WorldWideScience

Sample records for self-similar protein dynamics

  1. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

    Hu, Xiaohu; Hong, Liang; Dean Smith, Micholas; Neusius, Thomas; Cheng, Xiaolin; Smith, Jeremy C.

    2016-02-01

    Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behaviour with effective relaxation times existing over many decades in time, from ps up to ~102 s (refs ,,,). Here, using molecular dynamics simulations, we show that, on timescales from 10-12 to 10-5 s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behaviour persists up to timescales approaching the in vivo lifespan of individual protein molecules.

  2. Dynamic stability of self-similar solutions for a plasma pinch

    Ma, Sifeng.

    1988-01-01

    Linear Magnetohydrodynamic (MHD) stability theory is applied to a class of self-similar solutions which describe implosion, expansion and oscillation of an infinitely conducting plasma column. The equations of perturbation are derived in the Lagrangian coordinate system. Numerical procedures via the finite-element method are formulated, and general aspects of dynamic stability are discussed, The dynamic stability of the column when it is oscillatory is studied in detail using the Floquet theory, and the characteristic exponent is calculated numerically. A-pinch configuration is examined. It is found that self-similar oscillations in general destabilize the continua in the MHD spectrum, and parametric instability results

  3. Self-similar dynamic converging shocks - I. An isothermal gas sphere with self-gravity

    Lou, Yu-Qing; Shi, Chun-Hui

    2014-07-01

    We explore novel self-similar dynamic evolution of converging spherical shocks in a self-gravitating isothermal gas under conceivable astrophysical situations. The construction of such converging shocks involves a time-reversal operation on feasible flow profiles in self-similar expansion with a proper care for the increasing direction of the specific entropy. Pioneered by Guderley since 1942 but without self-gravity so far, self-similar converging shocks are important for implosion processes in aerodynamics, combustion, and inertial fusion. Self-gravity necessarily plays a key role for grossly spherical structures in very broad contexts of astrophysics and cosmology, such as planets, stars, molecular clouds (cores), compact objects, planetary nebulae, supernovae, gamma-ray bursts, supernova remnants, globular clusters, galactic bulges, elliptical galaxies, clusters of galaxies as well as relatively hollow cavity or bubble structures on diverse spatial and temporal scales. Large-scale dynamic flows associated with such quasi-spherical systems (including collapses, accretions, fall-backs, winds and outflows, explosions, etc.) in their initiation, formation, and evolution are likely encounter converging spherical shocks at times. Our formalism lays an important theoretical basis for pertinent astrophysical and cosmological applications of various converging shock solutions and for developing and calibrating numerical codes. As examples, we describe converging shock triggered star formation, supernova explosions, and void collapses.

  4. Levy Stable Processes. From Stationary to Self-Similar Dynamics and Back. An Application to Finance

    Burnecki, K.; Weron, A.

    2004-01-01

    We employ an ergodic theory argument to demonstrate the foundations of ubiquity of Levy stable self-similar processes in physics and present a class of models for anomalous and nonextensive diffusion. A relationship between stationary and self-similar models is clarified. The presented stochastic integral description of all Levy stable processes could provide new insights into the mechanism underlying a range of self-similar natural phenomena. Finally, this effect is illustrated by self-similar approach to financial modelling. (author)

  5. Visual Analysis of Nonlinear Dynamical Systems: Chaos, Fractals, Self-Similarity and the Limits of Prediction

    Geoff Boeing

    2016-11-01

    Full Text Available Nearly all nontrivial real-world systems are nonlinear dynamical systems. Chaos describes certain nonlinear dynamical systems that have a very sensitive dependence on initial conditions. Chaotic systems are always deterministic and may be very simple, yet they produce completely unpredictable and divergent behavior. Systems of nonlinear equations are difficult to solve analytically, and scientists have relied heavily on visual and qualitative approaches to discover and analyze the dynamics of nonlinearity. Indeed, few fields have drawn as heavily from visualization methods for their seminal innovations: from strange attractors, to bifurcation diagrams, to cobweb plots, to phase diagrams and embedding. Although the social sciences are increasingly studying these types of systems, seminal concepts remain murky or loosely adopted. This article has three aims. First, it argues for several visualization methods to critically analyze and understand the behavior of nonlinear dynamical systems. Second, it uses these visualizations to introduce the foundations of nonlinear dynamics, chaos, fractals, self-similarity and the limits of prediction. Finally, it presents Pynamical, an open-source Python package to easily visualize and explore nonlinear dynamical systems’ behavior.

  6. Universal self-similar dynamics of relativistic and nonrelativistic field theories near nonthermal fixed points

    Piñeiro Orioli, Asier; Boguslavski, Kirill; Berges, Jürgen

    2015-07-01

    We investigate universal behavior of isolated many-body systems far from equilibrium, which is relevant for a wide range of applications from ultracold quantum gases to high-energy particle physics. The universality is based on the existence of nonthermal fixed points, which represent nonequilibrium attractor solutions with self-similar scaling behavior. The corresponding dynamic universality classes turn out to be remarkably large, encompassing both relativistic as well as nonrelativistic quantum and classical systems. For the examples of nonrelativistic (Gross-Pitaevskii) and relativistic scalar field theory with quartic self-interactions, we demonstrate that infrared scaling exponents as well as scaling functions agree. We perform two independent nonperturbative calculations, first by using classical-statistical lattice simulation techniques and second by applying a vertex-resummed kinetic theory. The latter extends kinetic descriptions to the nonperturbative regime of overoccupied modes. Our results open new perspectives to learn from experiments with cold atoms aspects about the dynamics during the early stages of our universe.

  7. Dynamic scaling, data-collapse and self-similarity in Barabasi-Albert networks

    Hassan, M Kamrul; Pavel, Neeaj I [Theoretical Physics Group, Department of Physics, University of Dhaka, Dhaka 1000 (Bangladesh); Hassan, M Zahedul, E-mail: khassan@univdhaka.edu [Institute of Computer Science, Bangladesh Atomic Energy Commission, Dhaka 1000 (Bangladesh)

    2011-04-29

    In this paper, we show that if each node of the Barabasi-Albert (BA) network is characterized by the generalized degree q, i.e. the product of their degree k and the square root of their respective birth time, then the distribution function F(q, t) exhibits dynamic scaling F(q, t {yields} {infinity}) {approx} t{sup -1/2}{phi}(q/t{sup 1/2}) where {phi}(x) is the scaling function. We verified it by showing that a series of distinct F(q, t) versus q curves for different network sizes N collapse onto a single universal curve if we plot t{sup 1/2}F(q, t) versus q/t{sup 1/2} instead. Finally, we show that the BA network falls into two universality classes depending on whether new nodes arrive with single edge (m = 1) or with multiple edges (m > 1).

  8. Why are large cities faster? Universal scaling and self-similarity in urban organization and dynamics

    Bettencourt, L. M. A.; Lobo, J.; West, G. B.

    2008-06-01

    Cities have existed since the beginning of civilization and have always been intimately connected with humanity's cultural and technological development. Much about the human and social dynamics that takes place is cities is intuitively recognizable across time, space and culture; yet we still do not have a clear cut answer as to why cities exist or to what factors are critical to make them thrive or collapse. Here, we construct an extensive quantitative characterization of the variation of many urban indicators with city size, using large data sets for American, European and Chinese cities. We show that social and economic quantities, characterizing the creation of wealth and new ideas, show increasing returns to population scale, which appear quantitatively as a power law of city size with an exponent β≃ 1.15 > 1. Concurrently, quantities characterizing material infrastructure typically show economies of scale, namely β≃ 0.8 exponential growth, which inexorably lead to crises of urban organization. To avoid them we show that growth may proceed in cycles, separated by major urban adaptations, with the unintended consequence that the duration of such cycles decreases with larger urban population size and is now estimated to be shorter than a human lifetime.

  9. Self-similar cosmological models

    Chao, W Z [Cambridge Univ. (UK). Dept. of Applied Mathematics and Theoretical Physics

    1981-07-01

    The kinematics and dynamics of self-similar cosmological models are discussed. The degrees of freedom of the solutions of Einstein's equations for different types of models are listed. The relation between kinematic quantities and the classifications of the self-similarity group is examined. All dust local rotational symmetry models have been found.

  10. Self-similar factor approximants

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  11. Chemical dynamics between wells across a time-dependent barrier: Self-similarity in the Lagrangian descriptor and reactive basins.

    Junginger, Andrej; Duvenbeck, Lennart; Feldmaier, Matthias; Main, Jörg; Wunner, Günter; Hernandez, Rigoberto

    2017-08-14

    In chemical or physical reaction dynamics, it is essential to distinguish precisely between reactants and products for all times. This task is especially demanding in time-dependent or driven systems because therein the dividing surface (DS) between these states often exhibits a nontrivial time-dependence. The so-called transition state (TS) trajectory has been seen to define a DS which is free of recrossings in a large number of one-dimensional reactions across time-dependent barriers and thus, allows one to determine exact reaction rates. A fundamental challenge to applying this method is the construction of the TS trajectory itself. The minimization of Lagrangian descriptors (LDs) provides a general and powerful scheme to obtain that trajectory even when perturbation theory fails. Both approaches encounter possible breakdowns when the overall potential is bounded, admitting the possibility of returns to the barrier long after the trajectories have reached the product or reactant wells. Such global dynamics cannot be captured by perturbation theory. Meanwhile, in the LD-DS approach, it leads to the emergence of additional local minima which make it difficult to extract the optimal branch associated with the desired TS trajectory. In this work, we illustrate this behavior for a time-dependent double-well potential revealing a self-similar structure of the LD, and we demonstrate how the reflections and side-minima can be addressed by an appropriate modification of the LD associated with the direct rate across the barrier.

  12. Self-Similar Nonlinear Dynamical Solutions for One-Component Nonneutral Plasma in a Time-Dependent Linear Focusing Field

    Qin, Hong; Davidson, Ronald C.

    2011-01-01

    In a linear trap confining a one-component nonneutral plasma, the external focusing force is a linear function of the configuration coordinates and/or the velocity coordinates. Linear traps include the classical Paul trap and the Penning trap, as well as the newly proposed rotating-radio- frequency traps and the Mobius accelerator. This paper describes a class of self-similar nonlinear solutions of nonneutral plasma in general time-dependent linear focusing devices, with self-consistent electrostatic field. This class of nonlinear solutions includes many known solutions as special cases.

  13. Self-similar dynamics of air film entrained by a solid disk in confined space: A simple prototype of topological transitions

    Nakazato, Hana; Yamagishi, Yuki; Okumura, Ko

    2018-05-01

    In hydrodynamic topological transitions, one mass of fluid breaks into two or two merge into one. For example, in honey-drop formation when honey is dripping from a spoon, honey is extended to separate into two masses as the liquid neck bridging them thins down to the micron scale. At the moment when the topology changes due to the breakup, physical observables such as surface curvature locally diverge. Such singular dynamics has widely attracted physicists, revealing universality in self-similar dynamics, which shares much in common with critical phenomena in thermodynamics. Many experimental examples have been found, including an electric spout and vibration-induced jet eruption. However, only a few cases have been physically understood on the basis of equations that govern the singular dynamics and even in such a case the physical understanding is mathematically complicated, inevitably involving delicate numerical calculations. Here we study the breakup of air film entrained by a solid disk into viscous liquid in a confined space, which leads to formation, thinning, and breakup of the neck of air. As a result, we unexpectedly find that equations governing the neck dynamics can be solved analytically by virtue of two remarkable experimental features: Only a single length scale linearly dependent on time remains near the singularity and two universal scaling functions describing the singular neck shape and velocity field are both analytic. The present solvable case would be essential for a better understanding of the singular dynamics and will help reveal the physics of unresolved examples intimately related to daily-life phenomena and diverse practical applications.

  14. Self-similar gravitational clustering

    Efstathiou, G.; Fall, S.M.; Hogan, C.

    1979-01-01

    The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

  15. The baryonic self similarity of dark matter

    Alard, C.

    2014-01-01

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M 1/4 . These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  16. On different forms of self similarity

    Aswathy, R.K.; Mathew, Sunil

    2016-01-01

    Fractal geometry is mainly based on the idea of self-similar forms. To be self-similar, a shape must able to be divided into parts that are smaller copies, which are more or less similar to the whole. There are different forms of self similarity in nature and mathematics. In this paper, some of the topological properties of super self similar sets are discussed. It is proved that in a complete metric space with two or more elements, the set of all non super self similar sets are dense in the set of all non-empty compact sub sets. It is also proved that the product of self similar sets are super self similar in product metric spaces and that the super self similarity is preserved under isometry. A characterization of super self similar sets using contracting sub self similarity is also presented. Some relevant counterexamples are provided. The concepts of exact super and sub self similarity are introduced and a necessary and sufficient condition for a set to be exact super self similar in terms of condensation iterated function systems (Condensation IFS’s) is obtained. A method to generate exact sub self similar sets using condensation IFS’s and the denseness of exact super self similar sets are also discussed.

  17. Testing Self-Similarity Through Lamperti Transformations

    Lee, Myoungji; Genton, Marc G.; Jun, Mikyoung

    2016-01-01

    extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi

  18. Testing Self-Similarity Through Lamperti Transformations

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  19. On self-similar Tolman models

    Maharaj, S.D.

    1988-01-01

    The self-similar spherically symmetric solutions of the Einstein field equation for the case of dust are identified. These form a subclass of the Tolman models. These self-similar models contain the solution recently presented by Chi [J. Math. Phys. 28, 1539 (1987)], thereby refuting the claim of having found a new solution to the Einstein field equations

  20. Self-Similar Traffic In Wireless Networks

    Jerjomins, R.; Petersons, E.

    2005-01-01

    Many studies have shown that traffic in Ethernet and other wired networks is self-similar. This paper reveals that wireless network traffic is also self-similar and long-range dependant by analyzing big amount of data captured from the wireless router.

  1. Self-similar continued root approximants

    Gluzman, S.; Yukalov, V.I.

    2012-01-01

    A novel method of summing asymptotic series is advanced. Such series repeatedly arise when employing perturbation theory in powers of a small parameter for complicated problems of condensed matter physics, statistical physics, and various applied problems. The method is based on the self-similar approximation theory involving self-similar root approximants. The constructed self-similar continued roots extrapolate asymptotic series to finite values of the expansion parameter. The self-similar continued roots contain, as a particular case, continued fractions and Padé approximants. A theorem on the convergence of the self-similar continued roots is proved. The method is illustrated by several examples from condensed-matter physics.

  2. Gait Recognition Using Image Self-Similarity

    Chiraz BenAbdelkader

    2004-04-01

    Full Text Available Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have sufficient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of difficulty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98% is achieved for a data set of 6 people, and 70% for a data set of 54 people.

  3. On self-similarity of crack layer

    Botsis, J.; Kunin, B.

    1987-01-01

    The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

  4. Universal self-similarity of propagating populations.

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

    This paper explores the universal self-similarity of propagating populations. The following general propagation model is considered: particles are randomly emitted from the origin of a d-dimensional Euclidean space and propagate randomly and independently of each other in space; all particles share a statistically common--yet arbitrary--motion pattern; each particle has its own random propagation parameters--emission epoch, motion frequency, and motion amplitude. The universally self-similar statistics of the particles' displacements and first passage times (FPTs) are analyzed: statistics which are invariant with respect to the details of the displacement and FPT measurements and with respect to the particles' underlying motion pattern. Analysis concludes that the universally self-similar statistics are governed by Poisson processes with power-law intensities and by the Fréchet and Weibull extreme-value laws.

  5. Universal self-similarity of propagating populations

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

    This paper explores the universal self-similarity of propagating populations. The following general propagation model is considered: particles are randomly emitted from the origin of a d -dimensional Euclidean space and propagate randomly and independently of each other in space; all particles share a statistically common—yet arbitrary—motion pattern; each particle has its own random propagation parameters—emission epoch, motion frequency, and motion amplitude. The universally self-similar statistics of the particles’ displacements and first passage times (FPTs) are analyzed: statistics which are invariant with respect to the details of the displacement and FPT measurements and with respect to the particles’ underlying motion pattern. Analysis concludes that the universally self-similar statistics are governed by Poisson processes with power-law intensities and by the Fréchet and Weibull extreme-value laws.

  6. Stochastic self-similar and fractal universe

    Iovane, G.; Laserra, E.; Tortoriello, F.S.

    2004-01-01

    The structures formation of the Universe appears as if it were a classically self-similar random process at all astrophysical scales. An agreement is demonstrated for the present hypotheses of segregation with a size of astrophysical structures by using a comparison between quantum quantities and astrophysical ones. We present the observed segregated Universe as the result of a fundamental self-similar law, which generalizes the Compton wavelength relation. It appears that the Universe has a memory of its quantum origin as suggested by R. Penrose with respect to quasi-crystal. A more accurate analysis shows that the present theory can be extended from the astrophysical to the nuclear scale by using generalized (stochastically) self-similar random process. This transition is connected to the relevant presence of the electromagnetic and nuclear interactions inside the matter. In this sense, the presented rule is correct from a subatomic scale to an astrophysical one. We discuss the near full agreement at organic cell scale and human scale too. Consequently the Universe, with its structures at all scales (atomic nucleus, organic cell, human, planet, solar system, galaxy, clusters of galaxy, super clusters of galaxy), could have a fundamental quantum reason. In conclusion, we analyze the spatial dimensions of the objects in the Universe as well as space-time dimensions. The result is that it seems we live in an El Naschie's E-infinity Cantorian space-time; so we must seriously start considering fractal geometry as the geometry of nature, a type of arena where the laws of physics appear at each scale in a self-similar way as advocated long ago by the Swedish school of astrophysics

  7. Self-similar oscillations of the Extrap pinch

    Tendler, M.

    1987-11-01

    The method of the dynamic stabilization is invoked to explain the enhanced stability of a Z-pinch in EXTRAP configuration. The oscillatory motion is assumed to be forced on EXTRAP due to self-similar oscillations of a Z-pinch. Using a scaling for the net energy loss with plasma density and temperature typical for divertor configurations, a new analytic, self-similar solution of the fluid equations is presented. Strongly unharmonic oscillations of the plasma parameters in the pinch arise. These results are used in a discussion on the stability of EXTRAP, considered as a system with a time dependent internal magnetic field. The effect of the dynamic stabilization is considered by taking estimates. (author)

  8. Self-similarity in the inertial region of wall turbulence.

    Klewicki, J; Philip, J; Marusic, I; Chauhan, K; Morrill-Winter, C

    2014-12-01

    The inverse of the von Kármán constant κ is the leading coefficient in the equation describing the logarithmic mean velocity profile in wall bounded turbulent flows. Klewicki [J. Fluid Mech. 718, 596 (2013)] connects the asymptotic value of κ with an emerging condition of dynamic self-similarity on an interior inertial domain that contains a geometrically self-similar hierarchy of scaling layers. A number of properties associated with the asymptotic value of κ are revealed. This is accomplished using a framework that retains connection to invariance properties admitted by the mean statement of dynamics. The development leads toward, but terminates short of, analytically determining a value for κ. It is shown that if adjacent layers on the hierarchy (or their adjacent positions) adhere to the same self-similarity that is analytically shown to exist between any given layer and its position, then κ≡Φ(-2)=0.381966..., where Φ=(1+√5)/2 is the golden ratio. A number of measures, derived specifically from an analysis of the mean momentum equation, are subsequently used to empirically explore the veracity and implications of κ=Φ(-2). Consistent with the differential transformations underlying an invariant form admitted by the governing mean equation, it is demonstrated that the value of κ arises from two geometric features associated with the inertial turbulent motions responsible for momentum transport. One nominally pertains to the shape of the relevant motions as quantified by their area coverage in any given wall-parallel plane, and the other pertains to the changing size of these motions in the wall-normal direction. In accord with self-similar mean dynamics, these two features remain invariant across the inertial domain. Data from direct numerical simulations and higher Reynolds number experiments are presented and discussed relative to the self-similar geometric structure indicated by the analysis, and in particular the special form of self-similarity

  9. Emergent self-similarity of cluster coagulation

    Pushkin, Dmtiri O.

    A wide variety of nonequilibrium processes, such as coagulation of colloidal particles, aggregation of bacteria into colonies, coalescence of rain drops, bond formation between polymerization sites, and formation of planetesimals, fall under the rubric of cluster coagulation. We predict emergence of self-similar behavior in such systems when they are 'forced' by an external source of the smallest particles. The corresponding self-similar coagulation spectra prove to be power laws. Starting from the classical Smoluchowski coagulation equation, we identify the conditions required for emergence of self-similarity and show that the power-law exponent value for a particular coagulation mechanism depends on the homogeneity index of the corresponding coagulation kernel only. Next, we consider the current wave of mergers of large American banks as an 'unorthodox' application of coagulation theory. We predict that the bank size distribution has propensity to become a power law, and verify our prediction in a statistical study of the available economical data. We conclude this chapter by discussing economically significant phenomenon of capital condensation and predicting emergence of power-law distributions in other economical and social data. Finally, we turn to apparent semblance between cluster coagulation and turbulence and conclude that it is not accidental: both of these processes are instances of nonlinear cascades. This class of processes also includes river network formation models, certain force-chain models in granular mechanics, fragmentation due to collisional cascades, percolation, and growing random networks. We characterize a particular cascade by three indicies and show that the resulting power-law spectrum exponent depends on the indicies values only. The ensuing algebraic formula is remarkable for its simplicity.

  10. Spherically symmetric self-similar universe

    Dyer, C C [Toronto Univ., Ontario (Canada)

    1979-10-01

    A spherically symmetric self-similar dust-filled universe is considered as a simple model of a hierarchical universe. Observable differences between the model in parabolic expansion and the corresponding homogeneous Einstein-de Sitter model are considered in detail. It is found that an observer at the centre of the distribution has a maximum observable redshift and can in principle see arbitrarily large blueshifts. It is found to yield an observed density-distance law different from that suggested by the observations of de Vaucouleurs. The use of these solutions as central objects for Swiss-cheese vacuoles is discussed.

  11. Self-similar magnetohydrodynamic boundary layers

    Nunez, Manuel; Lastra, Alberto, E-mail: mnjmhd@am.uva.e [Departamento de Analisis Matematico, Universidad de Valladolid, 47005 Valladolid (Spain)

    2010-10-15

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  12. Self-similar magnetohydrodynamic boundary layers

    Nunez, Manuel; Lastra, Alberto

    2010-01-01

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  13. Self-similarity in applied superconductivity

    Dresner, Lawrence

    1981-09-01

    Self-similarity is a descriptive term applying to a family of curves. It means that the family is invariant to a one-parameter group of affine (stretching) transformations. The property of self-similarity has been exploited in a wide variety of problems in applied superconductivity, namely, (i) transient distribution of the current among the filaments of a superconductor during charge-up, (ii) steady distribution of current among the filaments of a superconductor near the current leads, (iii) transient heat transfer in superfluid helium, (iv) transient diffusion in cylindrical geometry (important in studying the growth rate of the reacted layer in A15 materials), (v) thermal expulsion of helium from quenching cable-in-conduit conductors, (vi) eddy current heating of irregular plates by slow, ramped fields, and (vii) the specific heat of type-II superconductors. Most, but not all, of the applications involve differential equations, both ordinary and partial. The novel methods explained in this report should prove of great value in other fields, just as they already have done in applied superconductivity. (author)

  14. Self-similar pattern formation and continuous mechanics of self-similar systems

    A. V. Dyskin

    2007-01-01

    Full Text Available In many cases, the critical state of systems that reached the threshold is characterised by self-similar pattern formation. We produce an example of pattern formation of this kind – formation of self-similar distribution of interacting fractures. Their formation starts with the crack growth due to the action of stress fluctuations. It is shown that even when the fluctuations have zero average the cracks generated by them could grow far beyond the scale of stress fluctuations. Further development of the fracture system is controlled by crack interaction leading to the emergence of self-similar crack distributions. As a result, the medium with fractures becomes discontinuous at any scale. We develop a continuum fractal mechanics to model its physical behaviour. We introduce a continuous sequence of continua of increasing scales covering this range of scales. The continuum of each scale is specified by the representative averaging volume elements of the corresponding size. These elements determine the resolution of the continuum. Each continuum hides the cracks of scales smaller than the volume element size while larger fractures are modelled explicitly. Using the developed formalism we investigate the stability of self-similar crack distributions with respect to crack growth and show that while the self-similar distribution of isotropically oriented cracks is stable, the distribution of parallel cracks is not. For the isotropically oriented cracks scaling of permeability is determined. For permeable materials (rocks with self-similar crack distributions permeability scales as cube of crack radius. This property could be used for detecting this specific mechanism of formation of self-similar crack distributions.

  15. Vertex labeling and routing in self-similar outerplanar unclustered graphs modeling complex networks

    Comellas, Francesc; Miralles, Alicia

    2009-01-01

    This paper introduces a labeling and optimal routing algorithm for a family of modular, self-similar, small-world graphs with clustering zero. Many properties of this family are comparable to those of networks associated with technological and biological systems with low clustering, such as the power grid, some electronic circuits and protein networks. For these systems, the existence of models with an efficient routing protocol is of interest to design practical communication algorithms in relation to dynamical processes (including synchronization) and also to understand the underlying mechanisms that have shaped their particular structure.

  16. Self-similar analysis of the spherical implosion process

    Ishiguro, Yukio; Katsuragi, Satoru.

    1976-07-01

    The implosion processes caused by laser-heating ablation has been studied by self-similarity analysis. Attention is paid to the possibility of existence of the self-similar solution which reproduces the implosion process of high compression. Details of the self-similar analysis are reproduced and conclusions are drawn quantitatively on the gas compression by a single shock. The compression process by a sequence of shocks is discussed in self-similarity. The gas motion followed by a homogeneous isentropic compression is represented by a self-similar motion. (auth.)

  17. Observations and analysis of self-similar branching topology in glacier networks

    Bahr, D.B.; Peckham, S.D.

    1996-01-01

    Glaciers, like rivers, have a branching structure which can be characterized by topological trees or networks. Probability distributions of various topological quantities in the networks are shown to satisfy the criterion for self-similarity, a symmetry structure which might be used to simplify future models of glacier dynamics. Two analytical methods of describing river networks, Shreve's random topology model and deterministic self-similar trees, are applied to the six glaciers of south central Alaska studied in this analysis. Self-similar trees capture the topological behavior observed for all of the glaciers, and most of the networks are also reasonably approximated by Shreve's theory. Copyright 1996 by the American Geophysical Union.

  18. Lipschitz equivalence of self-similar sets with touching structures

    Ruan, Huo-Jun; Wang, Yang; Xi, Li-Feng

    2014-01-01

    Lipschitz equivalence of self-similar sets is an important area in the study of fractal geometry. It is known that two dust-like self-similar sets with the same contraction ratios are always Lipschitz equivalent. However, when self-similar sets have touching structures the problem of Lipschitz equivalence becomes much more challenging and intriguing at the same time. So far, all the known results only cover self-similar sets in R with no more than three branches. In this study we establish results for the Lipschitz equivalence of self-similar sets with touching structures in R with arbitrarily many branches. Key to our study is the introduction of a geometric condition for self-similar sets called substitutable. (paper)

  19. A self-similar magnetohydrodynamic model for ball lightnings

    Tsui, K. H.

    2006-01-01

    Ball lightning is modeled by magnetohydrodynamic (MHD) equations in two-dimensional spherical geometry with azimuthal symmetry. Dynamic evolutions in the radial direction are described by the self-similar evolution function y(t). The plasma pressure, mass density, and magnetic fields are solved in terms of the radial label η. This model gives spherical MHD plasmoids with axisymmetric force-free magnetic field, and spherically symmetric plasma pressure and mass density, which self-consistently determine the polytropic index γ. The spatially oscillating nature of the radial and meridional field structures indicate embedded regions of closed field lines. These regions are named secondary plasmoids, whereas the overall self-similar spherical structure is named the primary plasmoid. According to this model, the time evolution function allows the primary plasmoid expand outward in two modes. The corresponding ejection of the embedded secondary plasmoids results in ball lightning offering an answer as how they come into being. The first is an accelerated expanding mode. This mode appears to fit plasmoids ejected from thundercloud tops with acceleration to ionosphere seen in high altitude atmospheric observations of sprites and blue jets. It also appears to account for midair high-speed ball lightning overtaking airplanes, and ground level high-speed energetic ball lightning. The second is a decelerated expanding mode, and it appears to be compatible to slowly moving ball lightning seen near ground level. The inverse of this second mode corresponds to an accelerated inward collapse, which could bring ball lightning to an end sometimes with a cracking sound

  20. Self-similar Hot Accretion Flow onto a Neutron Star

    Medvedev, Mikhail V.; Narayan, Ramesh

    2001-06-01

    We consider hot, two-temperature, viscous accretion onto a rotating, unmagnetized neutron star. We assume Coulomb coupling between the protons and electrons, as well as free-free cooling from the electrons. We show that the accretion flow has an extended settling region that can be described by means of two analytical self-similar solutions: a two-temperature solution that is valid in an inner zone, r~102.5. In both zones the density varies as ρ~r-2 and the angular velocity as Ω~r-3/2. We solve the flow equations numerically and confirm that the analytical solutions are accurate. Except for the radial velocity, all gas properties in the self-similar settling zone, such as density, angular velocity, temperature, luminosity, and angular momentum flux, are independent of the mass accretion rate; these quantities do depend sensitively on the spin of the neutron star. The angular momentum flux is outward under most conditions; therefore, the central star is nearly always spun down. The luminosity of the settling zone arises from the rotational energy that is released as the star is braked by viscosity, and the contribution from gravity is small; hence, the radiative efficiency, η=Lacc/Mc2, is arbitrarily large at low M. For reasonable values of the gas adiabatic index γ, the Bernoulli parameter is negative; therefore, in the absence of dynamically important magnetic fields, a strong outflow or wind is not expected. The flow is also convectively stable but may be thermally unstable. The described solution is not advection dominated; however, when the spin of the star is small enough, the flow transforms smoothly to an advection-dominated branch of solution.

  1. Self-similar solution for coupled thermal electromagnetic model ...

    An investigation into the existence and uniqueness solution of self-similar solution for the coupled Maxwell and Pennes Bio-heat equations have been done. Criteria for existence and uniqueness of self-similar solution are revealed in the consequent theorems. Journal of the Nigerian Association of Mathematical Physics ...

  2. Self-similarity in incompressible Navier-Stokes equations.

    Ercan, Ali; Kavvas, M Levent

    2015-12-01

    The self-similarity conditions of the 3-dimensional (3D) incompressible Navier-Stokes equations are obtained by utilizing one-parameter Lie group of point scaling transformations. It is found that the scaling exponents of length dimensions in i = 1, 2, 3 coordinates in 3-dimensions are not arbitrary but equal for the self-similarity of 3D incompressible Navier-Stokes equations. It is also shown that the self-similarity in this particular flow process can be achieved in different time and space scales when the viscosity of the fluid is also scaled in addition to other flow variables. In other words, the self-similarity of Navier-Stokes equations is achievable under different fluid environments in the same or different gravity conditions. Self-similarity criteria due to initial and boundary conditions are also presented. Utilizing the proposed self-similarity conditions of the 3D hydrodynamic flow process, the value of a flow variable at a specified time and space can be scaled to a corresponding value in a self-similar domain at the corresponding time and space.

  3. Scaling Relations and Self-Similarity of 3-Dimensional Reynolds-Averaged Navier-Stokes Equations.

    Ercan, Ali; Kavvas, M Levent

    2017-07-25

    Scaling conditions to achieve self-similar solutions of 3-Dimensional (3D) Reynolds-Averaged Navier-Stokes Equations, as an initial and boundary value problem, are obtained by utilizing Lie Group of Point Scaling Transformations. By means of an open-source Navier-Stokes solver and the derived self-similarity conditions, we demonstrated self-similarity within the time variation of flow dynamics for a rigid-lid cavity problem under both up-scaled and down-scaled domains. The strength of the proposed approach lies in its ability to consider the underlying flow dynamics through not only from the governing equations under consideration but also from the initial and boundary conditions, hence allowing to obtain perfect self-similarity in different time and space scales. The proposed methodology can be a valuable tool in obtaining self-similar flow dynamics under preferred level of detail, which can be represented by initial and boundary value problems under specific assumptions.

  4. Temporal self-similar synchronization patterns and scaling in ...

    Repulsively coupled oscillators; synchronization patterns; self-similar ... system, one expects multistable behavior in analogy to ..... More about the scaling relation between the long-period ... The third type of representation of phases is via.

  5. Mixed quantization dimensions of self-similar measures

    Dai Meifeng; Wang Xiaoli; Chen Dandan

    2012-01-01

    Highlights: ► We define the mixed quantization dimension of finitely many measures. ► Formula of mixed quantization dimensions of self-similar measures is given. ► Illustrate the behavior of mixed quantization dimension as a function of order. - Abstract: Classical multifractal analysis studies the local scaling behaviors of a single measure. However recently mixed multifractal has generated interest. The purpose of this paper is some results about the mixed quantization dimensions of self-similar measures.

  6. Self-similarity in the equation of motion of a ship

    Gyeong Joong Lee

    2014-06-01

    Full Text Available If we want to analyze the motion of a body in fluid, we should use rigid-body dynamics and fluid dynamics together. Even if the rigid-body and fluid dynamics are each self-consistent, there arises the problem of self-similar structure in the equation of motion when the two dynamics are coupled with each other. When the added mass is greater than the mass of a body, the calculated motion is divergent because of its self-similar structure. This study showed that the above problem is an inherent problem. This problem of self-similar structure may arise in the equation of motion in which the fluid dynamic forces are treated as external forces on the right hand side of the equation. A reconfiguration technique for the equation of motion using pseudo-added-mass was proposed to resolve the self-similar structure problem; specifically for the case when the fluid force is expressed by integration of the fluid pressure.

  7. Mechanics of ultra-stretchable self-similar serpentine interconnects

    Zhang, Yihui; Fu, Haoran; Su, Yewang; Xu, Sheng

    2013-01-01

    Graphical abstract: We developed analytical models of flexibility and elastic-stretchability for self-similar interconnect. The analytic solutions agree very well with the finite element analyses, both demonstrating that the elastic-stretchability more than doubles when the order of self-similar structure increases by one. Design optimization yields 90% and 50% elastic stretchability for systems with surface filling ratios of 50% and 70% of active devices, respectively. The analytic models are useful for the development of stretchable electronics that simultaneously demand large coverage of active devices, such as stretchable photovoltaics and electronic eye-ball cameras. -- Abstract: Electrical interconnects that adopt self-similar, serpentine layouts offer exceptional levels of stretchability in systems that consist of collections of small, non-stretchable active devices in the so-called island–bridge design. This paper develops analytical models of flexibility and elastic stretchability for such structures, and establishes recursive formulae at different orders of self-similarity. The analytic solutions agree well with finite element analysis, with both demonstrating that the elastic stretchability more than doubles when the order of the self-similar structure increases by one. Design optimization yields 90% and 50% elastic stretchability for systems with surface filling ratios of 50% and 70% of active devices, respectively

  8. Self-similar potential in the near wake

    Diebold, D.; Hershkowitz, N.; Intrator, T.; Bailey, A.

    1987-01-01

    The plasma potential is measured near the edge of an electrically floating obstacle placed in a steady-state, supersonic, unmagnetized, neutral plasma flow. Equipotential contours show the sheath of the upstream side of the obstacle wrapping around the edge of the obstacle and fanning out into the near wake. Both fluid theory and the data find the near-wake plasma potential to be self-similar when ionization, charge exchange, and magnetic field can be neglected. The theory also finds that fluid velocity is self-similar, the near wake is nonneutral, and plasma density is not self-similar. Strong electric fields are found near the obstacle and equipotential contours are found to conform to all boundaries

  9. Self-similarity of the negative binomial multiplicity distributions

    Calucci, G.; Treleani, D.

    1998-01-01

    The negative binomial distribution is self-similar: If the spectrum over the whole rapidity range gives rise to a negative binomial, in the absence of correlation and if the source is unique, also a partial range in rapidity gives rise to the same distribution. The property is not seen in experimental data, which are rather consistent with the presence of a number of independent sources. When multiplicities are very large, self-similarity might be used to isolate individual sources in a complex production process. copyright 1997 The American Physical Society

  10. Self-similar expansion of dusts in a plasma

    Luo, H.; Yu, M.Y.

    1992-01-01

    The self-similar expansion of two species of dust particles in an equilibrium plasma is investigated by means of fluid as well as Vlasov theories. It is found that under certain conditions the density of the dust with the smaller charge-to-mass ratio can vanish at a finite value of the self-similar variable, while the density of the remaining dust species attains a plateau. The kinetic theory predicts a secondary decay in which the latter density eventually also vanishes

  11. Self-similar solutions of the modified nonlinear schrodinger equation

    Kitaev, A.V.

    1986-01-01

    This paper considers a 2 x 2 matrix linear ordinary differential equation with large parameter t and irregular singular point of fourth order at infinity. The leading order of the monodromy data of this equation is calculated in terms of its coefficients. Isomonodromic deformations of the equation are self-similar solutions of the modified nonlinear Schrodinger equation, and therefore inversion of the expressions obtained for the monodromy data gives the leading term in the time-asymptotic behavior of the self-similar solution. The application of these results to the type IV Painleve equation is considered in detail

  12. Self-Similar Symmetry Model and Cosmic Microwave Background

    Tomohide eSonoda

    2016-05-01

    Full Text Available In this paper, we present the self-similar symmetry (SSS model that describes the hierarchical structure of the universe. The model is based on the concept of self-similarity, which explains the symmetry of the cosmic microwave background (CMB. The approximate length and time scales of the six hierarchies of the universe---grand unification, electroweak unification, the atom, the pulsar, the solar system, and the galactic system---are derived from the SSS model. In addition, the model implies that the electron mass and gravitational constant could vary with the CMB radiation temperature.

  13. Self-similar Langmuir collapse at critical dimension

    Berge, L.; Dousseau, Ph.; Pelletier, G.; Pesme, D.

    1991-01-01

    Two spherically symmetric versions of a self-similar collapse are investigated within the framework of the Zakharov equations, namely, one relative to a vectorial electric field and the other corresponding to a scalar modeling of the Langmuir field. Singular solutions of both of them depend on a linear time contraction rate ξ(t) = V(t * -t), where t * and V = -ξ denote, respectively, the collapse time and the constant collapse velocity. It is shown that under certain conditions, only the scalar model admits self-similar solutions, varying regularly as a function of the control parameter V from the subsonic (V >1) regime. (author)

  14. PHOG analysis of self-similarity in aesthetic images

    Amirshahi, Seyed Ali; Koch, Michael; Denzler, Joachim; Redies, Christoph

    2012-03-01

    In recent years, there have been efforts in defining the statistical properties of aesthetic photographs and artworks using computer vision techniques. However, it is still an open question how to distinguish aesthetic from non-aesthetic images with a high recognition rate. This is possibly because aesthetic perception is influenced also by a large number of cultural variables. Nevertheless, the search for statistical properties of aesthetic images has not been futile. For example, we have shown that the radially averaged power spectrum of monochrome artworks of Western and Eastern provenance falls off according to a power law with increasing spatial frequency (1/f2 characteristics). This finding implies that this particular subset of artworks possesses a Fourier power spectrum that is self-similar across different scales of spatial resolution. Other types of aesthetic images, such as cartoons, comics and mangas also display this type of self-similarity, as do photographs of complex natural scenes. Since the human visual system is adapted to encode images of natural scenes in a particular efficient way, we have argued that artists imitate these statistics in their artworks. In support of this notion, we presented results that artists portrait human faces with the self-similar Fourier statistics of complex natural scenes although real-world photographs of faces are not self-similar. In view of these previous findings, we investigated other statistical measures of self-similarity to characterize aesthetic and non-aesthetic images. In the present work, we propose a novel measure of self-similarity that is based on the Pyramid Histogram of Oriented Gradients (PHOG). For every image, we first calculate PHOG up to pyramid level 3. The similarity between the histograms of each section at a particular level is then calculated to the parent section at the previous level (or to the histogram at the ground level). The proposed approach is tested on datasets of aesthetic and

  15. Self-Similar Solutions for Viscous and Resistive Advection ...

    2016-01-27

    Jan 27, 2016 ... In this paper, self-similar solutions of resistive advection dominated accretion flows (ADAF) in the presence of a pure azimuthal magnetic field are investigated. The mechanism of energy dissipation is assumed to be the viscosity and the magnetic diffusivity due to turbulence in the accretion flow.

  16. Self-similar solutions of certain coupled integrable systems

    Chakravarty, S; Kent, S L

    2003-01-01

    Similarity reductions of the coupled nonlinear Schroedinger equation and an integrable version of the coupled Maxwell-Bloch system are obtained by applying non-translational symmetries. The reduced system of coupled ordinary differential equations are solved in terms of Painleve transcendents, leading to new exact self-similar solutions for these integrable equations.

  17. Self-similar solutions of certain coupled integrable systems

    Chakravarty, S; Halburd, R G; Kent, S L

    2003-01-01

    Similarity reductions of the coupled nonlinear Schroedinger equation and an integrable version of the coupled Maxwell-Bloch system are obtained by applying non-translational symmetries. The reduced system of coupled ordinary differential equations are solved in terms of Painleve transcendents, leading to new exact self-similar solutions for these integrable equations

  18. Spherical anharmonic oscillator in self-similar approximation

    Yukalova, E.P.; Yukalov, V.I.

    1992-01-01

    The method of self-similar approximation is applied here for calculating the eigenvalues of the three-dimensional spherical anharmonic oscillator. The advantage of this method is in its simplicity and high accuracy. The comparison with other known analytical methods proves that this method is more simple and accurate. 25 refs

  19. Tokunaga self-similarity arises naturally from time invariance

    Kovchegov, Yevgeniy; Zaliapin, Ilya

    2018-04-01

    The Tokunaga condition is an algebraic rule that provides a detailed description of the branching structure in a self-similar tree. Despite a solid empirical validation and practical convenience, the Tokunaga condition lacks a theoretical justification. Such a justification is suggested in this work. We define a geometric branching process G (s ) that generates self-similar rooted trees. The main result establishes the equivalence between the invariance of G (s ) with respect to a time shift and a one-parametric version of the Tokunaga condition. In the parameter region where the process satisfies the Tokunaga condition (and hence is time invariant), G (s ) enjoys many of the symmetries observed in a critical binary Galton-Watson branching process and reproduces the latter for a particular parameter value.

  20. Self-similar radiation from numerical Rosenau-Hyman compactons

    Rus, Francisco; Villatoro, Francisco R.

    2007-01-01

    The numerical simulation of compactons, solitary waves with compact support, is characterized by the presence of spurious phenomena, as numerically induced radiation, which is illustrated here using four numerical methods applied to the Rosenau-Hyman K(p, p) equation. Both forward and backward radiations are emitted from the compacton presenting a self-similar shape which has been illustrated graphically by the proper scaling. A grid refinement study shows that the amplitude of the radiations decreases as the grid size does, confirming its numerical origin. The front velocity and the amplitude of both radiations have been studied as a function of both the compacton and the numerical parameters. The amplitude of the radiations decreases exponentially in time, being characterized by a nearly constant scaling exponent. An ansatz for both the backward and forward radiations corresponding to a self-similar function characterized by the scaling exponent is suggested by the present numerical results

  1. Self-similar oscillations of a Z pinch

    Felber, F.S.

    1982-01-01

    A new analytic, self-similar solution of the equations of ideal magnetohydrodynamics describes cylindrically symmetric plasmas conducting constant current. The solution indicates that an adiabatic Z pinch oscillates radially with a period typically of the order of a few acoustic transit times. A stability analysis, which shows the growth rate of the sausage instability to be a saturating function of wavenumber, suggests that the oscillations are observable

  2. One dimensional beam. Asymptotic and self similar solutions

    Feix, M.R.; Duranceau, J.L.; Besnard, D.

    1982-06-01

    Rescaling transformations provide a useful tool to solve nonlinear problems described by partial derivative equations. A brief review of this method is presented together with the connection with the self similar solutions obtained by compacting the independent variable with one of them (the time). The general theory is reported through examples found in Plasma Physics with a careful distinction between systems described by Hamiltonian and others where irreversible phenomena, like diffusion, are taken into account

  3. Log-periodic self-similarity: an emerging financial law?

    S. Drozdz; F. Grummer; F. Ruf; J. Speth

    2002-01-01

    A hypothesis that the financial log-periodicity, cascading self-similarity through various time scales, carries signatures of a law is pursued. It is shown that the most significant historical financial events can be classified amazingly well using a single and unique value of the preferred scaling factor lambda=2, which indicates that its real value should be close to this number. This applies even to a declining decelerating log-periodic phase. Crucial in this connection is identification o...

  4. Naked singularities in self-similar spherical gravitational collapse

    Ori, A.; Piran, T.

    1987-01-01

    We present general-relativistic solutions of self-similar spherical collapse of an adiabatic perfect fluid. We show that if the equation of state is soft enough (Γ-1<<1), a naked singularity forms. The singularity resembles the shell-focusing naked singularities that arise in dust collapse. This solution increases significantly the range of matter fields that should be ruled out in order that the cosmic-censorship hypothesis will hold

  5. Self-similar slip distributions on irregular shaped faults

    Herrero, A.; Murphy, S.

    2018-06-01

    We propose a strategy to place a self-similar slip distribution on a complex fault surface that is represented by an unstructured mesh. This is possible by applying a strategy based on the composite source model where a hierarchical set of asperities, each with its own slip function which is dependent on the distance from the asperity centre. Central to this technique is the efficient, accurate computation of distance between two points on the fault surface. This is known as the geodetic distance problem. We propose a method to compute the distance across complex non-planar surfaces based on a corollary of the Huygens' principle. The difference between this method compared to others sample-based algorithms which precede it is the use of a curved front at a local level to calculate the distance. This technique produces a highly accurate computation of the distance as the curvature of the front is linked to the distance from the source. Our local scheme is based on a sequence of two trilaterations, producing a robust algorithm which is highly precise. We test the strategy on a planar surface in order to assess its ability to keep the self-similarity properties of a slip distribution. We also present a synthetic self-similar slip distribution on a real slab topography for a M8.5 event. This method for computing distance may be extended to the estimation of first arrival times in both complex 3D surfaces or 3D volumes.

  6. Self-similar solutions for implosion and reflection of strong and weak shocks in a plasma

    Desai, B.N.; Chavda, L.K.

    1980-06-01

    We present an improved approximation scheme for finding approximate solutions in analytic form to the self-similar equations of gas dynamics. The method gives better agreement with exact results not only for the weak shocks which were considered previously but also for strong shocks for which the previous method gave poor results. We have considered various shock configurations in spherical and cylindrical geometries. (author)

  7. Self-Similar Spin Images for Point Cloud Matching

    Pulido, Daniel

    based on the concept of self-similarity to aid in the scale and feature matching steps. An open problem in fusion is how best to extract features from two point clouds and then perform feature-based matching. The proposed approach for this matching step is the use of local self-similarity as an invariant measure to match features. In particular, the proposed approach is to combine the concept of local self-similarity with a well-known feature descriptor, Spin Images, and thereby define "Self-Similar Spin Images". This approach is then extended to the case of matching two points clouds in very different coordinate systems (e.g., a geo-referenced Lidar point cloud and stereo-image derived point cloud without geo-referencing). The use of Self-Similar Spin Images is again applied to address this problem by introducing a "Self-Similar Keyscale" that matches the spatial scales of two point clouds. Another open problem is how best to detect changes in content between two point clouds. A method is proposed to find changes between two point clouds by analyzing the order statistics of the nearest neighbors between the two clouds, and thereby define the "Nearest Neighbor Order Statistic" method. Note that the well-known Hausdorff distance is a special case as being just the maximum order statistic. Therefore, by studying the entire histogram of these nearest neighbors it is expected to yield a more robust method to detect points that are present in one cloud but not the other. This approach is applied at multiple resolutions. Therefore, changes detected at the coarsest level will yield large missing targets and at finer levels will yield smaller targets.

  8. Self-Similar Vacuums Arc Plasma Cloud Expansion

    Gidalevich, E.; Goldsmith, S.; Boxman, R.L.

    1999-01-01

    A spherical plasma cloud generated by a vacuum are, is considered as expanding in an ambient neutral gas in a self-similar approximation. Under the assumption that the cathode erosion rate as well as density of the ambient neutral gas are constant during the plasma expansion, the self-similarity parameter is A = (1/ρ 3 dM/dt) 1/3 where ρ 3 is the density of undisturbed gas, M is the mass of the expanding metal vapor, and t is time, while the dimensionless independent variable is ξ = r/At 1/3 , where r is the distance from the cloud center. The equations of plasma motion and continuity are: ∂v/∂t + ∂n/∂r +1∂p/ρ∂r = 0 ∂ρ/∂t + ∂ρ/∂r + ρ(∂v/∂r + 2v/r) = 0 where v, ρ, P are plasma velocity, density and pressure, transformed in the self-similar form and solved numerically. Boundary conditions were formulated on the front of the plasma expansion taking into account that 1) the front edge of the shock wave expanding in the ambient neutral gas and 2) the rate of cathode erosion is a constant. For an erosion rate of 104 g/C, a cathode ion current of about 20 A and an ambient gas pressure about 0.1 Torr, the radius of the plasma cloud is r (m) = 0.834 x t 1/3 . At t = 10 -5 s, the plasma cloud radius is about 0.018 m, while the front velocity is v f = 600 m/s

  9. Self-similar perturbations of a Friedmann universe

    Carr, B.J.; Yahil, A.

    1990-01-01

    The present analysis of spherically symmetric self-similar solutions to the Einstein equations gives attention to those solutions that are asymptotically k = 0 Friedmann at large z values, and possess finite but perturbed density at the origin. Such solutions represent nonlinear density fluctuations which grow at the same rate as the universe's particle horizon. The overdense solutions span only a narrow range of parameters, and resemble static isothermal gas spheres just within the sonic point; the underdense solutions may have arbitrarily low density at the origin while exhibiting a unique relationship between amplitude and scale. Their relevance to large-scale void formation is considered. 36 refs

  10. Algebraic decay in self-similar Markov chains

    Hanson, J.D.; Cary, J.R.; Meiss, J.D.

    1985-01-01

    A continuous-time Markov chain is used to model motion in the neighborhood of a critical invariant circle for a Hamiltonian map. States in the infinite chain represent successive rational approximants to the frequency of the invariant circle. For the case of a noble frequency, the chain is self-similar and the nonlinear integral equation for the first passage time distribution is solved exactly. The asymptotic distribution is a power law times a function periodic in the logarithm of the time. For parameters relevant to the critical noble circle, the decay proceeds as t/sup -4.05/

  11. Self similar asymptotics of the drift ion acoustic waves

    Taranov, V.B.

    2004-01-01

    A 3D model for the coupled drift and ion acoustic waves is considered. It is shown that self-similar solutions can exist due to the symmetry extension in asymptotic regimes. The form of these solutions is determined in the presence of the magnetic shear as well as in the shear less case. Some of the most symmetric exact solutions are obtained explicitly. In particular, solutions describing asymptotics of zonal flow interaction with monochromatic waves are presented and corresponding frequency shifts are determined

  12. ESSENTIAL DYNAMICS OF PROTEINS

    AMADEI, A; LINSSEN, ABM; BERENDSEN, HJC

    1993-01-01

    Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ''essential'' subspace containing only a few degrees of freedom in which anharmonic motion occurs that

  13. Self-similarity and scaling theory of complex networks

    Song, Chaoming

    Scale-free networks have been studied extensively due to their relevance to many real systems as diverse as the World Wide Web (WWW), the Internet, biological and social networks. We present a novel approach to the analysis of scale-free networks, revealing that their structure is self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a self-similar exponent, which classifies fractal and non-fractal networks. By using the concept of renormalization as a mechanism for the growth of fractal and non-fractal modular networks, we show that the key principle that gives rise to the fractal architecture of networks is a strong effective "repulsion" between the most connected nodes (hubs) on all length scales, rendering them very dispersed. We show that a robust network comprised of functional modules, such as a cellular network, necessitates a fractal topology, suggestive of a evolutionary drive for their existence. These fundamental properties help to understand the emergence of the scale-free property in complex networks.

  14. A self-similar isochoric implosion for fast ignition

    Clark, D.S.; Tabak, M.

    2007-01-01

    Various gain models have shown the potentially great advantages of fast ignition (FI) inertial confinement fusion (ICF) over its conventional hot spot ignition counterpart (e.g. Atzeni S. 1999 Phys. Plasmas 6 3316; Tabak M. et al 2006 Fusion Sci. Technol. 49 254). These gain models, however, all assume nearly uniform density fuel assemblies. In contrast, conventional ICF implosions yield hollowed fuel assemblies with a high-density shell of fuel surrounding a low-density, high-pressure hot spot. Hence, to realize fully the advantages of FI, an alternative implosion design must be found which yields nearly isochoric fuel assemblies without substantial hot spots. Here, it is shown that a self-similar spherical implosion of the type originally studied by Guderley (1942 Luftfahrtforschung 19 302) may be employed to yield precisely such quasi-isochoric imploded states. The difficulty remains, however, of accessing these self-similarly imploding configurations from initial conditions representing an actual ICF target, namely a uniform, solid-density shell at rest. Furthermore, these specialized implosions must be realized for practicable drive parameters and at the scales and energies of interest in ICF. A direct-drive implosion scheme is presented which meets all of these requirements and reaches a nearly isochoric assembled density of 300 g cm -3 and areal density of 2.4 g cm -2 using 485 kJ of laser energy

  15. A self-similar hierarchy of the Korean stock market

    Lim, Gyuchang; Min, Seungsik; Yoo, Kun-Woo

    2013-01-01

    A scaling analysis is performed on market values of stocks listed on Korean stock exchanges such as the KOSPI and the KOSDAQ. Different from previous studies on price fluctuations, market capitalizations are dealt with in this work. First, we show that the sum of the two stock exchanges shows a clear rank-size distribution, i.e., the Zipf's law, just as each separate one does. Second, by abstracting Zipf's law as a γ-sequence, we define a self-similar hierarchy consisting of many levels, with the numbers of firms at each level forming a geometric sequence. We also use two exponential functions to describe the hierarchy and derive a scaling law from them. Lastly, we propose a self-similar hierarchical process and perform an empirical analysis on our data set. Based on our findings, we argue that all money invested in the stock market is distributed in a hierarchical way and that a slight difference exists between the two exchanges.

  16. Self-similar compression of a magnetized plasma filled liner

    Felber, F.S.; Liberman, M.A.; Velikovich, A.L.

    1985-01-01

    New analytic, one-dimensional, self-similar solutions of magnetohydrodynamic equations describing the compression of a magnetized plasma by a thin cylindrical liner are presented. The solutions include several features that have not been included in an earlier self-similar solution of the equations of ideal magnetohydrodynamics. These features are the effects of finite plasma electrical conductivity, induction heating, thermal conductivity and related thermogalvanomagnetic effects, plasma turbulence, and plasma boundary effects. These solutions have been motivated by recent suggestions for production of ultrahigh magnetic fields by new methods. The methods involve radially imploding plasmas in which axial magnetic fields have been entrained. These methods may be capable of producing controlled magnetic fields up to approx. = 100 MG. Specific methods of implosion suggested were by ablative radial acceleration of a liner by a laser and by a gas-puff Z pinch. The model presented here addresses the first of these methods. The solutions derived here are used to estimate magnetic flux losses out of the compression volume, and to indicate conditions under which an impulsively-accelerated, plasma-filled liner may compress an axial magnetic field to large magnitude

  17. Similarity and self-similarity in high energy density physics: application to laboratory astrophysics

    Falize, E.

    2008-10-01

    The spectacular recent development of powerful facilities allows the astrophysical community to explore, in laboratory, astrophysical phenomena where radiation and matter are strongly coupled. The titles of the nine chapters of the thesis are: from high energy density physics to laboratory astrophysics; Lie groups, invariance and self-similarity; scaling laws and similarity properties in High-Energy-Density physics; the Burgan-Feix-Munier transformation; dynamics of polytropic gases; stationary radiating shocks and the POLAR project; structure, dynamics and stability of optically thin fluids; from young star jets to laboratory jets; modelling and experiences for laboratory jets

  18. Vere-Jones' self-similar branching model

    Saichev, A.; Sornette, D.

    2005-01-01

    Motivated by its potential application to earthquake statistics as well as for its intrinsic interest in the theory of branching processes, we study the exactly self-similar branching process introduced recently by Vere-Jones. This model extends the ETAS class of conditional self-excited branching point-processes of triggered seismicity by removing the problematic need for a minimum (as well as maximum) earthquake size. To make the theory convergent without the need for the usual ultraviolet and infrared cutoffs, the distribution of magnitudes m ' of daughters of first-generation of a mother of magnitude m has two branches m ' ' >m with exponent β+d, where β and d are two positive parameters. We investigate the condition and nature of the subcritical, critical, and supercritical regime in this and in an extended version interpolating smoothly between several models. We predict that the distribution of magnitudes of events triggered by a mother of magnitude m over all generations has also two branches m ' ' >m with exponent β+h, with h=d√(1-s), where s is the fraction of triggered events. This corresponds to a renormalization of the exponent d into h by the hierarchy of successive generations of triggered events. For a significant part of the parameter space, the distribution of magnitudes over a full catalog summed over an average steady flow of spontaneous sources (immigrants) reproduces the distribution of the spontaneous sources with a single branch and is blind to the exponents β,d of the distribution of triggered events. Since the distribution of earthquake magnitudes is usually obtained with catalogs including many sequences, we conclude that the two branches of the distribution of aftershocks are not directly observable and the model is compatible with real seismic catalogs. In summary, the exactly self-similar Vere-Jones model provides an attractive new approach to model triggered seismicity, which alleviates delicate questions on the role of

  19. Self-similarity of higher-order moving averages

    Arianos, Sergio; Carbone, Anna; Türk, Christian

    2011-10-01

    In this work, higher-order moving average polynomials are defined by straightforward generalization of the standard moving average. The self-similarity of the polynomials is analyzed for fractional Brownian series and quantified in terms of the Hurst exponent H by using the detrending moving average method. We prove that the exponent H of the fractional Brownian series and of the detrending moving average variance asymptotically agree for the first-order polynomial. Such asymptotic values are compared with the results obtained by the simulations. The higher-order polynomials correspond to trend estimates at shorter time scales as the degree of the polynomial increases. Importantly, the increase of polynomial degree does not require to change the moving average window. Thus trends at different time scales can be obtained on data sets with the same size. These polynomials could be interesting for those applications relying on trend estimates over different time horizons (financial markets) or on filtering at different frequencies (image analysis).

  20. Self-similar anomalous diffusion and Levy-stable laws

    Uchaikin, Vladimir V

    2003-01-01

    Stochastic principles for constructing the process of anomalous diffusion are considered, and corresponding models of random processes are reviewed. The self-similarity and the independent-increments principles are used to extend the notion of diffusion process to the class of Levy-stable processes. Replacing the independent-increments principle with the renewal principle allows us to take the next step in generalizing the notion of diffusion, which results in fractional-order partial space-time differential equations of diffusion. Fundamental solutions to these equations are represented in terms of stable laws, and their relationship to the fractality and memory of the medium is discussed. A new class of distributions, called fractional stable distributions, is introduced. (reviews of topical problems)

  1. Self-similar current decay experiment in RFX-mod

    Zanca, Paolo

    2007-01-01

    The self-similar current decay (SSCD) has been suggested as a promising operation for reversed field pinch devices by numerical simulations, which show a decrease in modes amplitude and stochasticity when the magnetic field is forced to decay at a suitable rate at a fixed radial profile (Nebel et al 2002 Phys. Plasmas 9 4968). The first experimental test of SSCD has recently been performed in RFX-mod. An initial fast decrease in the mode amplitudes (about 40% of the initial value) is observed. After that, a regime characterized by transient states close to the single-helicity condition (Cappello and Paccagnella 1992 Phys. Fluids B 4 611, Finn et al 1992 Phys. Fluids B 4 1262) is established. This brings about a 50% increase in the global confinement parameters

  2. Bianchi VI0 and III models: self-similar approach

    Belinchon, Jose Antonio

    2009-01-01

    We study several cosmological models with Bianchi VI 0 and III symmetries under the self-similar approach. We find new solutions for the 'classical' perfect fluid model as well as for the vacuum model although they are really restrictive for the equation of state. We also study a perfect fluid model with time-varying constants, G and Λ. As in other studied models we find that the behaviour of G and Λ are related. If G behaves as a growing time function then Λ is a positive decreasing time function but if G is decreasing then Λ 0 is negative. We end by studying a massive cosmic string model, putting special emphasis in calculating the numerical values of the equations of state. We show that there is no SS solution for a string model with time-varying constants.

  3. Observable relations in an inhomogeneous self-similar cosmology

    Wesson, P.S.

    1979-01-01

    An exact self-similar solution is taken in general relativity as a model for an inhomogeneous cosmology. The self-similarity property means (conceptually) that the model is scale-free and (mathematically) that its essential parameters are functions of only one dimensionless variable zeta (equivalentct/R, where R and t are distance and time coordinates and c is the velocity of light). It begins inhomogeneous (zeta=0 or t=0), and tends to a homogeneous Einstein--de Sitter type state as zeta (or t) →infinity. Such a model can be used (a) for evaluating the observational effects of a clumpy universe; (b) for studying astrophysical processes such as galaxy formation and the growth and decay of inhomogeneities in initially clumpy cosmologies; and (c) as a relativistic basis for cosmological models with extended clustering of the de Vaucouleurs and Peebles types. The model has two adjustable parameters, namely, the observer's coordinate zeta 0 and a constant α/sub s/ that fixes the effect of the inhomogeneity. Expressions are obtained for the redshift, Hubble parameter, deceleration parameter, magnitude-redshift relation, and (number density of objects) --redshift relation. Expected anisotropies in the 3 K microwave background are also examined. There is no conflict with observation if zeta 0 /α/sub s/> or approx. =10, and four tests of the model are suggested that can be used to further determine the acceptability of inhomogeneous cosmologies of this type. The ratio α/sub s//zeta 0 on presently available data is α/sub s//zeta 0 < or approx. =10% and this, loosely speaking, means that the universe at the present epoch is globally homogeneous to within about 10%

  4. The role of self-similarity in singularities of partial differential equations

    Eggers, Jens; Fontelos, Marco A

    2009-01-01

    We survey rigorous, formal and numerical results on the formation of point-like singularities (or blow-up) for a wide range of evolution equations. We use a similarity transformation of the original equation with respect to the blow-up point, such that self-similar behaviour is mapped to the fixed point of a dynamical system. We point out that analysing the dynamics close to the fixed point is a useful way of characterizing the singularity, in that the dynamics frequently reduces to very few dimensions. As far as we are aware, examples from the literature either correspond to stable fixed points, low-dimensional centre-manifold dynamics, limit cycles or travelling waves. For each 'class' of singularity, we give detailed examples. (invited article)

  5. Subshifts of finite type and self-similar sets

    Jiang, Kan; Dajani, Karma

    2017-02-01

    Let K\\subset {R} be a self-similar set generated by some iterated function system. In this paper we prove, under some assumptions, that K can be identified with a subshift of finite type. With this identification, we can calculate the Hausdorff dimension of K as well as the set of elements in K with unique codings using the machinery of Mauldin and Williams (1988 Trans. Am. Math. Soc. 309 811-29). We give three different applications of our main result. Firstly, we calculate the Hausdorff dimension of the set of points of K with multiple codings. Secondly, in the setting of β-expansions, when the set of all the unique codings is not a subshift of finite type, we can calculate in some cases the Hausdorff dimension of the univoque set. Motivated by this application, we prove that the set of all the unique codings is a subshift of finite type if and only if it is a sofic shift. This equivalent condition was not mentioned by de Vries and Komornik (2009 Adv. Math. 221 390-427, theorem 1.8). Thirdly, for the doubling map with asymmetrical holes, we give a sufficient condition such that the survivor set can be identified with a subshift of finite type. The third application partially answers a problem posed by Alcaraz Barrera (2014 PhD Thesis University of Manchester).

  6. Root Growth Optimizer with Self-Similar Propagation

    Xiaoxian He

    2015-01-01

    Full Text Available Most nature-inspired algorithms simulate intelligent behaviors of animals and insects that can move spontaneously and independently. The survival wisdom of plants, as another species of biology, has been neglected to some extent even though they have evolved for a longer period of time. This paper presents a new plant-inspired algorithm which is called root growth optimizer (RGO. RGO simulates the iterative growth behaviors of plant roots to optimize continuous space search. In growing process, main roots and lateral roots, classified by fitness values, implement different strategies. Main roots carry out exploitation tasks by self-similar propagation in relatively nutrient-rich areas, while lateral roots explore other places to seek for better chance. Inhibition mechanism of plant hormones is applied to main roots in case of explosive propagation in some local optimal areas. Once resources in a location are exhausted, roots would shrink away from infertile conditions to preserve their activity. In order to validate optimization effect of the algorithm, twelve benchmark functions, including eight classic functions and four CEC2005 test functions, are tested in the experiments. We compared RGO with other existing evolutionary algorithms including artificial bee colony, particle swarm optimizer, and differential evolution algorithm. The experimental results show that RGO outperforms other algorithms on most benchmark functions.

  7. Protein kinesis: The dynamics of protein trafficking and stability

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  8. Tokunaga and Horton self-similarity for level set trees of Markov chains

    Zaliapin, Ilia; Kovchegov, Yevgeniy

    2012-01-01

    Highlights: ► Self-similar properties of the level set trees for Markov chains are studied. ► Tokunaga and Horton self-similarity are established for symmetric Markov chains and regular Brownian motion. ► Strong, distributional self-similarity is established for symmetric Markov chains with exponential jumps. ► It is conjectured that fractional Brownian motions are Tokunaga self-similar. - Abstract: The Horton and Tokunaga branching laws provide a convenient framework for studying self-similarity in random trees. The Horton self-similarity is a weaker property that addresses the principal branching in a tree; it is a counterpart of the power-law size distribution for elements of a branching system. The stronger Tokunaga self-similarity addresses so-called side branching. The Horton and Tokunaga self-similarity have been empirically established in numerous observed and modeled systems, and proven for two paradigmatic models: the critical Galton–Watson branching process with finite progeny and the finite-tree representation of a regular Brownian excursion. This study establishes the Tokunaga and Horton self-similarity for a tree representation of a finite symmetric homogeneous Markov chain. We also extend the concept of Horton and Tokunaga self-similarity to infinite trees and establish self-similarity for an infinite-tree representation of a regular Brownian motion. We conjecture that fractional Brownian motions are also Tokunaga and Horton self-similar, with self-similarity parameters depending on the Hurst exponent.

  9. How proteins modify water dynamics

    Persson, Filip; Söderhjelm, Pär; Halle, Bertil

    2018-06-01

    Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)—the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the

  10. Self-similar measures in multi-sector endogenous growth models

    La Torre, Davide; Marsiglio, Simone; Mendivil, Franklin; Privileggi, Fabio

    2015-01-01

    We analyze two types of stochastic discrete time multi-sector endogenous growth models, namely a basic Uzawa–Lucas (1965, 1988) model and an extended three-sector version as in La Torre and Marsiglio (2010). As in the case of sustained growth the optimal dynamics of the state variables are not stationary, we focus on the dynamics of the capital ratio variables, and we show that, through appropriate log-transformations, they can be converted into affine iterated function systems converging to an invariant distribution supported on some (possibly fractal) compact set. This proves that also the steady state of endogenous growth models—i.e., the stochastic balanced growth path equilibrium—might have a fractal nature. We also provide some sufficient conditions under which the associated self-similar measures turn out to be either singular or absolutely continuous (for the three-sector model we only consider the singularity).

  11. Internal structures of self-organized relaxed states and self-similar decay phase

    Kondoh, Yoshiomi

    1992-03-01

    A thought analysis on relaxation due to nonlinear processes is presented to lead to a set of general thoughts applicable to general nonlinear dynamical systems for finding out internal structures of the self-organized relaxed state without using 'invariant'. Three applications of the set of general thoughts to energy relaxations in resistive MHD plasmas, incompressible viscous fluids, and incompressible viscous MHD fluids are shown to lead to the internal structures of the self-organized relaxed states. It is shown that all of the relaxed states in these three dynamical systems are followed by self-similar decay phase without significant change of the spatial structure. The well known relaxed state of ∇ x B = ±λ B is shown to be derived generally in the low β plasma limit. (author)

  12. Revelation of the Sun Self-Similarity Skeletal Structures

    Rantsev-Kartinov, V.A.

    2005-01-01

    The analysis of databases of photographic images of a surface of the Sun, its atmosphere and the closest its space environment taken at various spatial resolutions and for various types of radiation of a surface of the Sun by means of a method multilevel dynamic contrasting, has revealed presence skeletal structures as on the Sun directly such and in its environment. It is demonstrated the revealed a global structures of the Sun and powerful ejections of mass of its corona, as well as the structures of its atmosphere, protuberances, sun-spots and a globular structures of its photosphere

  13. Analytic self-similar solutions of the Oberbeck–Boussinesq equations

    Barna, I.F.; Mátyás, L.

    2015-01-01

    In this article we will present pure two-dimensional analytic solutions for the coupled non-compressible Newtonian–Navier–Stokes — with Boussinesq approximation — and the heat conduction equation. The system was investigated from E.N. Lorenz half a century ago with Fourier series and pioneered the way to the paradigm of chaos. We present a novel analysis of the same system where the key idea is the two-dimensional generalization of the well-known self-similar Ansatz of Barenblatt which will be interpreted in a geometrical way. The results, the pressure, temperature and velocity fields are all analytic and can be expressed with the help of the error functions. The temperature field shows a strongly damped single periodic oscillation which can mimic the appearance of Rayleigh–Bénard convection cells. Finally, it is discussed how our result may be related to nonlinear or chaotic dynamical regimes

  14. Water-Protein Interactions: The Secret of Protein Dynamics

    Silvia Martini

    2013-01-01

    Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

  15. Exact self-similar solutions of the Korteweg de Vries equation

    Nakach, R.

    1975-12-01

    It is shown that the exact analytic self-similar solution of the Korteweg de Vries equation is connected with the second Painleve transcendent. When the self-similar independant variable tends to infinity the asymptotic solutions are given by a nonlinear differential equation which can be integrated to yield Jacobian elliptic functions [fr

  16. Self-similar solutions for toroidal magnetic fields in a turbulent jet

    Komissarov, S.S.; Ovchinnikov, I.L.

    1989-01-01

    Self-similar solutions for weak toroidal magnetic fields transported by a turbulent jet of incompressible fluid are obtained. It is shown that radial profiles of the self-similar solutions form a discrete spectrum of eigenfunctions of a linear differential operator. The strong depatures from the magnetic flux conservation law, used frequently in turbulent jet models for extragalactic radio sources, are found

  17. Self-similar drop-size distributions produced by breakup in chaotic flows

    Muzzio, F.J.; Tjahjadi, M.; Ottino, J.M.; Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003; Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208)

    1991-01-01

    Deformation and breakup of immiscible fluids in deterministic chaotic flows is governed by self-similar distributions of stretching histories and stretching rates and produces populations of droplets of widely distributed sizes. Scaling reveals that distributions of drop sizes collapse into two self-similar families; each family exhibits a different shape, presumably due to changes in the breakup mechanism

  18. The self-similar field and its application to a diffusion problem

    Michelitsch, Thomas M

    2011-01-01

    We introduce a continuum approach which accounts for self-similarity as a symmetry property of an infinite medium. A self-similar Laplacian operator is introduced which is the source of self-similar continuous fields. In this way ‘self-similar symmetry’ appears in an analogous manner as transverse isotropy or cubic symmetry of a medium. As a consequence of the self-similarity the Laplacian is a non-local fractional operator obtained as the continuum limit of the discrete self-similar Laplacian introduced recently by Michelitsch et al (2009 Phys. Rev. E 80 011135). The dispersion relation of the Laplacian and its Green’s function is deduced in closed forms. As a physical application of the approach we analyze a self-similar diffusion problem. The statistical distributions, which constitute the solutions of this problem, turn out to be Lévi-stable distributions with infinite variances characterizing the statistics of one-dimensional Lévi flights. The self-similar continuum approach introduced in this paper has the potential to be applied on a variety of scale invariant and fractal problems in physics such as in continuum mechanics, electrodynamics and in other fields. (paper)

  19. Self-similar solutions for implosion and reflection of coalesced shocks in a plasma : spherical and cylindrical geometries

    Chavda, L.K.

    1978-01-01

    Approximate analytic solutions to the self-similar equations of gas dynamics for a plasma, treated as an ideal gas with specific heat ratio γ=5/3 are obtained for the implosion and subsequent reflection of various types of shock sequences in spherical and cylindrical geometries. This is based on the lowest-order polynomial approximation in the reduced fluid velocity, for a suitable nonlinear function of the sound velocity and the fluid velocity. However, the method developed here is powerful enough to be extended analytically to higher order polynomial approximations, to obtain successive approximations to the exact self-similar solutions. Also obtained, for the first time, are exact asymptotic solutions, in analytic form, for the reflected shocks. Criteria are given that may enable one to make a choice between the two geometries for maximising compression or temperature of the gas. These solutions should be useful in the study of inertial confinement of a plasma. (author)

  20. Hydration dynamics near a model protein surface

    Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

    2003-01-01

    The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces

  1. Kovasznay modes in the linear stability analysis of self-similar ablation flows

    Lombard, V.

    2008-12-01

    Exact self-similar solutions of gas dynamics equations with nonlinear heat conduction for semi-infinite slabs of perfect gases are used for studying the stability of ablative flows in inertial confinement fusion, when a shock wave propagates in front of a thermal front. Both the similarity solutions and their linear perturbations are numerically computed with a dynamical multi-domain Chebyshev pseudo-spectral method. Laser-imprint results, showing that maximum amplification occurs for a laser-intensity modulation of zero transverse wavenumber have thus been obtained (Abeguile et al. (2006); Clarisse et al. (2008)). Here we pursue this approach by proceeding for the first time to an analysis of perturbations in terms of Kovasznay modes. Based on the analysis of two compressible and incompressible flows, evolution equations of vorticity, acoustic and entropy modes are proposed for each flow region and mode couplings are assessed. For short times, perturbations are transferred from the external surface to the ablation front by diffusion and propagate as acoustic waves up to the shock wave. For long times, the shock region is governed by the free propagation of acoustic waves. A study of perturbations and associated sources allows us to identify strong mode couplings in the conduction and ablation regions. Moreover, the maximum instability depends on compressibility. Finally, a comparison with experiments of flows subjected to initial surface defects is initiated. (author)

  2. Levy flights and self-similar exploratory behaviour of termite workers: beyond model fitting.

    Octavio Miramontes

    Full Text Available Animal movements have been related to optimal foraging strategies where self-similar trajectories are central. Most of the experimental studies done so far have focused mainly on fitting statistical models to data in order to test for movement patterns described by power-laws. Here we show by analyzing over half a million movement displacements that isolated termite workers actually exhibit a range of very interesting dynamical properties--including Lévy flights--in their exploratory behaviour. Going beyond the current trend of statistical model fitting alone, our study analyses anomalous diffusion and structure functions to estimate values of the scaling exponents describing displacement statistics. We evince the fractal nature of the movement patterns and show how the scaling exponents describing termite space exploration intriguingly comply with mathematical relations found in the physics of transport phenomena. By doing this, we rescue a rich variety of physical and biological phenomenology that can be potentially important and meaningful for the study of complex animal behavior and, in particular, for the study of how patterns of exploratory behaviour of individual social insects may impact not only their feeding demands but also nestmate encounter patterns and, hence, their dynamics at the social scale.

  3. Scaling of peak flows with constant flow velocity in random self-similar networks

    R. Mantilla

    2011-07-01

    Full Text Available A methodology is presented to understand the role of the statistical self-similar topology of real river networks on scaling, or power law, in peak flows for rainfall-runoff events. We created Monte Carlo generated sets of ensembles of 1000 random self-similar networks (RSNs with geometrically distributed interior and exterior generators having parameters pi and pe, respectively. The parameter values were chosen to replicate the observed topology of real river networks. We calculated flow hydrographs in each of these networks by numerically solving the link-based mass and momentum conservation equation under the assumption of constant flow velocity. From these simulated RSNs and hydrographs, the scaling exponents β and φ characterizing power laws with respect to drainage area, and corresponding to the width functions and flow hydrographs respectively, were estimated. We found that, in general, φ > β, which supports a similar finding first reported for simulations in the river network of the Walnut Gulch basin, Arizona. Theoretical estimation of β and φ in RSNs is a complex open problem. Therefore, using results for a simpler problem associated with the expected width function and expected hydrograph for an ensemble of RSNs, we give heuristic arguments for theoretical derivations of the scaling exponents β(E and φ(E that depend on the Horton ratios for stream lengths and areas. These ratios in turn have a known dependence on the parameters of the geometric distributions of RSN generators. Good agreement was found between the analytically conjectured values of β(E and φ(E and the values estimated by the simulated ensembles of RSNs and hydrographs. The independence of the scaling exponents φ(E and φ with respect to the value of flow velocity and runoff intensity implies an interesting connection between unit

  4. Scaling of peak flows with constant flow velocity in random self-similar networks

    Troutman, Brent M.; Mantilla, Ricardo; Gupta, Vijay K.

    2011-01-01

    A methodology is presented to understand the role of the statistical self-similar topology of real river networks on scaling, or power law, in peak flows for rainfall-runoff events. We created Monte Carlo generated sets of ensembles of 1000 random self-similar networks (RSNs) with geometrically distributed interior and exterior generators having parameters pi and pe, respectively. The parameter values were chosen to replicate the observed topology of real river networks. We calculated flow hydrographs in each of these networks by numerically solving the link-based mass and momentum conservation equation under the assumption of constant flow velocity. From these simulated RSNs and hydrographs, the scaling exponents β and φ characterizing power laws with respect to drainage area, and corresponding to the width functions and flow hydrographs respectively, were estimated. We found that, in general, φ > β, which supports a similar finding first reported for simulations in the river network of the Walnut Gulch basin, Arizona. Theoretical estimation of β and φ in RSNs is a complex open problem. Therefore, using results for a simpler problem associated with the expected width function and expected hydrograph for an ensemble of RSNs, we give heuristic arguments for theoretical derivations of the scaling exponents β(E) and φ(E) that depend on the Horton ratios for stream lengths and areas. These ratios in turn have a known dependence on the parameters of the geometric distributions of RSN generators. Good agreement was found between the analytically conjectured values of β(E) and φ(E) and the values estimated by the simulated ensembles of RSNs and hydrographs. The independence of the scaling exponents φ(E) and φ with respect to the value of flow velocity and runoff intensity implies an interesting connection between unit hydrograph theory and flow dynamics. Our results provide a reference framework to study scaling exponents under more complex scenarios

  5. Models for discrete-time self-similar vector processes with application to network traffic

    Lee, Seungsin; Rao, Raghuveer M.; Narasimha, Rajesh

    2003-07-01

    The paper defines self-similarity for vector processes by employing the discrete-time continuous-dilation operation which has successfully been used previously by the authors to define 1-D discrete-time stochastic self-similar processes. To define self-similarity of vector processes, it is required to consider the cross-correlation functions between different 1-D processes as well as the autocorrelation function of each constituent 1-D process in it. System models to synthesize self-similar vector processes are constructed based on the definition. With these systems, it is possible to generate self-similar vector processes from white noise inputs. An important aspect of the proposed models is that they can be used to synthesize various types of self-similar vector processes by choosing proper parameters. Additionally, the paper presents evidence of vector self-similarity in two-channel wireless LAN data and applies the aforementioned systems to simulate the corresponding network traffic traces.

  6. Inactivation of Tor proteins affects the dynamics of endocytic proteins ...

    Tor2 is an activator of the Rom2/Rho1 pathway that regulates -factor internalization. Since the recruitment of endocytic proteins such as actin-binding proteins and the amphiphysins precedes the internalization of -factor, we hypothesized that loss of Tor function leads to an alteration in the dynamics of the endocytic ...

  7. Advanced Models and Algorithms for Self-Similar IP Network Traffic Simulation and Performance Analysis

    Radev, Dimitar; Lokshina, Izabella

    2010-11-01

    The paper examines self-similar (or fractal) properties of real communication network traffic data over a wide range of time scales. These self-similar properties are very different from the properties of traditional models based on Poisson and Markov-modulated Poisson processes. Advanced fractal models of sequentional generators and fixed-length sequence generators, and efficient algorithms that are used to simulate self-similar behavior of IP network traffic data are developed and applied. Numerical examples are provided; and simulation results are obtained and analyzed.

  8. A novel numerical framework for self-similarity in plasticity: Wedge indentation in single crystals

    Juul, K. J.; Niordson, C. F.; Nielsen, K. L.

    2018-01-01

    -viscoplastic single crystal. However, the framework may be readily adapted to any constitutive law of interest. The main focus herein is the development of the self-similar framework, while the indentation study serves primarily as verification of the technique by comparing to existing numerical and analytical......A novel numerical framework for analyzing self-similar problems in plasticity is developed and demonstrated. Self-similar problems of this kind include processes such as stationary cracks, void growth, indentation etc. The proposed technique offers a simple and efficient method for handling...

  9. Self-similar optical pulses in competing cubic-quintic nonlinear media with distributed coefficients

    Zhang Jiefang; Tian Qing; Wang Yueyue; Dai Chaoqing; Wu Lei

    2010-01-01

    We present a systematic analysis of the self-similar propagation of optical pulses within the framework of the generalized cubic-quintic nonlinear Schroedinger equation with distributed coefficients. By appropriately choosing the relations between the distributed coefficients, we not only retrieve the exact self-similar solitonic solutions, but also find both the approximate self-similar Gaussian-Hermite solutions and compact solutions. Our analytical and numerical considerations reveal that proper choices of the distributed coefficients could make the unstable solitons stable and could restrict the nonlinear interaction between the neighboring solitons.

  10. Simultaneous determination of protein structure and dynamics

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  11. Self-organization phenomena and decaying self-similar state in two-dimensional incompressible viscous fluids

    Kondoh, Yoshiomi; Serizawa, Shunsuke; Nakano, Akihiro; Takahashi, Toshiki; Van Dam, James W.

    2004-01-01

    The final self-similar state of decaying two-dimensional (2D) turbulence in 2D incompressible viscous flow is analytically and numerically investigated for the case with periodic boundaries. It is proved by theoretical analysis and simulations that the sinh-Poisson state cω=-sinh(βψ) is not realized in the dynamical system of interest. It is shown by an eigenfunction spectrum analysis that a sufficient explanation for the self-organization to the decaying self-similar state is the faster energy decay of higher eigenmodes and the energy accumulation to the lowest eigenmode for given boundary conditions due to simultaneous normal and inverse cascading by nonlinear mode couplings. The theoretical prediction is demonstrated to be correct by simulations leading to the lowest eigenmode of {(1,0)+(0,1)} of the dissipative operator for the periodic boundaries. It is also clarified that an important process during nonlinear self-organization is an interchange between the dominant operators, which leads to the final decaying self-similar state

  12. Self-similar regimes of turbulence in weakly coupled plasmas under compression

    Viciconte, Giovanni; Gréa, Benoît-Joseph; Godeferd, Fabien S.

    2018-02-01

    Turbulence in weakly coupled plasmas under compression can experience a sudden dissipation of kinetic energy due to the abrupt growth of the viscosity coefficient governed by the temperature increase. We investigate in detail this phenomenon by considering a turbulent velocity field obeying the incompressible Navier-Stokes equations with a source term resulting from the mean velocity. The system can be simplified by a nonlinear change of variable, and then solved using both highly resolved direct numerical simulations and a spectral model based on the eddy-damped quasinormal Markovian closure. The model allows us to explore a wide range of initial Reynolds and compression numbers, beyond the reach of simulations, and thus permits us to evidence the presence of a nonlinear cascade phase. We find self-similarity of intermediate regimes as well as of the final decay of turbulence, and we demonstrate the importance of initial distribution of energy at large scales. This effect can explain the global sensitivity of the flow dynamics to initial conditions, which we also illustrate with simulations of compressed homogeneous isotropic turbulence and of imploding spherical turbulent layers relevant to inertial confinement fusion.

  13. An accurate algorithm to calculate the Hurst exponent of self-similar processes

    Fernández-Martínez, M.; Sánchez-Granero, M.A.; Trinidad Segovia, J.E.; Román-Sánchez, I.M.

    2014-01-01

    In this paper, we introduce a new approach which generalizes the GM2 algorithm (introduced in Sánchez-Granero et al. (2008) [52]) as well as fractal dimension algorithms (FD1, FD2 and FD3) (first appeared in Sánchez-Granero et al. (2012) [51]), providing an accurate algorithm to calculate the Hurst exponent of self-similar processes. We prove that this algorithm performs properly in the case of short time series when fractional Brownian motions and Lévy stable motions are considered. We conclude the paper with a dynamic study of the Hurst exponent evolution in the S and P500 index stocks. - Highlights: • We provide a new approach to properly calculate the Hurst exponent. • This generalizes FD algorithms and GM2, introduced previously by the authors. • This method (FD4) results especially appropriate for short time series. • FD4 may be used in both unifractal and multifractal contexts. • As an empirical application, we show that S and P500 stocks improved their efficiency

  14. Fast Diffusion to Self-Similarity: Complete Spectrum, Long-Time Asymptotics, and Numerology

    Denzler, Jochen; McCann, Robert J.

    2005-03-01

    The complete spectrum is determined for the operator on the Sobolev space W1,2ρ(Rn) formed by closing the smooth functions of compact support with respect to the norm Here the Barenblatt profile ρ is the stationary attractor of the rescaled diffusion equation in the fast, supercritical regime m the same diffusion dynamics represent the steepest descent down an entropy E(u) on probability measures with respect to the Wasserstein distance d2. Formally, the operator H=HessρE is the Hessian of this entropy at its minimum ρ, so the spectral gap H≧α:=2-n(1-m) found below suggests the sharp rate of asymptotic convergence: from any centered initial data 0≦u(0,x) ∈ L1(Rn) with second moments. This bound improves various results in the literature, and suggests the conjecture that the self-similar solution u(t,x)=R(t)-nρ(x/R(t)) is always slowest to converge. The higher eigenfunctions which are polynomials with hypergeometric radial parts and the presence of continuous spectrum yield additional insight into the relations between symmetries of Rn and the flow. Thus the rate of convergence can be improved if we are willing to replace the distance to ρ with the distance to its nearest mass-preserving dilation (or still better, affine image). The strange numerology of the spectrum is explained in terms of the number of moments of ρ.

  15. An accurate algorithm to calculate the Hurst exponent of self-similar processes

    Fernández-Martínez, M., E-mail: fmm124@ual.es [Department of Mathematics, Faculty of Science, Universidad de Almería, 04120 Almería (Spain); Sánchez-Granero, M.A., E-mail: misanche@ual.es [Department of Mathematics, Faculty of Science, Universidad de Almería, 04120 Almería (Spain); Trinidad Segovia, J.E., E-mail: jetrini@ual.es [Department of Accounting and Finance, Faculty of Economics and Business, Universidad de Almería, 04120 Almería (Spain); Román-Sánchez, I.M., E-mail: iroman@ual.es [Department of Accounting and Finance, Faculty of Economics and Business, Universidad de Almería, 04120 Almería (Spain)

    2014-06-27

    In this paper, we introduce a new approach which generalizes the GM2 algorithm (introduced in Sánchez-Granero et al. (2008) [52]) as well as fractal dimension algorithms (FD1, FD2 and FD3) (first appeared in Sánchez-Granero et al. (2012) [51]), providing an accurate algorithm to calculate the Hurst exponent of self-similar processes. We prove that this algorithm performs properly in the case of short time series when fractional Brownian motions and Lévy stable motions are considered. We conclude the paper with a dynamic study of the Hurst exponent evolution in the S and P500 index stocks. - Highlights: • We provide a new approach to properly calculate the Hurst exponent. • This generalizes FD algorithms and GM2, introduced previously by the authors. • This method (FD4) results especially appropriate for short time series. • FD4 may be used in both unifractal and multifractal contexts. • As an empirical application, we show that S and P500 stocks improved their efficiency.

  16. A Numerical Framework for Self-Similar Problems in Plasticity: Indentation in Single Crystals

    Juul, Kristian Jørgensen; Niordson, Christian Frithiof; Nielsen, Kim Lau

    A new numerical framework specialized for analyzing self-similar problems in plasticity is developed. Self-similarity in plasticity is encountered in a number of different problems such as stationary cracks, void growth, indentation etc. To date, such problems are handled by traditional Lagrangian...... procedures that may be associated with severe numerical difficulties relating to sufficient discretization, moving contact points, etc. In the present work, self-similarity is exploited to construct the numerical framework that offers a simple and efficient method to handle self-similar problems in history...... numerical simulations [3] when possible. To mimic the condition for the analytical predictions, the wedge indenter is considered nearly flat and the material is perfectly plastic with a very low yield strain. Under these conditions, [1][2] proved analytically the existence of discontinuities in the slip...

  17. Self-similarity and turbulence characteristics of wind turbine wakes via large-eddy simulation (Invited)

    Xie, S.; Archer, C. L.

    2013-12-01

    In this study, a new large-eddy simulation code, the Wind Turbine and Turbulence Simulator (WiTTS), is developed to study the wake generated from a single wind turbine in the neutral ABL. The WiTTS formulation is based on a scale-dependent Lagrangian dynamical model of the sub-grid shear stress and uses actuator lines to simulate the effects of the rotating blades. WiTTS is first tested against wind tunnel experiments and then used to study the commonly-used assumptions of self-similarity and axis-symmetry of the wake under neutral conditions for a variety of wind speeds and turbine properties. The mean velocity deficit shows good self-similarity properties following a normal distribution in the horizontal plane at the hub-height level. Self-similarity is a less valid approximation in the vertical near the ground, due to strong wind shear and ground effects. The mean velocity deficit is strongly dependent on the thrust coefficient or induction factor. A new relationship is proposed to model the mean velocity deficit along the centerline at the hub-height level to fit the LES results piecewise throughout the wake. A logarithmic function is used in the near and intermediate wake regions whereas a power function is used in the far-wake. These two functions provide a better fit to both simulated and observed wind velocity deficits than other functions previously used in wake models such as WAsP. The wind shear and impact with the ground cause an anisotropy in the expansion of the wake such that the wake grows faster horizontally than vertically. The wake deforms upon impact with the ground and spreads laterally. WiTTS is also used to study the turbulence characteristics in the wake. Aligning with the mean wind direction, the streamwise component of turbulence intensity is the dominant among the three components and thus it is further studied. The highest turbulence intensity occurs near the top-tip level. The added turbulence intensity increases fast in the near

  18. Hausdorff dimension of the arithmetic sum of self-similar sets

    Jiang, Kan

    Let β>1. We define a class of similitudes S:=(fi(x)=xβni+ai:ni∈N+,ai∈R). Taking any finite collection of similitudes (fi(x))i=1m from S, it is well known that there is a unique self-similar set K1 satisfying K1=∪i=1mfi(K1). Similarly, another self-similar set K2 can be generated via the finite

  19. Effects of Self-Similar Collisions in the Theory of Pressure Broadening and Shift

    Kharintsev, S.S.; Salakhov, M.Kh.

    1999-01-01

    In the present paper the self-similar collision model is developed in terms of fractal Brownian motion. Within this model framework, collisions are assumed to carry a non-Markovian character and, therefore, possible memory collisional effects are not taken into account. Applying a self-similar collision model for the motion of the radiator and Anderson-Talman phase-shift theory of collisional broadening, a general formula for the correlation function in the impact limit is described. (author)

  20. Effective Summation and Interpolation of Series by Self-Similar Root Approximants

    Simon Gluzman

    2015-06-01

    Full Text Available We describe a simple analytical method for effective summation of series, including divergent series. The method is based on self-similar approximation theory resulting in self-similar root approximants. The method is shown to be general and applicable to different problems, as is illustrated by a number of examples. The accuracy of the method is not worse, and in many cases better, than that of Padé approximants, when the latter can be defined.

  1. Functional dynamics of cell surface membrane proteins.

    Nishida, Noritaka; Osawa, Masanori; Takeuchi, Koh; Imai, Shunsuke; Stampoulis, Pavlos; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio

    2014-04-01

    Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes, which convert the structure of the receptor into an active conformation. However, recent NMR studies of cell surface membrane proteins have revealed that their structures are more dynamic than previously envisioned, and they fluctuate between multiple conformations in an equilibrium on various timescales. In addition, NMR analyses, along with biochemical and cell biological experiments indicated that such dynamical properties are critical for the proper functions of the receptors. In this review, we will describe several NMR studies that revealed direct linkage between the structural dynamics and the functions of the cell surface membrane proteins, such as G-protein coupled receptors (GPCRs), ion channels, membrane transporters, and cell adhesion molecules. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Proteins with Novel Structure, Function and Dynamics

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  3. Testing statistical self-similarity in the topology of river networks

    Troutman, Brent M.; Mantilla, Ricardo; Gupta, Vijay K.

    2010-01-01

    Recent work has demonstrated that the topological properties of real river networks deviate significantly from predictions of Shreve's random model. At the same time the property of mean self-similarity postulated by Tokunaga's model is well supported by data. Recently, a new class of network model called random self-similar networks (RSN) that combines self-similarity and randomness has been introduced to replicate important topological features observed in real river networks. We investigate if the hypothesis of statistical self-similarity in the RSN model is supported by data on a set of 30 basins located across the continental United States that encompass a wide range of hydroclimatic variability. We demonstrate that the generators of the RSN model obey a geometric distribution, and self-similarity holds in a statistical sense in 26 of these 30 basins. The parameters describing the distribution of interior and exterior generators are tested to be statistically different and the difference is shown to produce the well-known Hack's law. The inter-basin variability of RSN parameters is found to be statistically significant. We also test generator dependence on two climatic indices, mean annual precipitation and radiative index of dryness. Some indication of climatic influence on the generators is detected, but this influence is not statistically significant with the sample size available. Finally, two key applications of the RSN model to hydrology and geomorphology are briefly discussed.

  4. Dynamics in electron transfer protein complexes

    Bashir, Qamar

    2010-01-01

    Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We have used paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize the ensemble of encounter orientations in the short-lived electron transfer complex of yeast Cc and CcP. The complete conformational space sampled by the protein molecules during the dynamic part of ...

  5. Effects of self-similar correlations on the spectral line shape in the neutral gas

    Kharintsev, S.S.; Salakhov, M.Kh.

    2001-01-01

    The paper is devoted to the study of the influence of self-similar correlations on the Doppler and pressure broadening within the non-equilibrium Boltzmann gas. The diffuse model for the thermal motion of the radiator and the self-similar mechanism of interference of scalar perturbations for phase shifts of an atomic oscillator are developed. It is shown that taking into account self-similar correlation in a description of the spectral line shape allows one to explain, on the one hand, the additional spectral line Dicke-narrowing in the Doppler regime, and, on the other hand, the asymmetry in wings of the spectral line in a high pressure region

  6. Self-similar transmission properties of aperiodic Cantor potentials in gapped graphene

    Rodríguez-González, Rogelio; Rodríguez-Vargas, Isaac; Díaz-Guerrero, Dan Sidney; Gaggero-Sager, Luis Manuel

    2016-01-01

    We investigate the transmission properties of quasiperiodic or aperiodic structures based on graphene arranged according to the Cantor sequence. In particular, we have found self-similar behaviour in the transmission spectra, and most importantly, we have calculated the scalability of the spectra. To do this, we implement and propose scaling rules for each one of the fundamental parameters: generation number, height of the barriers and length of the system. With this in mind we have been able to reproduce the reference transmission spectrum, applying the appropriate scaling rule, by means of the scaled transmission spectrum. These scaling rules are valid for both normal and oblique incidence, and as far as we can see the basic ingredients to obtain self-similar characteristics are: relativistic Dirac electrons, a self-similar structure and the non-conservation of the pseudo-spin.

  7. Discrete Self-Similarity in Interfacial Hydrodynamics and the Formation of Iterated Structures.

    Dallaston, Michael C; Fontelos, Marco A; Tseluiko, Dmitri; Kalliadasis, Serafim

    2018-01-19

    The formation of iterated structures, such as satellite and subsatellite drops, filaments, and bubbles, is a common feature in interfacial hydrodynamics. Here we undertake a computational and theoretical study of their origin in the case of thin films of viscous fluids that are destabilized by long-range molecular or other forces. We demonstrate that iterated structures appear as a consequence of discrete self-similarity, where certain patterns repeat themselves, subject to rescaling, periodically in a logarithmic time scale. The result is an infinite sequence of ridges and filaments with similarity properties. The character of these discretely self-similar solutions as the result of a Hopf bifurcation from ordinarily self-similar solutions is also described.

  8. Irreversible thermodynamics, parabolic law and self-similar state in grain growth

    Rios, P.R.

    2004-01-01

    The formalism of the thermodynamic theory of irreversible processes is applied to grain growth to investigate the nature of the self-similar state and its corresponding parabolic law. Grain growth does not reach a steady state in the sense that the entropy production remains constant. However, the entropy production can be written as a product of two factors: a scale factor that tends to zero for long times and a scaled entropy production. It is suggested that the parabolic law and the self-similar state may be associated with the minimum of this scaled entropy production. This result implies that the parabolic law and the self-similar state have a sound irreversible thermodynamical basis

  9. Is a malleable protein necessarily highly dynamic?

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare

    2012-01-01

    core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...

  10. Molecular dynamics of surfactant protein C

    Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

    2006-01-01

    Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...

  11. Discretely Self-Similar Solutions to the Navier-Stokes Equations with Besov Space Data

    Bradshaw, Zachary; Tsai, Tai-Peng

    2017-12-01

    We construct self-similar solutions to the three dimensional Navier-Stokes equations for divergence free, self-similar initial data that can be large in the critical Besov space {\\dot{B}_{p,∞}^{3/p-1}} where 3 1. These results extend those of uc(Bradshaw) and uc(Tsai) (Ann Henri Poincaré 2016. https://doi.org/10.1007/s00023-016-0519-0) which dealt with initial data in L 3 w since {L^3_w\\subsetneq \\dot{B}_{p,∞}^{3/p-1}} for p > 3. We also provide several concrete examples of vector fields in the relevant function spaces.

  12. Chirped self-similar solutions of a generalized nonlinear Schroedinger equation

    Fei Jin-Xi [Lishui Univ., Zhejiang (China). College of Mathematics and Physics; Zheng Chun-Long [Shaoguan Univ., Guangdong (China). School of Physics and Electromechanical Engineering; Shanghai Univ. (China). Shanghai Inst. of Applied Mathematics and Mechanics

    2011-01-15

    An improved homogeneous balance principle and an F-expansion technique are used to construct exact chirped self-similar solutions to the generalized nonlinear Schroedinger equation with distributed dispersion, nonlinearity, and gain coefficients. Such solutions exist under certain conditions and impose constraints on the functions describing dispersion, nonlinearity, and distributed gain function. The results show that the chirp function is related only to the dispersion coefficient, however, it affects all of the system parameters, which influence the form of the wave amplitude. As few characteristic examples and some simple chirped self-similar waves are presented. (orig.)

  13. Cosmological model with anisotropic dark energy and self-similarity of the second kind

    Brandt, Carlos F. Charret; Silva, Maria de Fatima A. da; Rocha, Jaime F. Villas da; Chan, Roberto

    2006-01-01

    We study the evolution of an anisotropic fluid with self-similarity of the second kind. We found a class of solution to the Einstein field equations by assuming an equation of state where the radial pressure of the fluid is proportional to its energy density (p r =ωρ) and that the fluid moves along time-like geodesics. The equation of state and the anisotropy with self-similarity of second kind imply ω = -1. The energy conditions, geometrical and physical properties of the solutions are studied. We have found that for the parameter α=-1/2 , it may represent a Big Rip cosmological model. (author)

  14. Stable non-Gaussian self-similar processes with stationary increments

    Pipiras, Vladas

    2017-01-01

    This book provides a self-contained presentation on the structure of a large class of stable processes, known as self-similar mixed moving averages. The authors present a way to describe and classify these processes by relating them to so-called deterministic flows. The first sections in the book review random variables, stochastic processes, and integrals, moving on to rigidity and flows, and finally ending with mixed moving averages and self-similarity. In-depth appendices are also included. This book is aimed at graduate students and researchers working in probability theory and statistics.

  15. Self-similar photonic crystal cavity with ultrasmall mode volume for single-photon nonlinearities

    Choi, Hyeongrak; Heuck, Mikkel; Englund, Dirk

    2017-01-01

    We propose a photonic crystal cavity design with self-similar structure to achieve ultrasmall mode volume. We describe the concept with a silicon-air nanobeam cavity at λ ∼ 1550nm, reaching a mode volume of ∼ 7.01 × 10∼5λ3.......We propose a photonic crystal cavity design with self-similar structure to achieve ultrasmall mode volume. We describe the concept with a silicon-air nanobeam cavity at λ ∼ 1550nm, reaching a mode volume of ∼ 7.01 × 10∼5λ3....

  16. Constraint theory and hierarchical protein dynamics

    Phillips, J C [Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019 (United States)

    2004-11-10

    The complexity and functionality of proteins requires that they occupy an exponentially small fraction of configuration space (perhaps 10{sup -300}). How did evolution manage to create such unlikely objects? Thorpe has solved the static half of this problem (known in protein chemistry as Levinthal's paradox) by observing that for stress-free chain segments the complexity of optimally constrained elastic networks scales not with expN (where N {approx} 100-1000 is the number of amino acids in a protein), but only with N. Newman's results for diffusion in N-dimensional spaces provide suggestive insights into the dynamical half of the problem. He showed that the distribution of residence (or pausing) time between sign reversals changes qualitatively at N {approx}40. The overall sign of a protein can be defined in terms of a product of curvature and hydrophobic(philic) character over all amino acid residues. This construction agrees with the sizes of the smallest known proteins and prions, and it suggests a universal clock for protein molecular dynamics simulations.

  17. Constraint theory and hierarchical protein dynamics

    Phillips, J C

    2004-01-01

    The complexity and functionality of proteins requires that they occupy an exponentially small fraction of configuration space (perhaps 10 -300 ). How did evolution manage to create such unlikely objects? Thorpe has solved the static half of this problem (known in protein chemistry as Levinthal's paradox) by observing that for stress-free chain segments the complexity of optimally constrained elastic networks scales not with expN (where N ∼ 100-1000 is the number of amino acids in a protein), but only with N. Newman's results for diffusion in N-dimensional spaces provide suggestive insights into the dynamical half of the problem. He showed that the distribution of residence (or pausing) time between sign reversals changes qualitatively at N ∼40. The overall sign of a protein can be defined in terms of a product of curvature and hydrophobic(philic) character over all amino acid residues. This construction agrees with the sizes of the smallest known proteins and prions, and it suggests a universal clock for protein molecular dynamics simulations

  18. Self-similarity of proton spin and asymmetry of jet production

    Tokarev, M. V.; Zborovský, Imrich

    2015-01-01

    Roč. 12, č. 2 (2015), s. 214-220 ISSN 1547-4771 R&D Projects: GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : asymmetry * high energy * jets * polarization * proton-proton collisions * Self-similarity Subject RIV: BE - Theoretical Physics

  19. Smooth Optical Self-similar Emission of Gamma-Ray Bursts

    Lipunov, Vladimir; Simakov, Sergey; Gorbovskoy, Evgeny; Vlasenko, Daniil, E-mail: lipunov2007@gmail.com [Lomonosov Moscow State University, Sternberg Astronomical Institute, Universitetsky prospect, 13, 119992, Moscow (Russian Federation)

    2017-08-10

    We offer a new type of calibration for gamma-ray bursts (GRB), in which some class of GRB can be marked and share a common behavior. We name this behavior Smooth Optical Self-similar Emission (SOS-similar Emission) and identify this subclasses of GRBs with optical light curves described by a universal scaling function.

  20. Isomonodromic deformations and self-similar solutions of the Einstein-Maxwell equations

    Kitaev, A.V.

    1992-01-01

    It is shown that the self-similar solutions of the Einstein-Maxwell equations in the cylindrical case describe the isomonodromic deformations of ordinary linear differential equations with rational coefficients. New types of such solutions, expressed in terms of the fifth Painleve transcendent, are found. 24 refs

  1. Non-self-similar cracking in unidirectional metal-matrix composites

    Rajesh, G.; Dharani, L.R.

    1993-01-01

    Experimental investigations on the fracture behavior of unidirectional Metal Matrix Composites (MMC) show the presence of extensive matrix damage and non-self-similar cracking of fibers near the notch tip. These failures are primarily observed in the interior layers of an MMC, presenting experimental difficulties in studying them. Hence an investigation of the matrix damage and fiber fracture near the notch tip is necessary to determine the stress concentration at the notch tip. The classical shear lag (CLSL) assumption has been used in the present study to investigate longitudinal matrix damage and nonself-similar cracking of fibers at the notch tip of an MMC. It is seen that non-self-similar cracking of fibers reduces the stress concentration at the notch tip considerably and the effect of matrix damage is negligible after a large number of fibers have broken beyond the notch tip in a non-self-similar manner. Finally, an effort has been made to include non-self-similar fiber fracture and matrix damage to model the fracture behavior of a unidirectional boron/aluminum composite for two different matrices viz. a 6061-0 fully annealed aluminum matrix and a heat treated 6061-T6 aluminum matrix. Results have been drawn for several characteristics pertaining to the shear stiffnesses and the shear yield stresses of the two matrices and compared with the available experimental results

  2. Self-similar cosmological solutions with dark energy. II. Black holes, naked singularities, and wormholes

    Maeda, Hideki; Harada, Tomohiro; Carr, B. J.

    2008-01-01

    We use a combination of numerical and analytical methods, exploiting the equations derived in a preceding paper, to classify all spherically symmetric self-similar solutions which are asymptotically Friedmann at large distances and contain a perfect fluid with equation of state p=(γ-1)μ with 0<γ<2/3. The expansion of the Friedmann universe is accelerated in this case. We find a one-parameter family of self-similar solutions representing a black hole embedded in a Friedmann background. This suggests that, in contrast to the positive pressure case, black holes in a universe with dark energy can grow as fast as the Hubble horizon if they are not too large. There are also self-similar solutions which contain a central naked singularity with negative mass and solutions which represent a Friedmann universe connected to either another Friedmann universe or some other cosmological model. The latter are interpreted as self-similar cosmological white hole or wormhole solutions. The throats of these wormholes are defined as two-dimensional spheres with minimal area on a spacelike hypersurface and they are all nontraversable because of the absence of a past null infinity

  3. Self-similar drag reduction in plug-flow of suspensions of macroscopic fibers

    Gillissen, J.J.J.; Hoving, J.P.

    2012-01-01

    Pipe flow experiments show that turbulent drag reduction in plug-flow of concentrated suspensions of macroscopic fibers is a self-similar function of the wall shear stress over the fiber network yield stress. We model the experimental observations, by assuming a central fiber network plug, whose

  4. Self-Similarity and helical symmetry in vortex generator flow simulations

    Fernandez, U.; Velte, Clara Marika; Réthoré, Pierre-Elouan

    2014-01-01

    According to experimental observations, the vortices generated by vortex generators have previously been observed to be self-similar for both the axial (uz) and azimuthal (uӨ) velocity profiles. Further, the measured vortices have been observed to obey the criteria for helical symmetry...

  5. Self-similarity of the union of 3-part Cantor set with its two translations

    Dai Meifeng [Nonlinear Scientific Research Center, Faculty of Science, Jiangsu University, Zhenjiang 212013 (China)], E-mail: daimf@ujs.edu.cn; Tian Lixin [Nonlinear Scientific Research Center, Faculty of Science, Jiangsu University, Zhenjiang 212013 (China)], E-mail: tianlx@ujs.edu.cn

    2008-07-15

    For 3-part Cantor set, we first discuss the relationship between iterated function systems and the union of the set with its two translations. Then we obtain the necessary and sufficient condition that the union is a self-similar set with the open set condition.

  6. Collapsing perfect fluid in self-similar five dimensional space-time and cosmic censorship

    Ghosh, S.G.; Sarwe, S.B.; Saraykar, R.V.

    2002-01-01

    We investigate the occurrence and nature of naked singularities in the gravitational collapse of a self-similar adiabatic perfect fluid in a five dimensional space-time. The naked singularities are found to be gravitationally strong in the sense of Tipler and thus violate the cosmic censorship conjecture

  7. A NUMERICAL STUDY OF UNIVERSALITY AND SELF-SIMILARITY IN SOME FAMILIES OF FORCED LOGISTIC MAPS

    Rabassa, Pau; Jorba, Angel; Carles Tatjer, Joan

    We explore different two-parametric families of quasi-periodically Forced Logistic Maps looking for universality and self-similarity properties. In the bifurcation diagram of the one-dimensional Logistic Map, it is well known that there exist parameter values s(n) where the 2(n)-periodic orbit is

  8. Dynamics of proteins aggregation. II. Dynamic scaling in confined media

    Zheng, Size; Shing, Katherine S.; Sahimi, Muhammad

    2018-03-01

    In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.

  9. Protein Dynamics in the Plant Extracellular Space

    Leonor Guerra-Guimarães

    2016-07-01

    Full Text Available The extracellular space (ECS or apoplast is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF. The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in “cell wall organization and biogenesis”, “response to stimulus” and “protein metabolism”. It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.

  10. Generalized Ornstein-Uhlenbeck processes and associated self-similar processes

    Lim, S C; Muniandy, S V

    2003-01-01

    We consider three types of generalized Ornstein-Uhlenbeck processes: the stationary process obtained from the Lamperti transformation of fractional Brownian motion, the process with stretched exponential covariance and the process obtained from the solution of the fractional Langevin equation. These stationary Gaussian processes have many common properties, such as the fact that their local covariances share a similar structure and they exhibit identical spectral densities at large frequency limit. In addition, the generalized Ornstein-Uhlenbeck processes can be shown to be local stationary representations of fractional Brownian motion. Two new self-similar Gaussian processes, in addition to fractional Brownian motion, are obtained by applying the (inverse) Lamperti transformation to the generalized Ornstein-Uhlenbeck processes. We study some of the properties of these self-similar processes such as the long-range dependence. We give a simulation of their sample paths based on numerical Karhunan-Loeve expansion

  11. Generalized Ornstein-Uhlenbeck processes and associated self-similar processes

    Lim, S C

    2003-01-01

    We consider three types of generalized Ornstein-Uhlenbeck processes: the stationary process obtained from the Lamperti transformation of fractional Brownian motion, the process with stretched exponential covariance and the process obtained from the solution of the fractional Langevin equation. These stationary Gaussian processes have many common properties, such as the fact that their local covariances share a similar structure and they exhibit identical spectral densities at large frequency limit. In addition, the generalized Ornstein-Uhlenbeck processes can be shown to be local stationary representations of fractional Brownian motion. Two new self-similar Gaussian processes, in addition to fractional Brownian motion, are obtained by applying the (inverse) Lamperti transformation to the generalized Ornstein-Uhlenbeck processes. We study some of the properties of these self-similar processes such as the long-range dependence. We give a simulation of their sample paths based on numerical Karhunan-Loeve expansi...

  12. Tests of peak flow scaling in simulated self-similar river networks

    Menabde, M.; Veitzer, S.; Gupta, V.; Sivapalan, M.

    2001-01-01

    The effect of linear flow routing incorporating attenuation and network topology on peak flow scaling exponent is investigated for an instantaneously applied uniform runoff on simulated deterministic and random self-similar channel networks. The flow routing is modelled by a linear mass conservation equation for a discrete set of channel links connected in parallel and series, and having the same topology as the channel network. A quasi-analytical solution for the unit hydrograph is obtained in terms of recursion relations. The analysis of this solution shows that the peak flow has an asymptotically scaling dependence on the drainage area for deterministic Mandelbrot-Vicsek (MV) and Peano networks, as well as for a subclass of random self-similar channel networks. However, the scaling exponent is shown to be different from that predicted by the scaling properties of the maxima of the width functions. ?? 2001 Elsevier Science Ltd. All rights reserved.

  13. Reply to ''Comment on 'Extended self-similarity in turbulent flows' ''

    Benzi, R.; Ciliberto, S.; Tripiccione, R.; Baudet, C.; Massaioli, F.; Succi, S.

    1995-01-01

    In this Reply we question the conclusion of van de Water and Herweijer (WH) [preceding Comment, Phys. Rev. E 51, 2669 (1995)] about the evidence of multiscaling behavior in the dissipation range of turbulence. We perform the same analysis suggested by WH for the data set used by Benzi et al. [Phys. Rev. E 48, 29, (1993)] to establish extended self-similarity. At variance with WH, we do not observe any evidence of multiscaling. We argue that data filtering in WH could produce a misleading effect at very small scales. The combined effect of multiscaling and extended self-similarity is an important question that needs to be investigated in more detail, both theoretically and experimentally

  14. Self-similar formation of the Kolmogorov spectrum in the Leith model of turbulence

    Nazarenko, S V; Grebenev, V N

    2017-01-01

    The last stage of evolution toward the stationary Kolmogorov spectrum of hydrodynamic turbulence is studied using the Leith model [1]. This evolution is shown to manifest itself as a reflection wave in the wavenumber space propagating from the largest toward the smallest wavenumbers, and is described by a self-similar solution of a new (third) kind. This stage follows the previously studied stage of an initial explosive propagation of the spectral front from the smallest to the largest wavenumbers reaching arbitrarily large wavenumbers in a finite time, and which was described by a self-similar solution of the second kind [2–4]. Nonstationary solutions corresponding to ‘warm cascades’ characterised by a thermalised spectrum at large wavenumbers are also obtained. (paper)

  15. Violation of self-similarity in the expansion of a one-dimensional Bose gas

    Pedri, P.; Santos, L.; Oehberg, P.; Stringari, S.

    2003-01-01

    The expansion of a one-dimensional Bose gas after releasing its initial harmonic confinement is investigated employing the Lieb-Liniger equation of state within the local-density approximation. We show that during the expansion the density profile of the gas does not follow a self-similar solution, as one would expect from a simple scaling ansatz. We carry out a variational calculation, which recovers the numerical results for the expansion, the equilibrium properties of the density profile, and the frequency of the lowest compressional mode. The variational approach allows for the analysis of the expansion in all interaction regimes between the mean-field and the Tonks-Girardeau limits, and in particular shows the range of parameters for which the expansion violates self-similarity

  16. Self-similarity of proton spin and asymmetry of jet production

    Tokarev, M.V.; Zborovsky, I.

    2014-01-01

    Self-similarity of jet production in polarized p + p collisions is studied. The concept of z-scaling is applied for description of inclusive spectra obtained with different orientations of proton spin. New data on the double longitudinal spin asymmetry, A LL , of jets produced in proton-proton collisions at √s = 200 GeV measured by the STAR Collaboration at RHIC are analyzed in the z-scaling approach. Hypotheses of self-similarity and fractality of internal spin structure are formulated. A possibility to extract information on spin-dependent fractal dimensions of proton from the asymmetry of jet production is justified. The spin-dependent fractal dimensions for the process p-bar+p-bar→jet+X are estimated.

  17. Exact self-similar solutions for the magnetized Noh Z pinch problem

    Velikovich, A. L.; Giuliani, J. L.; Thornhill, J. W.; Zalesak, S. T.; Gardiner, T. A.

    2012-01-01

    A self-similar solution is derived for a radially imploding cylindrical plasma with an embedded, azimuthal magnetic field. The plasma stagnates through a strong, outward propagating shock wave of constant velocity. This analysis is an extension of the classic Noh gasdynamics problem to its ideal magnetohydrodynamics (MHD) counterpart. The present exact solution is especially suitable as a test for MHD codes designed to simulate linear Z pinches. To demonstrate the application of the new solution to code verification, simulation results from the cylindrical R-Z version of Mach2 and the 3D Cartesian code Athena are compared against the analytic solution. Alternative routines from the default ones in Athena lead to significant improvement of the results, thereby demonstrating the utility of the self-similar solution for verification.

  18. Wind loads and competition for light sculpt trees into self-similar structures.

    Eloy, Christophe; Fournier, Meriem; Lacointe, André; Moulia, Bruno

    2017-10-18

    Trees are self-similar structures: their branch lengths and diameters vary allometrically within the tree architecture, with longer and thicker branches near the ground. These tree allometries are often attributed to optimisation of hydraulic sap transport and safety against elastic buckling. Here, we show that these allometries also emerge from a model that includes competition for light, wind biomechanics and no hydraulics. We have developed MECHATREE, a numerical model of trees growing and evolving on a virtual island. With this model, we identify the fittest growth strategy when trees compete for light and allocate their photosynthates to grow seeds, create new branches or reinforce existing ones in response to wind-induced loads. Strikingly, we find that selected trees species are self-similar and follow allometric scalings similar to those observed on dicots and conifers. This result suggests that resistance to wind and competition for light play an essential role in determining tree allometries.

  19. Rayleigh-Taylor instability of a self-similar spherical expansion

    Bernstein, I.B.; Book, D.L.

    1978-01-01

    The self-similar motion of a spherically symmetric isentropic cloud of ideal gas driven outward by an expanding low-density medium (e.g., radiation pressure from a pulsar) is shown to be unstable to Rayleigh-Taylor modes which develop in the neighborhood of the interface. A complete solution of the linearized equations of motion is obtained. The implications for astrophysical phenomena are discussed

  20. Self-similar regimes of fast ionization waves in shielded discharge tubes

    Gerasimov, D.N.; Sinkevich, O.A.

    1999-01-01

    An analytical self-similar solution to the problem of the propagation of a fast ionization wave (FIW) in a long shielded tube is constructed. An expression determining the influence of the device parameters on the FIW velocity is obtained; the velocity is found to be the nonmonotonic function of the working-gas pressure. The theoretical predictions are compared with the results of experiments carried out with helium and nitrogen. The calculation and experimental results agree within experimental errors

  1. Self-Similar Nanocavity Design with Ultrasmall Mode Volume for Single-Photon Nonlinearities

    Choi, Hyeongrak; Heuck, Mikkel; Englund, Dirk R.

    2017-01-01

    We propose a photonic crystal nanocavity design with self-similar electromagnetic boundary conditions, achieving ultrasmall mode volume (V-eff). The electric energy density of a cavity mode can be maximized in the air or dielectric region, depending on the choice of boundary conditions. We illust...... at the single-photon level. These features open new directions in cavity quantum electrodynamics, spectroscopy, and quantum nonlinear optics....

  2. Self-similar structure in the distribution and density of the partition function zeros

    Huang, M.-C.; Luo, Y.-P.; Liaw, T.-M.

    2003-01-01

    Based on the knowledge of the partition function zeros for the cell-decorated triangular Ising model, we analyze the similar structures contained in the distribution pattern and density function of the zeros. The two own the same symmetries, and the arising of the similar structure in the road toward the infinite decoration-level is exhibited explicitly. The distinct features of the formation of the self-similar structure revealed from this model may be quite general

  3. Self-similar spherical gravitational collapse and the cosmic censorship hypothesis

    Ori, A.; Piran, T.

    1988-01-01

    The authors show that a self-similar general relativistic spherical collapse of a perfect fluid with an adiabatic equation of state p = (lambda -1)rho and low enough lambda values, results in a naked singularity. The singularity is tangent to an event horizon which surrounds a massive singularity and the redshift along a null geodesic from the singularity to an external observer is infinite. The authors believe that this is the most serious counter example to cosmic censorship obtained so far.

  4. Self-similarities of periodic structures for a discrete model of a two-gene system

    Souza, S.L.T. de; Lima, A.A.; Caldas, I.L.; Medrano-T, R.O.; Guimarães-Filho, Z.O.

    2012-01-01

    We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. -- Highlights: ► The existence of noticeable periodic windows has been reported recently for several nonlinear systems. ► The periodic window distributions appear highly organized in two-parameter space. ► We characterize self-similar properties of Arnold tongues and shrimps for a two-gene model. ► We determine the period of the Arnold tongues recognizing a Fibonacci-type sequence. ► We explore self-similar features of the shrimps identifying multiple period-three structures.

  5. Self-Similarity of Plasmon Edge Modes on Koch Fractal Antennas.

    Bellido, Edson P; Bernasconi, Gabriel D; Rossouw, David; Butet, Jérémy; Martin, Olivier J F; Botton, Gianluigi A

    2017-11-28

    We investigate the plasmonic behavior of Koch snowflake fractal geometries and their possible application as broadband optical antennas. Lithographically defined planar silver Koch fractal antennas were fabricated and characterized with high spatial and spectral resolution using electron energy loss spectroscopy. The experimental data are supported by numerical calculations carried out with a surface integral equation method. Multiple surface plasmon edge modes supported by the fractal structures have been imaged and analyzed. Furthermore, by isolating and reproducing self-similar features in long silver strip antennas, the edge modes present in the Koch snowflake fractals are identified. We demonstrate that the fractal response can be obtained by the sum of basic self-similar segments called characteristic edge units. Interestingly, the plasmon edge modes follow a fractal-scaling rule that depends on these self-similar segments formed in the structure after a fractal iteration. As the size of a fractal structure is reduced, coupling of the modes in the characteristic edge units becomes relevant, and the symmetry of the fractal affects the formation of hybrid modes. This analysis can be utilized not only to understand the edge modes in other planar structures but also in the design and fabrication of fractal structures for nanophotonic applications.

  6. Self-similarities of periodic structures for a discrete model of a two-gene system

    Souza, S.L.T. de, E-mail: thomaz@ufsj.edu.br [Departamento de Física e Matemática, Universidade Federal de São João del-Rei, Ouro Branco, MG (Brazil); Lima, A.A. [Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG (Brazil); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, São Paulo, SP (Brazil); Medrano-T, R.O. [Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, SP (Brazil); Guimarães-Filho, Z.O. [Aix-Marseille Univ., CNRS PIIM UMR6633, International Institute for Fusion Science, Marseille (France)

    2012-03-12

    We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. -- Highlights: ► The existence of noticeable periodic windows has been reported recently for several nonlinear systems. ► The periodic window distributions appear highly organized in two-parameter space. ► We characterize self-similar properties of Arnold tongues and shrimps for a two-gene model. ► We determine the period of the Arnold tongues recognizing a Fibonacci-type sequence. ► We explore self-similar features of the shrimps identifying multiple period-three structures.

  7. Neural processing of race during imitation: self-similarity versus social status

    Reynolds Losin, Elizabeth A.; Cross, Katy A.; Iacoboni, Marco; Dapretto, Mirella

    2017-01-01

    People preferentially imitate others who are similar to them or have high social status. Such imitative biases are thought to have evolved because they increase the efficiency of cultural acquisition. Here we focused on distinguishing between self-similarity and social status as two candidate mechanisms underlying neural responses to a person’s race during imitation. We used fMRI to measure neural responses when 20 African American (AA) and 20 European American (EA) young adults imitated AA, EA and Chinese American (CA) models and also passively observed their gestures and faces. We found that both AA and EA participants exhibited more activity in lateral fronto-parietal and visual regions when imitating AAs compared to EAs or CAs. These results suggest that racial self-similarity is not likely to modulate neural responses to race during imitation, in contrast with findings from previous neuroimaging studies of face perception and action observation. Furthermore, AA and EA participants associated AAs with lower social status than EAs or CAs, suggesting that the social status associated with different racial groups may instead modulate neural activity during imitation of individuals from those groups. Taken together, these findings suggest that neural responses to race during imitation are driven by socially-learned associations rather than self-similarity. This may reflect the adaptive role of imitation in social learning, where learning from higher-status models can be more beneficial. This study provides neural evidence consistent with evolutionary theories of cultural acquisition. PMID:23813738

  8. Soliton shock wave fronts and self-similar discontinuities in dispersion hydrodynamics

    Gurevich, A.V.; Meshcherkin, A.P.

    1987-01-01

    Nonlinear flows in nondissipative dispersion hydrodynamics are examined. It is demonstrated that in order to describe such flows it is necessary to incorporate a new concept: a special discontinuity called a ''self-similar'' discontinuity consisting of a nondissipative shock wave and a powerful slow wave discontinuity in regular hydrodynamics. The ''self similar discontinuity'' expands linearly over time. It is demonstrated that this concept may be introduced in a solution to Euler equations. The boundary conditions of the ''self similar discontinuity'' that allow closure of Euler equations for dispersion hydrodynamics are formulated, i.e., those that replace the shock adiabatic curve of standard dissipative hydrodynamics. The structure of the soliton front and of the trailing edge of the shock wave is investigated. A classification and complete solution are given to the problem of the decay of random initial discontinuities in the hydrodynamics of highly nonisothermic plasma. A solution is derived to the problem of the decay of initial discontinuities in the hydrodynamics of magnetized plasma. It is demonstrated that in this plasma, a feature of current density arises at the point of soliton inversion

  9. Self-similarity in high Atwood number Rayleigh-Taylor experiments

    Mikhaeil, Mark; Suchandra, Prasoon; Pathikonda, Gokul; Ranjan, Devesh

    2017-11-01

    Self-similarity is a critical concept in turbulent and mixing flows. In the Rayleigh-Taylor instability, theory and simulations have shown that the flow exhibits properties of self-similarity as the mixing Reynolds number exceeds 20000 and the flow enters the turbulent regime. Here, we present results from the first large Atwood number (0.7) Rayleigh-Taylor experimental campaign for mixing Reynolds number beyond 20000 in an effort to characterize the self-similar nature of the instability. Experiments are performed in a statistically steady gas tunnel facility, allowing for the evaluation of turbulence statistics. A visualization diagnostic is used to study the evolution of the mixing width as the instability grows. This allows for computation of the instability growth rate. For the first time in such a facility, stereoscopic particle image velocimetry is used to resolve three-component velocity information in a plane. Velocity means, fluctuations, and correlations are considered as well as their appropriate scaling. Probability density functions of velocity fields, energy spectra, and higher-order statistics are also presented. The energy budget of the flow is described, including the ratio of the kinetic energy to the released potential energy. This work was supported by the DOE-NNSA SSAA Grant DE-NA0002922.

  10. Waveguiding and mirroring effects in stochastic self-similar and Cantorian ε(∞) universe

    Iovane, G.

    2005-01-01

    A waveguiding effect is considered with respect to the large scale structure of the Universe, where the structures formation appears as if it were a classically self-similar random process at all astrophysical scales. The result is that it seems we live in an El Naschie's ε (∞) Cantorian space-time, where gravitational lensing and waveguiding effects can explain the appearing Universe. In particular, we consider filamentary and planar large scale structures as possible refraction channels for electromagnetic radiation coming from cosmological structures. From this vision the Universe appears like a large self-similar adaptive mirrors set. Consequently, an infinite Universe is just an optical illusion that is produced by mirroring effects connected with the large scale structure of a finite and not so large Universe. Thanks to the presented analytical model supported by a numerical simulation, it is possible to explain the quasar luminosity distribution and the presence of 'twin' or 'brother' objects. More generally, the infinity and the abundance of astrophysical objects could be just a mirroring effect due to the peculiar self-similarity of the Universe

  11. A novel numerical framework for self-similarity in plasticity: Wedge indentation in single crystals

    Juul, K. J.; Niordson, C. F.; Nielsen, K. L.; Kysar, J. W.

    2018-03-01

    A novel numerical framework for analyzing self-similar problems in plasticity is developed and demonstrated. Self-similar problems of this kind include processes such as stationary cracks, void growth, indentation etc. The proposed technique offers a simple and efficient method for handling this class of complex problems by avoiding issues related to traditional Lagrangian procedures. Moreover, the proposed technique allows for focusing the mesh in the region of interest. In the present paper, the technique is exploited to analyze the well-known wedge indentation problem of an elastic-viscoplastic single crystal. However, the framework may be readily adapted to any constitutive law of interest. The main focus herein is the development of the self-similar framework, while the indentation study serves primarily as verification of the technique by comparing to existing numerical and analytical studies. In this study, the three most common metal crystal structures will be investigated, namely the face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal close packed (HCP) crystal structures, where the stress and slip rate fields around the moving contact point singularity are presented.

  12. Self-Similarity Superresolution for Resource-Constrained Image Sensor Node in Wireless Sensor Networks

    Yuehai Wang

    2014-01-01

    Full Text Available Wireless sensor networks, in combination with image sensors, open up a grand sensing application field. It is a challenging problem to recover a high resolution (HR image from its low resolution (LR counterpart, especially for low-cost resource-constrained image sensors with limited resolution. Sparse representation-based techniques have been developed recently and increasingly to solve this ill-posed inverse problem. Most of these solutions are based on an external dictionary learned from huge image gallery, consequently needing tremendous iteration and long time to match. In this paper, we explore the self-similarity inside the image itself, and propose a new combined self-similarity superresolution (SR solution, with low computation cost and high recover performance. In the self-similarity image super resolution model (SSIR, a small size sparse dictionary is learned from the image itself by the methods such as KSVD. The most similar patch is searched and specially combined during the sparse regulation iteration. Detailed information, such as edge sharpness, is preserved more faithfully and clearly. Experiment results confirm the effectiveness and efficiency of this double self-learning method in the image super resolution.

  13. Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

    Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

    2011-01-01

    The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

  14. Dynamic prestress in a globular protein.

    Scott A Edwards

    Full Text Available A protein at equilibrium is commonly thought of as a fully relaxed structure, with the intra-molecular interactions showing fluctuations around their energy minimum. In contrast, here we find direct evidence for a protein as a molecular tensegrity structure, comprising a balance of tensed and compressed interactions, a concept that has been put forward for macroscopic structures. We quantified the distribution of inter-residue prestress in ubiquitin and immunoglobulin from all-atom molecular dynamics simulations. The network of highly fluctuating yet significant inter-residue forces in proteins is a consequence of the intrinsic frustration of a protein when sampling its rugged energy landscape. In beta sheets, this balance of forces is found to compress the intra-strand hydrogen bonds. We estimate that the observed magnitude of this pre-compression is enough to induce significant changes in the hydrogen bond lifetimes; thus, prestress, which can be as high as a few 100 pN, can be considered a key factor in determining the unfolding kinetics and pathway of proteins under force. Strong pre-tension in certain salt bridges on the other hand is connected to the thermodynamic stability of ubiquitin. Effective force profiles between some side-chains reveal the signature of multiple, distinct conformational states, and such static disorder could be one factor explaining the growing body of experiments revealing non-exponential unfolding kinetics of proteins. The design of prestress distributions in engineering proteins promises to be a new tool for tailoring the mechanical properties of made-to-order nanomaterials.

  15. Multidimensional Riemann problem with self-similar internal structure. Part II - Application to hyperbolic conservation laws on unstructured meshes

    Balsara, Dinshaw S.; Dumbser, Michael

    2015-04-01

    Multidimensional Riemann solvers that have internal sub-structure in the strongly-interacting state have been formulated recently (D.S. Balsara (2012, 2014) [5,16]). Any multidimensional Riemann solver operates at the grid vertices and takes as its input all the states from its surrounding elements. It yields as its output an approximation of the strongly interacting state, as well as the numerical fluxes. The multidimensional Riemann problem produces a self-similar strongly-interacting state which is the result of several one-dimensional Riemann problems interacting with each other. To compute this strongly interacting state and its higher order moments we propose the use of a Galerkin-type formulation to compute the strongly interacting state and its higher order moments in terms of similarity variables. The use of substructure in the Riemann problem reduces numerical dissipation and, therefore, allows a better preservation of flow structures, like contact and shear waves. In this second part of a series of papers we describe how this technique is extended to unstructured triangular meshes. All necessary details for a practical computer code implementation are discussed. In particular, we explicitly present all the issues related to computational geometry. Because these Riemann solvers are Multidimensional and have Self-similar strongly-Interacting states that are obtained by Consistency with the conservation law, we call them MuSIC Riemann solvers. (A video introduction to multidimensional Riemann solvers is available on http://www.elsevier.com/xml/linking-roles/text/html". The MuSIC framework is sufficiently general to handle general nonlinear systems of hyperbolic conservation laws in multiple space dimensions. It can also accommodate all self-similar one-dimensional Riemann solvers and subsequently produces a multidimensional version of the same. In this paper we focus on unstructured triangular meshes. As examples of different systems of conservation laws we

  16. Size distribution of dust grains: A problem of self-similarity

    Henning, TH.; Dorschner, J.; Guertler, J.

    1989-01-01

    Distribution functions describing the results of natural processes frequently show the shape of power laws. It is an open question whether this behavior is a result simply coming about by the chosen mathematical representation of the observational data or reflects a deep-seated principle of nature. The authors suppose the latter being the case. Using a dust model consisting of silicate and graphite grains Mathis et al. (1977) showed that the interstellar extinction curve can be represented by taking a grain radii distribution of power law type n(a) varies as a(exp -p) with 3.3 less than or equal to p less than or equal to 3.6 (example 1) as a basis. A different approach to understanding power laws like that in example 1 becomes possible by the theory of self-similar processes (scale invariance). The beta model of turbulence (Frisch et al., 1978) leads in an elementary way to the concept of the self-similarity dimension D, a special case of Mandelbrot's (1977) fractal dimension. In the frame of this beta model, it is supposed that on each stage of a cascade the system decays to N clumps and that only the portion beta N remains active further on. An important feature of this model is that the active eddies become less and less space-filling. In the following, the authors assume that grain-grain collisions are such a scale-invarient process and that the remaining grains are the inactive (frozen) clumps of the cascade. In this way, a size distribution n(a) da varies as a(exp -(D+1))da (example 2) results. It seems to be highly probable that the power law character of the size distribution of interstellar dust grains is the result of a self-similarity process. We can, however, not exclude that the process leading to the interstellar grain size distribution is not fragmentation at all

  17. Self-similar solutions for multi-species plasma mixing by gradient driven transport

    Vold, E.; Kagan, G.; Simakov, A. N.; Molvig, K.; Yin, L.

    2018-05-01

    Multi-species transport of plasma ions across an initial interface between DT and CH is shown to exhibit self-similar species density profiles under 1D isobaric conditions. Results using transport theory from recent studies and using a Maxwell–Stephan multi-species approximation are found to be in good agreement for the self-similar mix profiles of the four ions under isothermal and isobaric conditions. The individual ion species mass flux and molar flux profile results through the mixing layer are examined using transport theory. The sum over species mass flux is confirmed to be zero as required, and the sum over species molar flux is related to a local velocity divergence needed to maintain pressure equilibrium during the transport process. The light ion species mass fluxes are dominated by the diagonal coefficients of the diffusion transport matrix, while for the heaviest ion species (C in this case), the ion flux with only the diagonal term is reduced by about a factor two from that using the full diffusion matrix, implying the heavy species moves more by frictional collisions with the lighter species than by its own gradient force. Temperature gradient forces were examined by comparing profile results with and without imposing constant temperature gradients chosen to be of realistic magnitude for ICF experimental conditions at a fuel-capsule interface (10 μm scale length or greater). The temperature gradients clearly modify the relative concentrations of the ions, for example near the fuel center, however the mixing across the fuel-capsule interface appears to be minimally influenced by the temperature gradient forces within the expected compression and burn time. Discussion considers the application of the self-similar profiles to specific conditions in ICF.

  18. Seismodynamics of extended underground structures and soils: Statement of the problem and self-similar solutions

    Georgievskii, D. V.; Israilov, M. Sh.

    2015-07-01

    In the problems of common vibrations of extended underground structures (pipelines and tunnels) and soil, an approach of the one-dimensional deformation of the medium is developed; this approach is based on the assumption that the soil deformation in the direction of seismic wave propagation coinciding with the pipeline axis is prevailing. The analytic solutions are obtained in the cases where the wave velocity in the soil is respectively less or greater than the wave velocity in the pipeline. The parameters influencing the pipeline fracture are revealed and methods for increasing the seismic stability of such structures are given. The possibility of the pipeline fatigue fracture is pointed out. The statements and solutions of parabolic problems modeling the physical phenomena in soils in the case of discontinuous velocity on the boundaries at the initial time are given. The notion of generalized vorticity diffusion is introduced and the cases of self-similarity existence are classified. A detailed analysis is performed for the non-Newtonian polynomial fluid, the medium close in properties to the rigidly ideally plastic body, and the viscoplastic Shvedov—Bingham body. In the case of physically linear medium, new self-similar solutions are obtained which describe the process of unsteady axially symmetric shear in spherical coordinates. The first approximation to the asymptotic solution of the problem of the vortex sheet diffusion is constructed in a medium with small polynomial nonlinearity. The solutions polynomially decreasing to zero as the self-similar variable increases are proposed in the class of two-constant fluids.

  19. Earthquake source scaling and self-similarity estimation from stacking P and S spectra

    Prieto, GermáN. A.; Shearer, Peter M.; Vernon, Frank L.; Kilb, Debi

    2004-08-01

    We study the scaling relationships of source parameters and the self-similarity of earthquake spectra by analyzing a cluster of over 400 small earthquakes (ML = 0.5 to 3.4) recorded by the Anza seismic network in southern California. We compute P, S, and preevent noise spectra from each seismogram using a multitaper technique and approximate source and receiver terms by iteratively stacking the spectra. To estimate scaling relationships, we average the spectra in size bins based on their relative moment. We correct for attenuation by using the smallest moment bin as an empirical Green's function (EGF) for the stacked spectra in the larger moment bins. The shapes of the log spectra agree within their estimated uncertainties after shifting along the ω-3 line expected for self-similarity of the source spectra. We also estimate corner frequencies and radiated energy from the relative source spectra using a simple source model. The ratio between radiated seismic energy and seismic moment (proportional to apparent stress) is nearly constant with increasing moment over the magnitude range of our EGF-corrected data (ML = 1.8 to 3.4). Corner frequencies vary inversely as the cube root of moment, as expected from the observed self-similarity in the spectra. The ratio between P and S corner frequencies is observed to be 1.6 ± 0.2. We obtain values for absolute moment and energy by calibrating our results to local magnitudes for these earthquakes. This yields a S to P energy ratio of 9 ± 1.5 and a value of apparent stress of about 1 MPa.

  20. Effective self-similar expansion for the Gross-Pitaevskii equation

    Modugno, Michele; Pagnini, Gianni; Valle-Basagoiti, Manuel Angel

    2018-04-01

    We consider an effective scaling approach for the free expansion of a one-dimensional quantum wave packet, consisting in a self-similar evolution to be satisfied on average, i.e., by integrating over the coordinates. A direct comparison with the solution of the Gross-Pitaevskii equation shows that the effective scaling reproduces with great accuracy the exact evolution—the actual wave function is reproduced with a fidelity close to one—for arbitrary values of the interactions. This result represents a proof of concept of the effectiveness of the scaling ansatz, which has been used in different forms in the literature but never compared against the exact evolution.

  1. Anomalous Traffic Detection and Self-Similarity Analysis in the Environment of ATMSim

    Hae-Duck J. Jeong

    2017-12-01

    Full Text Available Internet utilisation has steadily increased, predominantly due to the rapid recent development of information and communication networks and the widespread distribution of smartphones. As a result of this increase in Internet consumption, various types of services, including web services, social networking services (SNS, Internet banking, and remote processing systems have been created. These services have significantly enhanced global quality of life. However, as a negative side-effect of this rapid development, serious information security problems have also surfaced, which has led to serious to Internet privacy invasions and network attacks. In an attempt to contribute to the process of addressing these problems, this paper proposes a process to detect anomalous traffic using self-similarity analysis in the Anomaly Teletraffic detection Measurement analysis Simulator (ATMSim environment as a research method. Simulations were performed to measure normal and anomalous traffic. First, normal traffic for each attack, including the Address Resolution Protocol (ARP and distributed denial-of-service (DDoS was measured for 48 h over 10 iterations. Hadoop was used to facilitate processing of the large amount of collected data, after which MapReduce was utilised after storing the data in the Hadoop Distributed File System (HDFS. A new platform on Hadoop, the detection system ATMSim, was used to identify anomalous traffic after which a comparative analysis of the normal and anomalous traffic was performed through a self-similarity analysis. There were four categories of collected traffic that were divided according to the attack methods used: normal local area network (LAN traffic, DDoS attack, and ARP spoofing, as well as DDoS and ARP attack. ATMSim, the anomaly traffic detection system, was used to determine if real attacks could be identified effectively. To achieve this, the ATMSim was used in simulations for each scenario to test its ability to

  2. Self-similar solutions for poloidal magnetic field in turbulent jet

    Komissarov, S.S.; Ovchinnikov, I.L.

    1990-01-01

    Evolution of a large-scale magnetic field in a turbulent extragalactic source radio jets is considered. Self-similar solutions for a weak poloidal magnetic field transported by turbulent jet of incompressible fluid are found. It is shown that the radial profiles of the solutions are the eigenfunctions of a linear differential operator. In all the solutions, the strength of a large-scale field decreases more rapidly than that of a small-scale turbulent field. This can be understood as a decay of a large-scale field in the turbulent jet

  3. Non self-similar collapses described by the non-linear Schroedinger equation

    Berge, L.; Pesme, D.

    1992-01-01

    We develop a rapid method in order to find the contraction rates of the radially symmetric collapsing solutions of the nonlinear Schroedinger equation defined for space dimensions exceeding a threshold value. We explicitly determine the asymptotic behaviour of these latter solutions by solving the non stationary linear problem relative to the nonlinear Schroedinger equation. We show that the self-similar states associated with the collapsing solutions are characterized by a spatial extent which is bounded from the top by a cut-off radius

  4. Dimensional analysis and self-similarity methods for engineers and scientists

    Zohuri, Bahman

    2015-01-01

    This ground-breaking reference provides an overview of key concepts in dimensional analysis, and then pushes well beyond traditional applications in fluid mechanics to demonstrate how powerful this tool can be in solving complex problems across many diverse fields. Of particular interest is the book's coverage of  dimensional analysis and self-similarity methods in nuclear and energy engineering. Numerous practical examples of dimensional problems are presented throughout, allowing readers to link the book's theoretical explanations and step-by-step mathematical solutions to practical impleme

  5. Self-similar spectral structures and edge-locking hierarchy in open-boundary spin chains

    Haque, Masudul

    2010-01-01

    For an anisotropic Heisenberg (XXZ) spin chain, we show that an open boundary induces a series of approximately self-similar features at different energy scales, high up in the eigenvalue spectrum. We present a nonequilibrium phenomenon related to this fractal structure, involving states in which a connected block near the edge is polarized oppositely to the rest of the chain. We show that such oppositely polarized blocks can be 'locked' to the edge of the spin chain and that there is a hierarchy of edge-locking effects at various orders of the anisotropy. The phenomenon enables dramatic control of quantum-state transmission and magnetization control.

  6. A self-similar model for conduction in the plasma erosion opening switch

    Mosher, D.; Grossmann, J.M.; Ottinger, P.F.; Colombant, D.G.

    1987-01-01

    The conduction phase of the plasma erosion opening switch (PEOS) is characterized by combining a 1-D fluid model for plasma hydrodynamics, Maxwell's equations, and a 2-D electron-orbit analysis. A self-similar approximation for the plasma and field variables permits analytic expressions for their space and time variations to be derived. It is shown that a combination of axial MHD compression and magnetic insulation of high-energy electrons emitted from the switch cathode can control the character of switch conduction. The analysis highlights the need to include additional phenomena for accurate fluid modeling of PEOS conduction

  7. Self-similar collapse with cooling and heating in an expanding universe

    Uchida, Shuji; Yoshida, Tatsuo

    2003-01-01

    We derive self-similar solutions including cooling and heating in an Einstein de-Sitter universe, and investigate the effects of cooling and heating on the gas density and temperature distributions. We assume that the cooling rate has a power-law dependence on the gas density and temperature, $\\Lambda$$\\propto$$\\rho^{A}T^{B}$, and the heating rate is $\\Gamma$$\\propto$$\\rho T$. The values of $A$ and $B$ are chosen by requiring that the cooling time is proportional to the Hubble time in order t...

  8. On the nature and impact of self-similarity in real-time systems

    Enrique Hernández-Orallo; Vila Carbó, Juan Antonio

    2012-01-01

    In real-time systems with highly variable task execution times simplistic task models are insufficient to accurately model and to analyze the system. Variability can be tackled using distributions rather than a single value, but the proper charac- terization depends on the degree of variability. Self-similarity is one of the deep- est kinds of variability. It characterizes the fact that a workload is not only highly variable, but it is also bursty on many time-scales. This paper identifies in...

  9. A self-similar transformation for a dodecagonal quasiperiodic covering with T-clusters

    Liao, Longguang; Zhang, Wenbin; Yu, Tongxu; Cao, Zexian

    2013-01-01

    A single cluster covering for the ship tiling of a dodecagonal quasiperiodic structure is obtained via a self-similar transformation, by which a turtle-like cluster, dubbed as a T-cluster, comprising seven squares, twenty regular triangles and two 30°-rhombuses, is changed into twenty scaled-down T-clusters, each centering at a vertex of the original one. Remarkably, there are three types of transformations according to the distinct configuration of the 20 scaled-down T-clusters. Detailed data for the transformations are specified. The results are expected to be helpful for the study of the physical and structural properties of dodecagonal quasicrystals. (paper)

  10. Protein dynamics by neutron scattering: The protein dynamical transition and the fragile-to-strong dynamical crossover in hydrated lysozyme

    Magazù, Salvatore; Migliardo, Federica; Benedetto, Antonio; Vertessy, Beata

    2013-01-01

    Highlights: • The role played by the instrumental energy resolution in neutron scattering is presented. • The effect of natural bioprotectants on protein dynamics is shown. • A connection between the protein dynamical transition and the fragile-to-strong dynamical crossover is formulated. - Abstract: In this work Elastic Incoherent Neutron Scattering (EINS) results on lysozyme water mixtures in absence and in presence of bioprotectant systems are presented. The EINS data have been collected by using the IN13 and the IN10 spectrometers at the Institut Laue-Langevin (ILL, Grenoble, France) allowing to evaluate the temperature behaviour of the mean square displacement and of the relaxation time for the investigated systems. The obtained experimental findings together with theoretical calculations allow to put into evidence the role played by the spectrometer resolution and to clarify the connexion between the registered protein dynamical transition, the system relaxation time, and the instrumental energy resolution

  11. An application of superpositions of two-state Markovian sources to the modelling of self-similar behaviour

    Andersen, Allan T.; Nielsen, Bo Friis

    1997-01-01

    We present a modelling framework and a fitting method for modelling second order self-similar behaviour with the Markovian arrival process (MAP). The fitting method is based on fitting to the autocorrelation function of counts a second order self-similar process. It is shown that with this fittin...

  12. Self-Similar Solutions of Variable-Coefficient Cubic-Quintic Nonlinear Schroedinger Equation with an External Potential

    Wu Hongyu; Fei Jinxi; Zheng Chunlong

    2010-01-01

    An improved homogeneous balance principle and an F-expansion technique are used to construct exact self-similar solutions to the cubic-quintic nonlinear Schroedinger equation. Such solutions exist under certain conditions, and impose constraints on the functions describing dispersion, nonlinearity, and the external potential. Some simple self-similar waves are presented. (general)

  13. Characterization of self-similarity properties of turbulence in magnetized plasmas

    Scipioni, A.; Rischette, P.; Bonhomme, G.; Devynck, P.

    2008-01-01

    The understanding of turbulence in magnetized plasmas and its role in the cross field transport is still greatly incomplete. Several previous works reported on evidences of long-time correlations compatible with an avalanche-type of radial transport. Persistence properties in time records have been deduced from high values of the Hurst exponent obtained with the rescaled range R/S analysis applied to experimental probe data acquired in the edge of tokamaks. In this paper the limitations of this R/S method, in particular when applied to signals having mixed statistics are investigated, and the great advantages of the wavelets decomposition as a tool to characterize the self-similarity properties of experimental signals are highlighted. Furthermore the analysis of modified simulated fractional Brownian motions (fBm) and fractional Gaussian noises (fGn) allows us to discuss the relationship between high values of the Hurst exponent and long range correlations. It is shown that for such simulated signals with mixed statistics persistence at large time scales can still reflect the self-similarity properties of the original fBm and do not imply the existence of long range correlations, which are destroyed. It is thus questionable to assert the existence of long range correlations for experimental signals with non-Gaussian and mixed statistics just from high values of the Hurst exponent.

  14. A solvable self-similar model of the sausage instability in a resistive Z pinch

    Lampe, M.

    1991-01-01

    A solvable model is developed for the linearized sausage mode within the context of resistive magnetohydrodynamics. The model is based on the assumption that the fluid motion of the plasma is self-similar, as well as several assumptions pertinent to the limit of wavelength long compared to the pinch radius. The perturbations to the magnetic field are not assumed to be self-similar, but rather are calculated. Effects arising from time dependences of the z-independent perturbed state, e.g., current rising as t α , Ohmic heating, and time variation of the pinch radius, are included in the analysis. The formalism appears to provide a good representation of ''global'' modes that involve coherent sausage distortion of the entire cross section of the pinch, but excludes modes that are localized radially, and higher radial eigenmodes. For this and other reasons, it is expected that the model underestimates the maximum instability growth rates, but is reasonable for global sausage modes. The net effect of resistivity and time variation of the unperturbed state is to decrease the growth rate if α approx-lt 1, but never by more than a factor of about 2. The effect is to increase the growth rate if α approx-gt 1

  15. Spectral analysis of multi-dimensional self-similar Markov processes

    Modarresi, N; Rezakhah, S

    2010-01-01

    In this paper we consider a discrete scale invariant (DSI) process {X(t), t in R + } with scale l > 1. We consider a fixed number of observations in every scale, say T, and acquire our samples at discrete points α k , k in W, where α is obtained by the equality l = α T and W = {0, 1, ...}. We thus provide a discrete time scale invariant (DT-SI) process X(.) with the parameter space {α k , k in W}. We find the spectral representation of the covariance function of such a DT-SI process. By providing the harmonic-like representation of multi-dimensional self-similar processes, spectral density functions of them are presented. We assume that the process {X(t), t in R + } is also Markov in the wide sense and provide a discrete time scale invariant Markov (DT-SIM) process with the above scheme of sampling. We present an example of the DT-SIM process, simple Brownian motion, by the above sampling scheme and verify our results. Finally, we find the spectral density matrix of such a DT-SIM process and show that its associated T-dimensional self-similar Markov process is fully specified by {R H j (1), R j H (0), j = 0, 1, ..., T - 1}, where R H j (τ) is the covariance function of jth and (j + τ)th observations of the process.

  16. Self-similar cosmological solutions with dark energy. I. Formulation and asymptotic analysis

    Harada, Tomohiro; Maeda, Hideki; Carr, B. J.

    2008-01-01

    Based on the asymptotic analysis of ordinary differential equations, we classify all spherically symmetric self-similar solutions to the Einstein equations which are asymptotically Friedmann at large distances and contain a perfect fluid with equation of state p=(γ-1)μ with 0 1). However, in the latter case there is an additional parameter associated with the weak discontinuity at the sonic point and the solutions are only asymptotically 'quasi-Friedmann', in the sense that they exhibit an angle deficit at large distances. In the 0<γ<2/3 case, there is no sonic point and there exists a one-parameter family of solutions which are genuinely asymptotically Friedmann at large distances. We find eight classes of asymptotic behavior: Friedmann or quasi-Friedmann or quasistatic or constant-velocity at large distances, quasi-Friedmann or positive-mass singular or negative-mass singular at small distances, and quasi-Kantowski-Sachs at intermediate distances. The self-similar asymptotically quasistatic and quasi-Kantowski-Sachs solutions are analytically extendible and of great cosmological interest. We also investigate their conformal diagrams. The results of the present analysis are utilized in an accompanying paper to obtain and physically interpret numerical solutions

  17. Quantum mechanical analysis of fractal conductance fluctuations: a picture using self-similar periodic orbits

    Ogura, Tatsuo; Miyamoto, Masanori; Budiyono, Agung; Nakamura, Katsuhiro

    2007-01-01

    Fractal magnetoconductance fluctuations are often observed in experiments on ballistic quantum dots. Although the analysis of the exact self-affine fractal has been given by the semiclassical theory using self-similar periodic orbits in systems with a soft-walled potential with a saddle, there has been no corresponding quantum mechanical investigation. We numerically calculate the quantum conductance with use of the recursive Green's function method applied to open cavities characterized by a Henon-Heiles type potential. The conductance fluctuations show exact self-affinity just as in some of the experimental observations. The enlargement factor for the horizontal axis can be explained by the scaling factor of the area of self-similar periodic orbits, and therefore be attributed to the curvature of the saddle in the cavity potential. The fractal dimension obtained through the box counting method agrees with those evaluated with use of the Hurst exponent, and coincides with the semiclassical prediction. We further investigate the variation of the fractal dimension by changing the control parameters between the classical and quantum domains. (fast track communication)

  18. Scaling and interaction of self-similar modes in models of high Reynolds number wall turbulence.

    Sharma, A S; Moarref, R; McKeon, B J

    2017-03-13

    Previous work has established the usefulness of the resolvent operator that maps the terms nonlinear in the turbulent fluctuations to the fluctuations themselves. Further work has described the self-similarity of the resolvent arising from that of the mean velocity profile. The orthogonal modes provided by the resolvent analysis describe the wall-normal coherence of the motions and inherit that self-similarity. In this contribution, we present the implications of this similarity for the nonlinear interaction between modes with different scales and wall-normal locations. By considering the nonlinear interactions between modes, it is shown that much of the turbulence scaling behaviour in the logarithmic region can be determined from a single arbitrarily chosen reference plane. Thus, the geometric scaling of the modes is impressed upon the nonlinear interaction between modes. Implications of these observations on the self-sustaining mechanisms of wall turbulence, modelling and simulation are outlined.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

  19. CAN AGN FEEDBACK BREAK THE SELF-SIMILARITY OF GALAXIES, GROUPS, AND CLUSTERS?

    Gaspari, M. [Max Planck Institute for Astrophysics, Karl-Schwarzschild-Strasse 1, D-85741 Garching (Germany); Brighenti, F. [Astronomy Department, University of Bologna, Via Ranzani 1, I-40127 Bologna (Italy); Temi, P. [Astrophysics Branch, NASA/Ames Research Center, MS 245-6, Moffett Field, CA 94035 (United States); Ettori, S., E-mail: mgaspari@mpa-garching.mpg.de [INAF, Osservatorio Astronomico di Bologna, Via Ranzani 1, I-40127 Bologna (Italy)

    2014-03-01

    It is commonly thought that active galactic nucleus (AGN) feedback can break the self-similar scaling relations of galaxies, groups, and clusters. Using high-resolution three-dimensional hydrodynamic simulations, we isolate the impact of AGN feedback on the L {sub x}-T {sub x} relation, testing the two archetypal and common regimes, self-regulated mechanical feedback and a quasar thermal blast. We find that AGN feedback has severe difficulty in breaking the relation in a consistent way. The similarity breaking is directly linked to the gas evacuation within R {sub 500}, while the central cooling times are inversely proportional to the core density. Breaking self-similarity thus implies breaking the cool core, morphing all systems to non-cool-core objects, which is in clear contradiction with the observed data populated by several cool-core systems. Self-regulated feedback, which quenches cooling flows and preserves cool cores, prevents dramatic evacuation and similarity breaking at any scale; the relation scatter is also limited. The impulsive thermal blast can break the core-included L {sub x}-T {sub x} at T {sub 500} ≲ 1 keV, but substantially empties and overheats the halo, generating a perennial non-cool-core group, as experienced by cosmological simulations. Even with partial evacuation, massive systems remain overheated. We show that the action of purely AGN feedback is to lower the luminosity and heat the gas, perpendicular to the fit.

  20. Self-similarity of solitary waves on inertia-dominated falling liquid films.

    Denner, Fabian; Pradas, Marc; Charogiannis, Alexandros; Markides, Christos N; van Wachem, Berend G M; Kalliadasis, Serafim

    2016-03-01

    We propose consistent scaling of solitary waves on inertia-dominated falling liquid films, which accurately accounts for the driving physical mechanisms and leads to a self-similar characterization of solitary waves. Direct numerical simulations of the entire two-phase system are conducted using a state-of-the-art finite volume framework for interfacial flows in an open domain that was previously validated against experimental film-flow data with excellent agreement. We present a detailed analysis of the wave shape and the dispersion of solitary waves on 34 different water films with Reynolds numbers Re=20-120 and surface tension coefficients σ=0.0512-0.072 N m(-1) on substrates with inclination angles β=19°-90°. Following a detailed analysis of these cases we formulate a consistent characterization of the shape and dispersion of solitary waves, based on a newly proposed scaling derived from the Nusselt flat film solution, that unveils a self-similarity as well as the driving mechanism of solitary waves on gravity-driven liquid films. Our results demonstrate that the shape of solitary waves, i.e., height and asymmetry of the wave, is predominantly influenced by the balance of inertia and surface tension. Furthermore, we find that the dispersion of solitary waves on the inertia-dominated falling liquid films considered in this study is governed by nonlinear effects and only driven by inertia, with surface tension and gravity having a negligible influence.

  1. Method of synthesis of abstract images with high self-similarity

    Matveev, Nikolay V.; Shcheglov, Sergey A.; Romanova, Galina E.; Koneva, Ð.¢atiana A.

    2017-06-01

    Abstract images with high self-similarity could be used for drug-free stress therapy. This based on the fact that a complex visual environment has a high affective appraisal. To create such an image we can use the setup based on the three laser sources of small power and different colors (Red, Green, Blue), the image is the pattern resulting from the reflecting and refracting by the complicated form object placed into the laser ray paths. The images were obtained experimentally which showed the good therapy effect. However, to find and to choose the object which gives needed image structure is very difficult and requires many trials. The goal of the work is to develop a method and a procedure of finding the object form which if placed into the ray paths can provide the necessary structure of the image In fact the task means obtaining the necessary irradiance distribution on the given surface. Traditionally such problems are solved using the non-imaging optics methods. In the given case this task is very complicated because of the complicated structure of the illuminance distribution and its high non-linearity. Alternative way is to use the projected image of a mask with a given structure. We consider both ways and discuss how they can help to speed up the synthesis procedure for the given abstract image of the high self-similarity for the setups of drug-free therapy.

  2. CAN AGN FEEDBACK BREAK THE SELF-SIMILARITY OF GALAXIES, GROUPS, AND CLUSTERS?

    Gaspari, M.; Brighenti, F.; Temi, P.; Ettori, S.

    2014-01-01

    It is commonly thought that active galactic nucleus (AGN) feedback can break the self-similar scaling relations of galaxies, groups, and clusters. Using high-resolution three-dimensional hydrodynamic simulations, we isolate the impact of AGN feedback on the L x -T x relation, testing the two archetypal and common regimes, self-regulated mechanical feedback and a quasar thermal blast. We find that AGN feedback has severe difficulty in breaking the relation in a consistent way. The similarity breaking is directly linked to the gas evacuation within R 500 , while the central cooling times are inversely proportional to the core density. Breaking self-similarity thus implies breaking the cool core, morphing all systems to non-cool-core objects, which is in clear contradiction with the observed data populated by several cool-core systems. Self-regulated feedback, which quenches cooling flows and preserves cool cores, prevents dramatic evacuation and similarity breaking at any scale; the relation scatter is also limited. The impulsive thermal blast can break the core-included L x -T x at T 500 ≲ 1 keV, but substantially empties and overheats the halo, generating a perennial non-cool-core group, as experienced by cosmological simulations. Even with partial evacuation, massive systems remain overheated. We show that the action of purely AGN feedback is to lower the luminosity and heat the gas, perpendicular to the fit

  3. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

    Ulf Hensen

    Full Text Available Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.

  4. The dynamic multisite interactions between two intrinsically disordered proteins

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

    2017-01-01

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

  5. Flame Speed and Self-Similar Propagation of Expanding Turbulent Premixed Flames

    Chaudhuri, Swetaprovo; Wu, Fujia; Zhu, Delin; Law, Chung K.

    2012-01-01

    In this Letter we present turbulent flame speeds and their scaling from experimental measurements on constant-pressure, unity Lewis number expanding turbulent flames, propagating in nearly homogeneous isotropic turbulence in a dual-chamber, fan-stirred vessel. It is found that the normalized turbulent flame speed as a function of the average radius scales as a turbulent Reynolds number to the one-half power, where the average radius is the length scale and the thermal diffusivity is the transport property, thus showing self-similar propagation. Utilizing this dependence it is found that the turbulent flame speeds from the present expanding flames and those from the Bunsen geometry in the literature can be unified by a turbulent Reynolds number based on flame length scales using recent theoretical results obtained by spectral closure of the transformed G equation.

  6. Bianchi VI{sub 0} and III models: self-similar approach

    Belinchon, Jose Antonio, E-mail: abelcal@ciccp.e [Departamento de Fisica, ETS Arquitectura, UPM, Av. Juan de Herrera 4, Madrid 28040 (Spain)

    2009-09-07

    We study several cosmological models with Bianchi VI{sub 0} and III symmetries under the self-similar approach. We find new solutions for the 'classical' perfect fluid model as well as for the vacuum model although they are really restrictive for the equation of state. We also study a perfect fluid model with time-varying constants, G and LAMBDA. As in other studied models we find that the behaviour of G and LAMBDA are related. If G behaves as a growing time function then LAMBDA is a positive decreasing time function but if G is decreasing then LAMBDA{sub 0} is negative. We end by studying a massive cosmic string model, putting special emphasis in calculating the numerical values of the equations of state. We show that there is no SS solution for a string model with time-varying constants.

  7. Renormalization of the fragmentation equation: Exact self-similar solutions and turbulent cascades

    Saveliev, V. L.; Gorokhovski, M. A.

    2012-12-01

    Using an approach developed earlier for renormalization of the Boltzmann collision integral [Saveliev and Nanbu, Phys. Rev. E1539-375510.1103/PhysRevE.65.051205 65, 051205 (2002)], we derive an exact divergence form for the fragmentation operator. Then we reduce the fragmentation equation to the continuity equation in size space, with the flux given explicitly. This allows us to obtain self-similar solutions and to find the integral of motion for these solutions (we call it the bare flux). We show how these solutions can be applied as a description of cascade processes in three- and two-dimensional turbulence. We also suggested an empirical cascade model of impact fragmentation of brittle materials.

  8. Compression of dark halos by baryon infall - Self-similar solutions

    Ryden, B.S.

    1991-01-01

    The compression of dissipationless halos by dissipative baryon infall is examined through the use of self-similar models. The models are spherically symmetric, with asymptotic density profiles of given form. A fraction f of the matter consists of freely falling baryons; the remainder of the matter, consisting of dark matter with initial dispersion anisotropy beta is gravitationally compressed by the infalling baryons. Analytic results are presented in the limiting cases f = 1 and f = 0. Numerical results are given for halos with varying values of alpha, beta, and f. The compression of the dark matter is found to be adiabatic and has a Mach number less than 1 throughout the halo. 10 refs

  9. Local self-similarity descriptor for point-of-interest reconstruction of real-world scenes

    Gao, Xianglu; Wan, Weibing; Zhao, Qunfei; Zhang, Xianmin

    2015-01-01

    Scene reconstruction is utilized commonly in close-range photogrammetry, with diverse applications in fields such as industry, biology, and aerospace industries. Presented surfaces or wireframe three-dimensional (3D) model reconstruction applications are either too complex or too inflexible to accommodate various types of real-world scenes, however. This paper proposes an algorithm for acquiring point-of-interest (referred to throughout the study as POI) coordinates in 3D space, based on multi-view geometry and a local self-similarity descriptor. After reconstructing several POIs specified by a user, a concise and flexible target object measurement method, which obtains the distance between POIs, is described in detail. The proposed technique is able to measure targets with high accuracy even in the presence of obstacles and non-Lambertian surfaces. The method is so flexible that target objects can be measured with a handheld digital camera. Experimental results further demonstrate the effectiveness of the algorithm. (paper)

  10. Observation of Self-Similar Behavior of the 3D, Nonlinear Rayleigh-Taylor Instability

    Sadot, O.; Smalyuk, V.A.; Delettrez, J.A.; Sangster, T.C.; Goncharov, V.N.; Meyerhofer, D.D.; Betti, R.; Shvarts, D.

    2005-01-01

    The Rayleigh-Taylor unstable growth of laser-seeded, 3D broadband perturbations was experimentally measured in the laser-accelerated, planar plastic foils. The first experimental observation showing the self-similar behavior of the bubble size and amplitude distributions under ablative conditions is presented. In the nonlinear regime, the modulation σ rms grows as α σ gt 2 , where g is the foil acceleration, t is the time, and α σ is constant. The number of bubbles evolves as N(t)∝(ωt√(g)+C) -4 and the average size evolves as (t)∝ω 2 gt 2 , where C is a constant and ω=0.83±0.1 is the measured scaled bubble-merging rate

  11. Anomaly Detection in Nanofibrous Materials by CNN-Based Self-Similarity

    Paolo Napoletano

    2018-01-01

    Full Text Available Automatic detection and localization of anomalies in nanofibrous materials help to reduce the cost of the production process and the time of the post-production visual inspection process. Amongst all the monitoring methods, those exploiting Scanning Electron Microscope (SEM imaging are the most effective. In this paper, we propose a region-based method for the detection and localization of anomalies in SEM images, based on Convolutional Neural Networks (CNNs and self-similarity. The method evaluates the degree of abnormality of each subregion of an image under consideration by computing a CNN-based visual similarity with respect to a dictionary of anomaly-free subregions belonging to a training set. The proposed method outperforms the state of the art.

  12. The effective thermal conductivity of porous media based on statistical self-similarity

    Kou Jianlong; Wu Fengmin; Lu Hangjun; Xu Yousheng; Song Fuquan

    2009-01-01

    A fractal model is presented based on the thermal-electrical analogy technique and statistical self-similarity of fractal saturated porous media. A dimensionless effective thermal conductivity of saturated fractal porous media is studied by the relationship between the dimensionless effective thermal conductivity and the geometrical parameters of porous media with no empirical constant. Through this study, it is shown that the dimensionless effective thermal conductivity decreases with the increase of porosity (φ) and pore area fractal dimension (D f ) when k s /k g >1. The opposite trends is observed when k s /k g t ). The model predictions are compared with existing experimental data and the results show that they are in good agreement with existing experimental data.

  13. Odd-parity perturbations of the self-similar LTB spacetime

    Duffy, Emily M; Nolan, Brien C, E-mail: emilymargaret.duffy27@mail.dcu.ie, E-mail: brien.nolan@dcu.ie [School of Mathematical Sciences, Dublin City University, Glasnevin, Dublin 9 (Ireland)

    2011-05-21

    We consider the behaviour of odd-parity perturbations of those self-similar LemaItre-Tolman-Bondi spacetimes which admit a naked singularity. We find that a perturbation which evolves from initially regular data remains finite on the Cauchy horizon. Finiteness is demonstrated by considering the behaviour of suitable energy norms of the perturbation (and pointwise values of these quantities) on natural spacelike hypersurfaces. This result holds for a general choice of initial data and initial data surface. Finally, we examine the perturbed Weyl scalars in order to provide a physical interpretation of our results. Taken on its own, this result does not support cosmic censorship; however, a full perturbation of this spacetime would include even-parity perturbations, so we cannot conclude that this spacetime is stable to all linear perturbations.

  14. Self-similar density turbulence in the TCV tokamak scrape-off layer

    Graves, J P; Horacek, J; Pitts, R A; Hopcraft, K I

    2005-01-01

    Plasma fluctuations in the scrape-off layer (SOL) of the TCV tokamak exhibit statistical properties which are universal across a broad range of discharge conditions. Electron density fluctuations, from just inside the magnetic separatrix to the plasma-wall interface, are described well by a gamma distributed random variable. The density fluctuations exhibit clear evidence of self-similarity in the far SOL, such that the corresponding probability density functions collapse upon renormalization solely by the mean particle density. This constitutes a demonstration that the amplitude of the density fluctuations is simply proportional to the mean density and is consistent with the further observation that the radial particle flux fluctuations scale solely with the mean density over two orders of magnitude. Such findings indicate that it may be possible to improve the prediction of transport in the critical plasma-wall interaction region of future large scale tokamaks. (letter to the editor)

  15. Water dynamics clue to key residues in protein folding

    Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su

    2010-01-01

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  16. Self-similarity and flow characteristics of vertical-axis wind turbine wakes: an LES study

    Abkar, Mahdi; Dabiri, John O.

    2017-04-01

    Large eddy simulation (LES) is coupled with a turbine model to study the structure of the wake behind a vertical-axis wind turbine (VAWT). In the simulations, a tuning-free anisotropic minimum dissipation model is used to parameterise the subfilter stress tensor, while the turbine-induced forces are modelled with an actuator line technique. The LES framework is first validated in the simulation of the wake behind a model straight-bladed VAWT placed in the water channel and then used to study the wake structure downwind of a full-scale VAWT sited in the atmospheric boundary layer. In particular, the self-similarity of the wake is examined, and it is found that the wake velocity deficit can be well characterised by a two-dimensional multivariate Gaussian distribution. By assuming a self-similar Gaussian distribution of the velocity deficit, and applying mass and momentum conservation, an analytical model is developed and tested to predict the maximum velocity deficit downwind of the turbine. Also, a simple parameterisation of VAWTs for LES with very coarse grid resolutions is proposed, in which the turbine is modelled as a rectangular porous plate with the same thrust coefficient. The simulation results show that, after some downwind distance (x/D ≈ 6), both actuator line and rectangular porous plate models have similar predictions for the mean velocity deficit. These results are of particular importance in simulations of large wind farms where, due to the coarse spatial resolution, the flow around individual VAWTs is not resolved.

  17. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  18. 3D Protein Dynamics in the Cell Nucleus.

    Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E

    2017-01-10

    The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Organization and Dynamics of Receptor Proteins in a Plasma Membrane.

    Koldsø, Heidi; Sansom, Mark S P

    2015-11-25

    The interactions of membrane proteins are influenced by their lipid environment, with key lipid species able to regulate membrane protein function. Advances in high-resolution microscopy can reveal the organization and dynamics of proteins and lipids within living cells at resolutions membranes of in vivo-like complexity. We explore the dynamics of proteins and lipids in crowded and complex plasma membrane models, thereby closing the gap in length and complexity between computations and experiments. Our simulations provide insights into the mutual interplay between lipids and proteins in determining mesoscale (20-100 nm) fluctuations of the bilayer, and in enabling oligomerization and clustering of membrane proteins.

  20. Detailed investigation of the bifurcation diagram of capacitively coupled Josephson junctions in high-Tc superconductors and its self similarity

    Hamdipour, Mohammad

    2018-04-01

    We study an array of coupled Josephson junction of superconductor/insulator/superconductor type (SIS junction) as a model for high temperature superconductors with layered structure. In the current-voltage characteristics of this system there is a breakpoint region in which a net electric charge appear on superconducting layers, S-layers, of junctions which motivate us to study the charge dynamics in this region. In this paper first of all we show a current voltage characteristics (CVC) of Intrinsic Josephson Junctions (IJJs) with N=3 Junctions, then we show the breakpoint region in that CVC, then we try to investigate the chaos in this region. We will see that at the end of the breakpoint region, behavior of the system is chaotic and Lyapunov exponent become positive. We also study the route by which the system become chaotic and will see this route is bifurcation. Next goal of this paper is to show the self similarity in the bifurcation diagram of the system and detailed analysis of bifurcation diagram.

  1. Contributions to the stability analysis of self-similar supersonic heat waves related to inertial confinement fusion

    Dastugue, Laurent

    2013-01-01

    Exact self-similar solutions of gas dynamics equations with nonlinear heat conduction for semi-infinite slabs of perfect gases are used for studying the stability of flows in inertial confinement fusion. Both the similarity solutions and their linear perturbations are computed with a multi domain Chebyshev pseudo-spectral method, allowing us to account for, without any other approximation, compressibility and unsteadiness. Following previous results (Clarisse et al., 2008; Lombard, 2008) representative of the early ablation of a target by a nonuniform laser flux (electronic conduction, subsonic heat front downstream of a quasi-perfect shock front), we explore here other configurations. For this early ablation phase, but for a nonuniform incident X-radiation (radiative conduction), we study a compressible and a weakly compressible flow. In both cases, we recover the behaviours obtained for compressible flows with electronic heat conduction with a maximal instability for a zero wavenumber. Besides, the spectral method is extended to compute similarity solutions taking into account the supersonic heat wave ahead of the shock front. Based on an analysis of the reduced equations singularities (infinitely stiff front), this method allows us to describe the supersonic heat wave regime proper to the initial irradiation of the target and to recover the ablative solutions which were obtained under a negligible fore-running heat wave approximation. (author) [fr

  2. Computing the variations in the self-similar properties of the various gait intervals in Parkinson disease patients.

    Manjeri Keloth, Sana; Arjunan, Sridhar P; Kumar, Dinesh

    2017-07-01

    This study has investigated the stride, swing, stance and double support intervals of gait for Parkinson's disease (PD) patients with different levels of severity. Self-similar properties of the gait signal were analyzed to investigate the changes in the gait pattern of the healthy and PD patients. To understand the self-similar property, detrended fluctuation analysis was performed. The analysis shows that the PD patients have less defined gait when compared to healthy. The study also shows that among the stance and swing phase of stride interval, the self-similarity is less for swing interval when compared to the stance interval of gait and decreases with the severity of gait. Also, PD patients show decreased self-similar patterns in double support interval of gait. This suggest that there are less rhythmic gait intervals and a sense of urgency to remain in support phase of gait by the PD patients.

  3. Momentum transport process in the quasi self-similar region of free shear mixing layer

    Takamure, K.; Ito, Y.; Sakai, Y.; Iwano, K.; Hayase, T.

    2018-01-01

    In this study, we performed a direct numerical simulation (DNS) of a spatially developing shear mixing layer covering both developing and developed regions. The aim of this study is to clarify the driving mechanism and the vortical structure of the partial counter-gradient momentum transport (CGMT) appearing in the quasi self-similar region. In the present DNS, the self-similarity is confirmed in x/L ≥ 0.67 (x/δU0 ≥ 137), where L and δU0 are the vertical length of the computational domain and the initial momentum thickness, respectively. However, the trend of CGMT is observed at around kδU = 0.075 and 0.15, where k is the wavenumber, δU is the normalized momentum thickness at x/L = 0.78 (x/δU0 = 160), and kδU = 0.075 corresponds to the distance between the vortical/stretching regions of the coherent structure. The budget analysis for the Reynolds shear stress reveals that it is caused by the pressure diffusion term at the off-central region and by -p (∂ u /∂ y ) ¯ in the pressure-strain correlation term at the central region. As the flow moves toward the downstream direction, the appearance of those terms becomes random and the unique trend of CGMT at the specific wavenumber bands disappears. Furthermore, we investigated the relationship between the CGMT and vorticity distribution in the vortex region of the mixing layer, in association with the spatial development. In the upstream location, the high-vorticity region appears in the boundary between the areas of gradient momentum transport and CGMT, although the high-vorticity region is not actively producing turbulence. The negative production area gradually spreads by flowing toward the downstream direction, and subsequently, the fluid mass with high-vorticity is transported from the forehead stretching region toward the counter-gradient direction. In this location, the velocity fluctuation in the high-vorticity region is large and turbulence is actively produced. In view of this, the trend of

  4. Human-based percussion and self-similarity detection in electroacoustic music

    Mills, John Anderson, III

    Electroacoustic music is music that uses electronic technology for the compositional manipulation of sound, and is a unique genre of music for many reasons. Analyzing electroacoustic music requires special measures, some of which are integrated into the design of a preliminary percussion analysis tool set for electroacoustic music. This tool set is designed to incorporate the human processing of music and sound. Models of the human auditory periphery are used as a front end to the analysis algorithms. The audio properties of percussivity and self-similarity are chosen as the focus because these properties are computable and informative. A collection of human judgments about percussion was undertaken to acquire clearly specified, sound-event dimensions that humans use as a percussive cue. A total of 29 participants was asked to make judgments about the percussivity of 360 pairs of synthesized snare-drum sounds. The grouped results indicate that of the dimensions tested rise time is the strongest cue for percussivity. String resonance also has a strong effect, but because of the complex nature of string resonance, it is not a fundamental dimension of a sound event. Gross spectral filtering also has an effect on the judgment of percussivity but the effect is weaker than for rise time and string resonance. Gross spectral filtering also has less effect when the stronger cue of rise time is modified simultaneously. A percussivity-profile algorithm (PPA) is designed to identify those instants in pieces of music that humans also would identify as percussive. The PPA is implemented using a time-domain, channel-based approach and psychoacoustic models. The input parameters are tuned to maximize performance at matching participants' choices in the percussion-judgment collection. After the PPA is tuned, the PPA then is used to analyze pieces of electroacoustic music. Real electroacoustic music introduces new challenges for the PPA, though those same challenges might affect

  5. The management and containment of self-similar rogue waves in the inhomogeneous nonlinear Schrödinger equation

    Dai Chaoqing; Wang Yueyue; Tian Qing; Zhang Jiefang

    2012-01-01

    We present, analytically, self-similar rogue wave solutions (rational solutions) of the inhomogeneous nonlinear Schrödinger equation (NLSE) via a similarity transformation connected with the standard NLSE. Then we discuss the propagation behaviors of controllable rogue waves under dispersion and nonlinearity management. In an exponentially dispersion-decreasing fiber, the postponement, annihilation and sustainment of self-similar rogue waves are modulated by the exponential parameter σ. Finally, we investigate the nonlinear tunneling effect for self-similar rogue waves. Results show that rogue waves can tunnel through the nonlinear barrier or well with increasing, unchanged or decreasing amplitudes via the modulation of the ratio of the amplitudes of rogue waves to the barrier or well height. - Highlights: ► Self-similar rogue wave solutions of the inhomogeneous NLSE are obtained.► Postponement, annihilation and sustainment of self-similar rogue waves are discussed. ► Nonlinear tunneling effects for self-similar rogue waves are investigated.

  6. The dynamic multisite interactions between two intrinsically disordered proteins

    Wu, Shaowen

    2017-05-11

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

  7. Small-world organization of self-similar modules in functional brain networks

    Sigman, Mariano; Gallos, Lazaros; Makse, Hernan

    2012-02-01

    The modular organization of the brain implies the parallel nature of brain computations. These modules have to remain functionally independent, but at the same time they need to be sufficiently connected to guarantee the unitary nature of brain perception. Small-world architectures have been suggested as probable structures explaining this behavior. However, there is intrinsic tension between shortcuts generating small-worlds and the persistence of modularity. In this talk, we study correlations between the activity in different brain areas. We suggest that the functional brain network formed by the percolation of strong links is highly modular. Contrary to the common view, modules are self-similar and therefore are very far from being small-world. Incorporating the weak ties to the network converts it into a small-world preserving an underlying backbone of well-defined modules. Weak ties are shown to follow a pattern that maximizes information transfer with minimal wiring costs. This architecture is reminiscent of the concept of weak-ties strength in social networks and provides a natural solution to the puzzle of efficient infomration flow in the highly modular structure of the brain.

  8. MAGNETIC FIELDS AND COSMIC RAYS IN GRBs: A SELF-SIMILAR COLLISIONLESS FORESHOCK

    Medvedev, Mikhail V.; Zakutnyaya, Olga V.

    2009-01-01

    Cosmic rays accelerated by a shock form a streaming distribution of outgoing particles in the foreshock region. If the ambient fields are negligible compared to the shock and cosmic ray energetics, a stronger magnetic field can be generated in the shock upstream via the streaming (Weibel-type) instability. Here we develop a self-similar model of the foreshock region and calculate its structure, e.g., the magnetic field strength, its coherence scale, etc., as a function of the distance from the shock. Our model indicates that the entire foreshock region of thickness ∼R/(2Γ 2 sh ), being comparable to the shock radius in the late afterglow phase when Γ sh ∼ 1, can be populated with large-scale and rather strong magnetic fields (of subgauss strengths with the coherence length of order 10 16 cm) compared with the typical interstellar medium magnetic fields. The presence of such fields in the foreshock region is important for high efficiency of Fermi acceleration at the shock. Radiation from accelerated electrons in the foreshock fields can constitute a separate emission region radiating in the UV/optical through radio band, depending on time and shock parameters. We also speculate that these fields being eventually transported into the shock downstream can greatly increase radiative efficiency of a gamma-ray burst afterglow shock.

  9. Fundamental statistical features and self-similar properties of tagged networks

    Palla, Gergely; Farkas, Illes J; Pollner, Peter; Vicsek, Tamas; Derenyi, Imre

    2008-01-01

    We investigate the fundamental statistical features of tagged (or annotated) networks having a rich variety of attributes associated with their nodes. Tags (attributes, annotations, properties, features, etc) provide essential information about the entity represented by a given node, thus, taking them into account represents a significant step towards a more complete description of the structure of large complex systems. Our main goal here is to uncover the relations between the statistical properties of the node tags and those of the graph topology. In order to better characterize the networks with tagged nodes, we introduce a number of new notions, including tag-assortativity (relating link probability to node similarity), and new quantities, such as node uniqueness (measuring how rarely the tags of a node occur in the network) and tag-assortativity exponent. We apply our approach to three large networks representing very different domains of complex systems. A number of the tag related quantities display analogous behaviour (e.g. the networks we studied are tag-assortative, indicating possible universal aspects of tags versus topology), while some other features, such as the distribution of the node uniqueness, show variability from network to network allowing for pin-pointing large scale specific features of real-world complex networks. We also find that for each network the topology and the tag distribution are scale invariant, and this self-similar property of the networks can be well characterized by the tag-assortativity exponent, which is specific to each system.

  10. Brief communication: A nonlinear self-similar solution to barotropic flow over varying topography

    Ibanez, Ruy; Kuehl, Joseph; Shrestha, Kalyan; Anderson, William

    2018-03-01

    Beginning from the shallow water equations (SWEs), a nonlinear self-similar analytic solution is derived for barotropic flow over varying topography. We study conditions relevant to the ocean slope where the flow is dominated by Earth's rotation and topography. The solution is found to extend the topographic β-plume solution of Kuehl (2014) in two ways. (1) The solution is valid for intensifying jets. (2) The influence of nonlinear advection is included. The SWEs are scaled to the case of a topographically controlled jet, and then solved by introducing a similarity variable, η = cxnxyny. The nonlinear solution, valid for topographies h = h0 - αxy3, takes the form of the Lambert W-function for pseudo velocity. The linear solution, valid for topographies h = h0 - αxy-γ, takes the form of the error function for transport. Kuehl's results considered the case -1 ≤ γ < 1 which admits expanding jets, while the new result considers the case γ < -1 which admits intensifying jets and a nonlinear case with γ = -3.

  11. Self-similar Lagrangian hydrodynamics of beam-heated solar flare atmospheres

    Brown, J.C.; Emslie, A.G.

    1989-01-01

    The one-dimensional hydrodynamic problem in Lagrangian coordinates (Y, t) is considered for which the specific energy input Q has a power-law dependence on both Y and t, and the initial density distribution is rho(0) which is directly proportional to Y exp gamma. In regimes where the contributions of radiation, conduction, quiescent heating, and gravitational terms in the energy equation are negligible compared to those arising from Q, the problem has a self-similar solution, with the hydrodynamic variables depending only on a single independent variable which is a combination of Y, t, and the dimensional constants of the problem. It is then shown that the problem of solar flare chromospheric heating due to collisional interaction of a beam of electrons (or protons) with a power-law energy spectrum can be approximated by such forms of Q(Y, t) and rho(0)(Y), and that other terms are negligible compared to Q over a restricted regime early in the flare. 29 refs

  12. Landau-Ginzburg Limit of Black Hole's Quantum Portrait: Self Similarity and Critical Exponent

    Dvali, Gia

    2012-01-01

    Recently we have suggested that the microscopic quantum description of a black hole is an overpacked self-sustained Bose-condensate of N weakly-interacting soft gravitons, which obeys the rules of 't Hooft's large-N physics. In this note we derive an effective Landau-Ginzburg Lagrangian for the condensate and show that it becomes an exact description in a semi-classical limit that serves as the black hole analog of 't Hooft's planar limit. The role of a weakly-coupled Landau-Ginzburg order parameter is played by N. This description consistently reproduces the known properties of black holes in semi-classical limit. Hawking radiation, as the quantum depletion of the condensate, is described by the slow-roll of the field N. In the semiclassical limit, where black holes of arbitrarily small size are allowed, the equation of depletion is self similar leading to a scaling law for the black hole size with critical exponent 1/3.

  13. A generalized self-similar spectrum for decaying homogeneous and isotropic turbulence

    Yang, Pingfan; Pumir, Alain; Xu, Haitao

    2017-11-01

    The spectrum of turbulence in dissipative and inertial range can be described by the celebrated Kolmogorov theory. However, there is no general solution of the spectrum in the large scales, especially for statistically unsteady turbulent flows. Here we propose a generalized self-similar form that contains two length-scales, the integral scale and the Kolmogorov scale, for decaying homogeneous and isotropic turbulence. With the help of the local spectral energy transfer hypothesis by Pao (Phys. Fluids, 1965), we derive and solve for the explicit form of the energy spectrum and the energy transfer function, from which the second- and third-order velocity structure functions can also be obtained. We check and verify our assumptions by direct numerical simulations (DNS), and our solutions of the velocity structure functions compare well with hot-wire measurements of high-Reynolds number wind-tunnel turbulence. Financial supports from NSFC under Grant Number 11672157, from the Alexander von Humboldt Foundation, and from the MPG are gratefully acknowledged.

  14. Dark energy in six nearby galaxy flows: Synthetic phase diagrams and self-similarity

    Chernin, A. D.; Teerikorpi, P.; Dolgachev, V. P.; Kanter, A. A.; Domozhilova, L. M.; Valtonen, M. J.; Byrd, G. G.

    2012-09-01

    Outward flows of galaxies are observed around groups of galaxies on spatial scales of about 1 Mpc, and around galaxy clusters on scales of 10 Mpc. Using recent data from the Hubble Space Telescope (HST), we have constructed two synthetic velocity-distance phase diagrams: one for four flows on galaxy-group scales and the other for two flows on cluster scales. It has been shown that, in both cases, the antigravity produced by the cosmic dark-energy background is stronger than the gravity produced by the matter in the outflow volume. The antigravity accelerates the flows and introduces a phase attractor that is common to all scales, corresponding to a linear velocity-distance relation (the local Hubble law). As a result, the bundle of outflow trajectories mostly follow the trajectory of the attractor. A comparison of the two diagrams reveals the universal self-similar nature of the outflows: their gross phase structure in dimensionless variables is essentially independent of their physical spatial scales, which differ by approximately a factor of 10 in the two diagrams.

  15. Self-similar solutions with compactly supported profile of some nonlinear Schrodinger equations

    Pascal Begout

    2014-04-01

    Full Text Available ``Sharp localized'' solutions (i.e. with compact support for each given time t of a singular nonlinear type Schr\\"odinger equation in the whole space $\\mathbb{R}^N$ are constructed here under the assumption that they have a self-similar structure. It requires the assumption that the external forcing term satisfies that $\\mathbf{f}(t,x=t^{-(\\mathbf{p}-2/2}\\mathbf{F}(t^{-1/2}x$ for some complex exponent $\\mathbf{p}$ and for some profile function $\\mathbf{F}$ which is assumed to be with compact support in $\\mathbb{R}^N$. We show the existence of solutions of the form $\\mathbf{u}(t,x=t^{\\mathbf{p}/2}\\mathbf{U}(t^{-1/2}x$, with a profile $\\mathbf{U}$, which also has compact support in $\\mathbb{R}^N$. The proof of the localization of the support of the profile $\\mathbf{U}$ uses some suitable energy method applied to the stationary problem satisfied by $\\mathbf{U}$ after some unknown transformation.

  16. The self-similar turbulent flow of low-pressure water vapor

    Konyukhov, V. K.; Stepanov, E. V.; Borisov, S. K.

    2018-05-01

    We studied turbulent flows of water vapor in a pipe connecting two closed vessels of equal volume. The vessel that served as a source of water vapor was filled with adsorbent in the form of corundum ceramic balls. These ceramic balls were used to obtain specific conditions to lower the vapor pressure in the source vessel that had been observed earlier. A second vessel, which served as a receiver, was empty of either air or vapor before each vapor sampling. The rate of the pressure increase in the receiver vessel was measured in a series of six samplings performed with high precision. The pressure reduction rate in the source vessel was found to be three times lower than the pressure growth rate in the receiver vessel. We found that the pressure growth rates in all of the adjacent pairs of samples could be arranged in a combination that appeared to be identical for all pairs, and this revealed the existence of a rather interesting and peculiar self-similarity law for the sampling processes under consideration.

  17. Analyzing self-similar and fractal properties of the C. elegans neural network.

    Tyler M Reese

    Full Text Available The brain is one of the most studied and highly complex systems in the biological world. While much research has concentrated on studying the brain directly, our focus is the structure of the brain itself: at its core an interconnected network of nodes (neurons. A better understanding of the structural connectivity of the brain should elucidate some of its functional properties. In this paper we analyze the connectome of the nematode Caenorhabditis elegans. Consisting of only 302 neurons, it is one of the better-understood neural networks. Using a Laplacian Matrix of the 279-neuron "giant component" of the network, we use an eigenvalue counting function to look for fractal-like self similarity. This matrix representation is also used to plot visualizations of the neural network in eigenfunction coordinates. Small-world properties of the system are examined, including average path length and clustering coefficient. We test for localization of eigenfunctions, using graph energy and spacial variance on these functions. To better understand results, all calculations are also performed on random networks, branching trees, and known fractals, as well as fractals which have been "rewired" to have small-world properties. We propose algorithms for generating Laplacian matrices of each of these graphs.

  18. Self-similar distribution of oil spills in European coastal waters

    Redondo, Jose M; Platonov, Alexei K

    2009-01-01

    Marine pollution has been highlighted thanks to the advances in detection techniques as well as increasing coverage of catastrophes (e.g. the oil tankers Amoco Cadiz, Exxon Valdez, Erika, and Prestige) and of smaller oil spills from ships. The new satellite based sensors SAR and ASAR and new methods of oil spill detection and analysis coupled with self-similar statistical techniques allow surveys of environmental pollution monitoring large areas of the ocean. We present a statistical analysis of more than 700 SAR images obtained during 1996-2000, also comparing the detected small pollution events with the historical databases of great marine accidents during 1966-2004 in European coastal waters. We show that the statistical distribution of the number of oil spills as a function of their size corresponds to Zipf's law, and that the common small spills are comparable to the large accidents due to the high frequency of the smaller pollution events. Marine pollution from tankers and ships, which has been detected as oil spills between 0.01 and 100 km 2 , follows the marine transit routes. Multi-fractal methods are used to distinguish between natural slicks and spills, in order to estimate the oil spill index in European coastal waters, and in particular, the north-western Mediterranean Sea, which, due to the influence of local winds, shows optimal conditions for oil spill detection.

  19. Self-similar variables and the problem of nonlocal electron heat conductivity

    Krasheninnikov, S.I.; Bakunin, O.G.

    1993-10-01

    Self-similar solutions of the collisional electron kinetic equation are obtained for the plasmas with one (1D) and three (3D) dimensional plasma parameter inhomogeneities and arbitrary Z eff . For the plasma parameter profiles characterized by the ratio of the mean free path of thermal electrons with respect to electron-electron collisions, γ T , to the scale length of electron temperature variation, L, one obtains a criterion for determining the effect that tail particles with motion of the non-diffusive type have on the electron heat conductivity. For these conditions it is shown that the use of a open-quotes symmetrizedclose quotes kinetic equation for the investigation of the strong nonlocal effect of suprathermal electrons on the electron heat conductivity is only possible at sufficiently high Z eff (Z eff ≥ (L/γ T ) 1/2 ). In the case of 3D inhomogeneous plasma (spherical symmetry), the effect of the tail electrons on the heat transport is less pronounced since they are spread across the radius r

  20. Linear perturbations of a self-similar solution of hydrodynamics with non-linear heat conduction

    Dubois-Boudesocque, Carine

    2000-01-01

    The stability of an ablative flow, where a shock wave is located upstream a thermal front, is of importance in inertial confinement fusion. The present model considers an exact self-similar solution to the hydrodynamic equations with non-linear heat conduction for a semi-infinite slab. For lack of an analytical solution, a high resolution numerical procedure is devised, which couples a finite difference method with a relaxation algorithm using a two-domain pseudo-spectral method. Stability of this solution is studied by introducing linear perturbation method within a Lagrangian-Eulerian framework. The initial and boundary value problem is solved by a splitting of the equations between a hyperbolic system and a parabolic equation. The boundary conditions of the hyperbolic system are treated, in the case of spectral methods, according to Thompson's approach. The parabolic equation is solved by an influence matrix method. These numerical procedures have been tested versus exact solutions. Considering a boundary heat flux perturbation, the space-time evolution of density, velocity and temperature are shown. (author) [fr

  1. Polymer dynamics from synthetic polymers to proteins

    Keywords. Polymer dynamics; reptation; domain dynamics biomolecules. Abstract. Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the ...

  2. On the dynamical incompleteness of the Protein Data Bank.

    Marino-Buslje, Cristina; Monzon, Alexander Miguel; Zea, Diego Javier; Fornasari, María Silvina; Parisi, Gustavo

    2017-08-02

    Major scientific challenges that are beyond the capability of individuals need to be addressed by multi-disciplinary and multi-institutional consortia. Examples of these endeavours include the Human Genome Project, and more recently, the Structural Genomics (SG) initiative. The SG initiative pursues the expansion of structural coverage to include at least one structural representative for each protein family to derive the remaining structures using homology modelling. However, biological function is inherently connected with protein dynamics that can be studied by knowing different structures of the same protein. This ensemble of structures provides snapshots of protein conformational diversity under native conditions. Thus, sequence redundancy in the Protein Data Bank (PDB) (i.e. crystallization of the same protein under different conditions) is therefore an essential input contributing to experimentally based studies of protein dynamics and providing insights into protein function. In this work, we show that sequence redundancy, a key concept for exploring protein dynamics, is highly biased and fundamentally incomplete in the PDB. Additionally, our results show that dynamical behaviour of proteins cannot be inferred using homologous proteins. Minor to moderate changes in sequence can produce great differences in dynamical behaviour. Nonetheless, the structural and dynamical incompleteness of the PDB is apparently unrelated concepts in SG. While the first could be reversed by promoting the extension of the structural coverage, we would like to emphasize that further focused efforts will be needed to amend the incompleteness of the PDB in terms of dynamical information content, essential to fully understand protein function. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Dynamic protein assembly by programmable DNA strand displacement

    Chen, Rebecca P.; Blackstock, Daniel; Sun, Qing; Chen, Wilfred

    2018-03-01

    Inspired by the remarkable ability of natural protein switches to sense and respond to a wide range of environmental queues, here we report a strategy to engineer synthetic protein switches by using DNA strand displacement to dynamically organize proteins with highly diverse and complex logic gate architectures. We show that DNA strand displacement can be used to dynamically control the spatial proximity and the corresponding fluorescence resonance energy transfer between two fluorescent proteins. Performing Boolean logic operations enabled the explicit control of protein proximity using multi-input, reversible and amplification architectures. We further demonstrate the power of this technology beyond sensing by achieving dynamic control of an enzyme cascade. Finally, we establish the utility of the approach as a synthetic computing platform that drives the dynamic reconstitution of a split enzyme for targeted prodrug activation based on the sensing of cancer-specific miRNAs.

  4. Self-similarity of temperature profiles in distant galaxy clusters: the quest for a universal law

    Baldi, A.; Ettori, S.; Molendi, S.; Gastaldello, F.

    2012-09-01

    Context. We present the XMM-Newton temperature profiles of 12 bright (LX > 4 × 1044 erg s-1) clusters of galaxies at 0.4 high-redshift clusters, to investigate their properties, and to define a universal law to describe the temperature radial profiles in galaxy clusters as a function of both cosmic time and their state of relaxation. Methods: We performed a spatially resolved spectral analysis, using Cash statistics, to measure the temperature in the intracluster medium at different radii. Results: We extracted temperature profiles for the clusters in our sample, finding that all profiles are declining toward larger radii. The normalized temperature profiles (normalized by the mean temperature T500) are found to be generally self-similar. The sample was subdivided into five cool-core (CC) and seven non cool-core (NCC) clusters by introducing a pseudo-entropy ratio σ = (TIN/TOUT) × (EMIN/EMOUT)-1/3 and defining the objects with σ ratio σ is detected by fitting a function of r and σ, showing an indication that the outer part of the profiles becomes steeper for higher values of σ (i.e. transitioning toward the NCC clusters). No significant evidence of redshift evolution could be found within the redshift range sampled by our clusters (0.4 high-z sample with intermediate clusters at 0.1 0.4 has been attempted. We were able to define the closest possible relation to a universal law for the temperature profiles of galaxy clusters at 0.1 < z < 0.9, showing a dependence on both the relaxation state of the clusters and the redshift. Appendix A is only available in electronic form at http://www.aanda.org

  5. Signal-noise separation based on self-similarity testing in 1D-timeseries data

    Bourdin, Philippe A.

    2015-08-01

    The continuous improvement of the resolution delivered by modern instrumentation is a cost-intensive part of any new space- or ground-based observatory. Typically, scientists later reduce the resolution of the obtained raw-data, for example in the spatial, spectral, or temporal domain, in order to suppress the effects of noise in the measurements. In practice, only simple methods are used that just smear out the noise, instead of trying to remove it, so that the noise can nomore be seen. In high-precision 1D-timeseries data, this usually results in an unwanted quality-loss and corruption of power spectra at selected frequency ranges. Novel methods exist that are based on non-local averaging, which would conserve much of the initial resolution, but these methods are so far focusing on 2D or 3D data. We present here a method specialized for 1D-timeseries, e.g. as obtained by magnetic field measurements from the recently launched MMS satellites. To identify the noise, we use a self-similarity testing and non-local averaging method in order to separate different types of noise and signals, like the instrument noise, non-correlated fluctuations in the signal from heliospheric sources, and correlated fluctuations such as harmonic waves or shock fronts. In power spectra of test data, we are able to restore significant parts of a previously know signal from a noisy measurement. This method also works for high frequencies, where the background noise may have a larger contribution to the spectral power than the signal itself. We offer an easy-to-use software tools set, which enables scientists to use this novel technique on their own noisy data. This allows to use the maximum possible capacity of the instrumental hardware and helps to enhance the quality of the obtained scientific results.

  6. Asymmetric Effects of Subaerial and Subaqueous Basement Slopes on Self-Similar Morphology of Prograding Deltas

    Lai, Steven Yueh Jen; Hsiao, Yung-Tai; Wu, Fu-Chun

    2017-12-01

    Deltas form over basements of various slope configurations. While the morphodynamics of prograding deltas over single-slope basements have been studied previously, our understanding of delta progradation over segmented basements is still limited. Here we use experimental and analytical approaches to investigate the deltaic morphologies developing over two-slope basements with unequal subaerial and subaqueous slopes. For each case considered, the scaled profiles of the evolving delta collapse to a single profile for constant water and sediment influxes, allowing us to use the analytical self-similar profiles to investigate the individual effects of subaerial/subaqueous slopes. Individually varying the subaerial/subaqueous slopes exerts asymmetric effects on the morphologies. Increasing the subaerial slope advances the entire delta; increasing the subaqueous slope advances the upstream boundary of the topset yet causes the downstream boundary to retreat. The delta front exhibits a first-retreat-then-advance migrating trend with increasing subaqueous slope. A decrease in subaerial topset length is always accompanied by an increase in subaqueous volume fraction, no matter which segment is steepened. Applications are presented for estimating shoreline retreat caused by steepening of basement slopes, and estimating subaqueous volume and delta front using the observed topset length. The results may have implications for real-world delta systems subjected to upstream tectonic uplift and/or downstream subsidence. Both scenarios would exhibit reduced topset lengths, which are indicative of the accompanied increases in subaqueous volume and signal tectonic uplift and/or subsidence that are at play. We highlight herein the importance of geometric controls on partitioning of sediment between subaerial and subaqueous delta components.

  7. Inter-relationship between scaling exponents for describing self-similar river networks

    Yang, Soohyun; Paik, Kyungrock

    2015-04-01

    Natural river networks show well-known self-similar characteristics. Such characteristics are represented by various power-law relationships, e.g., between upstream length and drainage area (exponent h) (Hack, 1957), and in the exceedance probability distribution of upstream area (exponent ɛ) (Rodriguez-Iturbe et al., 1992). It is empirically revealed that these power-law exponents are within narrow ranges. Power-law is also found in the relationship between drainage density (the total stream length divided by the total basin area) and specified source area (the minimum drainage area to form a stream head) (exponent η) (Moussa and Bocquillon, 1996). Considering that above three scaling relationships all refer to fundamental measures of 'length' and 'area' of a given drainage basin, it is natural to hypothesize plausible inter-relationship between these three scaling exponents. Indeed, Rigon et al. (1996) demonstrated the relationship between ɛ and h. In this study, we expand this to a more general ɛ-η-h relationship. We approach ɛ-η relationship in an analytical manner while η-h relationship is demonstrated for six study basins in Korea. Detailed analysis and implications will be presented. References Hack, J. T. (1957). Studies of longitudinal river profiles in Virginia and Maryland. US, Geological Survey Professional Paper, 294. Moussa, R., & Bocquillon, C. (1996). Fractal analyses of tree-like channel networks from digital elevation model data. Journal of Hydrology, 187(1), 157-172. Rigon, R., Rodriguez-Iturbe, I., Maritan, A., Giacometti. A., Tarboton, D. G., & Rinaldo, A. (1996). On Hack's Law. Water Resources Research, 32(11), 3367-3374. Rodríguez-Iturbe, I., Ijjasz-Vasquez, E. J., Bras, R. L., & Tarboton, D. G. (1992). Power law distributions of discharge mass and energy in river basins. Water Resources Research, 28(4), 1089-1093.

  8. Modelling Protein Dynamics on the Microsecond Time Scale

    Siuda, Iwona Anna

    Recent years have shown an increase in coarse-grained (CG) molecular dynamics simulations, providing structural and dynamic details of large proteins and enabling studies of self-assembly of biological materials. It is not easy to acquire such data experimentally, and access is also still limited...... in atomistic simulations. During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger......ELNEDIN was therefore proposed as part of the work. Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins...

  9. Discriminating lysosomal membrane protein types using dynamic neural network.

    Tripathi, Vijay; Gupta, Dwijendra Kumar

    2014-01-01

    This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.

  10. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    Xia, Kelin; Wei, Guo-Wei

    2014-01-01

    This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365

  11. Development and Parameters of a Non-Self-Similar CME Caused by the Eruption of a Quiescent Prominence

    Kuzmenko, I. V.; Grechnev, V. V.

    2017-10-01

    The eruption of a large quiescent prominence on 17 August 2013 and an associated coronal mass ejection (CME) were observed from different vantage points by the Solar Dynamics Observatory (SDO), the Solar-Terrestrial Relations Observatory (STEREO), and the Solar and Heliospheric Observatory (SOHO). Screening of the quiet Sun by the prominence produced an isolated negative microwave burst. We estimated the parameters of the erupting prominence from a radio absorption model and measured them from 304 Å images. The variations of the parameters as obtained by these two methods are similar and agree within a factor of two. The CME development was studied from the kinematics of the front and different components of the core and their structural changes. The results were verified using movies in which the CME expansion was compensated for according to the measured kinematics. We found that the CME mass (3.6 × 10^{15} g) was mainly supplied by the prominence (≈ 6 × 10^{15} g), while a considerable part drained back. The mass of the coronal-temperature component did not exceed 10^{15} g. The CME was initiated by the erupting prominence, which constituted its core and remained active. The structural and kinematical changes started in the core and propagated outward. The CME structures continued to form during expansion, which did not become self-similar up to 25 R_{⊙}. The aerodynamic drag was insignificant. The core formed during the CME rise to 4 R_{⊙} and possibly beyond. Some of its components were observed to straighten and stretch outward, indicating the transformation of tangled structures of the core into a simpler flux rope, which grew and filled the cavity as the CME expanded.

  12. Collapse of a self-similar cylindrical scalar field with non-minimal coupling II: strong cosmic censorship

    Condron, Eoin; Nolan, Brien C

    2014-01-01

    We investigate self-similar scalar field solutions to the Einstein equations in whole cylinder symmetry. Imposing self-similarity on the spacetime gives rise to a set of single variable functions describing the metric. Furthermore, it is shown that the scalar field is dependent on a single unknown function of the same variable and that the scalar field potential has exponential form. The Einstein equations then take the form of a set of ODEs. Self-similarity also gives rise to a singularity at the scaling origin. We extend the work of Condron and Nolan (2014 Class. Quantum Grav. 31 015015), which determined the global structure of all solutions with a regular axis in the causal past of the singularity. We identified a class of solutions that evolves through the past null cone of the singularity. We give the global structure of these solutions and show that the singularity is censored in all cases. (paper)

  13. A nonlinear eigenvalue problem for self-similar spherical force-free magnetic fields

    Lerche, I. [Institut für Geowissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther Universität, D-06099 Halle (Germany); Low, B. C. [High Altitude Observatory, National Center for Atmospheric Research, Boulder, Colorado 80307 (United States)

    2014-10-15

    An axisymmetric force-free magnetic field B(r, θ) in spherical coordinates is defined by a function r sin θB{sub φ}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r sin θB{sub φ}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(θ))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(θ) as its eigenfunction [B. C. Low and Y. Q Lou, Astrophys. J. 352, 343 (1990)]. A complete analysis is presented of the eigenvalue spectrum for a given n, providing a unified understanding of the eigenfunctions and the physical relationship between the field's degree of multi-polarity and rate of radial decay via the parameter n. These force-free fields, self-similar on spheres of constant r, have basic astrophysical applications. As explicit solutions they have, over the years, served as standard benchmarks for testing 3D numerical codes developed to compute general force-free fields in the solar corona. The study presented includes a set of illustrative multipolar field solutions to address the magnetohydrodynamics (MHD) issues underlying the observation that the solar corona has a statistical preference for negative and positive magnetic helicities in its northern and southern hemispheres, respectively; a hemispherical effect, unchanging as the Sun's global field reverses polarity in successive eleven-year cycles. Generalizing these force-free fields to the separable form B=(H(θ,φ))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for φ-dependence greatly complicates the governing equations that have remained intractable. The axisymmetric results obtained are discussed in relation to this generalization and the Parker Magnetostatic Theorem. The axisymmetric solutions are mathematically related to a family of 3D time-dependent ideal MHD solutions for a polytropic fluid of index γ = 4

  14. Self-similar hierarchical energetics in the ICM of massive galaxy clusters

    Miniati, Francesco; Beresnyak, Andrey

    type of self-similarity in cosmology. Their specific values, while consistent with current data, indicate that thermal energy dominates the ICM energetics and the turbulent dynamo is always far from saturation, unlike the condition in other familiar astrophysical fluids (stars, interstellar medium of galaxies, compact objects, etc.). In addition, they have important physical meaning as their specific values encodes information about the efficiency of turbulent heating (the fraction of ICM thermal energy produced by turbulent dissipation) and the efficiency of dynamo action in the ICM (CE ).

  15. Simulation of Protein Structure, Dynamics and Function in Organic Media

    Daggett, Valerie

    1998-01-01

    The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...

  16. Protein dynamics in individual human cells: experiment and theory.

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  17. Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

    Lee, Hui Sun; Qi, Yifei; Im, Wonpil

    2015-03-09

    N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

  18. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  19. Self-similarity of high-pT hadron production in π-p and π- A collisions

    Tokarev, M.V.; Panebrattsev, Yu.A.; Skoro, G.P.; Zborovsky, I.

    2002-01-01

    Self-similar properties of hadron production in π - p and π - A collisions over a high-p T region are studied. The analysis if experimental data is performed in the framework of z-scaling. The scaling variable depends on the anomalous fractal dimension of the incoming pion. Its value is found to be δ π ≅ 0.1. Independence of the scaling function Ψ(z) on the collision energy is shown. A-dependence of data z-presentation confirms self-similarity of particle formation in πA collisions

  20. Protein-protein docking with dynamic residue protonation states.

    Krishna Praneeth Kilambi

    2014-12-01

    Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.

  1. Graphical user interface based computer simulation of self-similar modes of a paraxial slow self-focusing laser beam for saturating plasma nonlinearities

    Batra, Karuna; Mitra, Sugata; Subbarao, D.; Sharma, R.P.; Uma, R.

    2005-01-01

    The task for the present study is to make an investigation of self-similarity in a self-focusing laser beam both theoretically and numerically using graphical user interface based interactive computer simulation model in MATLAB (matrix laboratory) software in the presence of saturating ponderomotive force based and relativistic electron quiver based plasma nonlinearities. The corresponding eigenvalue problem is solved analytically using the standard eikonal formalism and the underlying dynamics of self-focusing is dictated by the corrected paraxial theory for slow self-focusing. The results are also compared with computer simulation of self-focusing by the direct fast Fourier transform based spectral methods. It is found that the self-similar solution obtained analytically oscillates around the true numerical solution equating it at regular intervals. The simulation results are the main ones although a feasible semianalytical theory under many assumptions is given to understand the process. The self-similar profiles are called as self-organized profiles (not in a strict sense), which are found to be close to Laguerre-Gaussian curves for all the modes, the shape being conserved. This terminology is chosen because it has already been shown from a phase space analysis that the width of an initially Gaussian beam undergoes periodic oscillations that are damped when any absorption is added in the model, i.e., the beam width converges to a constant value. The research paper also tabulates the specific values of the normalized phase shift for solutions decaying to zero at large transverse distances for first three modes which can, however, be extended to higher order modes

  2. Dynamics of a Highly Flexible Protein

    Andersen, Lisbeth

    malleability are the subject of this defense. Using nuclear magnetic resonance (NMR) spectroscopy, the dynamics of NCBD have been investigated on timescales ranging from picoseconds to milliseconds using relaxation dispersion experiments, residual dipolar couplings and methyl group deuterium relaxation. From...

  3. Dynamics in electron transfer protein complexes

    Bashir, Qamar

    2010-01-01

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

  4. A comparison of techniques for calculating protein essential dynamics

    van Aalten, D.M.F.; de Groot, B.L.; Findlay, J.B.C.; Berendsen, H.J.C.; Amadei, A

    1997-01-01

    Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to

  5. Dynamic properties of motor proteins with two subunits

    Kolomeisky, Anatoly B; III, Hubert Phillips

    2005-01-01

    The dynamics of motor protein molecules consisting of two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate states and conformations between the corresponding binding states of proteins. These models enable us to provide a detailed description and comparison of two different mechanisms of the motion of motor proteins along the linear tracks: the hand-over-hand mechanism, when the motion of subunits alternate; and the inchworm mechanism, when one subunit is always trailing another one. It is shown that the proteins in the hand-over-hand mechanism move faster and fluctuate more than the molecules in the inchworm mechanism. The effect of external forces on dynamic properties of motor proteins is also discussed. Finally, a quantitative method, based on experimental observations for single motor proteins, is proposed for distinguishing between two mechanisms of motion

  6. PDB2CD visualises dynamics within protein structures.

    Janes, Robert W

    2017-10-01

    Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

  7. Self-similarity of hard cumulative processes in fixed target experiment for BES-II at STAR

    Tokarev, M. V.; Zborovský, Imrich; Aparin, A. A.

    2015-01-01

    Roč. 12, č. 2 (2015), s. 221-229 ISSN 1547-4771 R&D Projects: GA MŠk(CZ) LG13031 Institutional support: RVO:61389005 Keywords : critical point * cumulative process * heavy ions * high energy * phase transition * self-similarity Subject RIV: BE - Theoretical Physics

  8. Self-Similarity of Jet Production in pp and p{/bar p} Collisions at RHIC, Tevatron and LHC

    Tokarev, M. V.; Dedovich, T. G.; Zborovský, Imrich

    2012-01-01

    Roč. 27, č. 21 (2012), s. 815-820 ISSN 0217-751X R&D Projects: GA MŠk LA08002; GA MŠk LA08015 Institutional support: RVO:61389005 Keywords : jets * self-similarity * high energy * scaling Subject RIV: BE - Theoretical Physics Impact factor: 1.127, year: 2012

  9. Uniqueness of Mass-Conserving Self-similar Solutions to Smoluchowski's Coagulation Equation with Inverse Power Law Kernels

    Laurençot, Philippe

    2018-03-01

    Uniqueness of mass-conserving self-similar solutions to Smoluchowski's coagulation equation is shown when the coagulation kernel K is given by K(x,x_*)=2(x x_*)^{-α } , (x,x_*)\\in (0,∞)^2 , for some α >0.

  10. Hindered protein dynamics in the presence of a cryoprotecting agent

    Koeper, I. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Physikdepartment E13, TU Muenchen, 85747 Garching (Germany); Bellissent-Funel, M.C. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France)

    2002-07-01

    We present a study of the influence of trehalose, a well-known cryoprotecting disaccharide, on the dynamics of a protein, the C-phycocyanin. The dynamics is investigated in a time range from some picoseconds to several nanoseconds using different neutron-scattering techniques. Data obtained on samples containing hydrated powders of the protein in the presence of trehalose are compared to that of the protein alone, studied by neutron-scattering techniques as well as by molecular dynamics simulations. The analysis of time-of-flight data gives access to the geometry of the observed motions. These motions can be described via a model of a particle diffusing inside a sphere. We observe a slowing down of the movements of the protein due to the presence of trehalose of one to two orders of magnitude, while the geometry of the motions is conserved. (orig.)

  11. Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis

    Klinman, Judith P.; Kohen, Amnon

    2014-01-01

    The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C–H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial. PMID:23746260

  12. Dynamics of DNA conformations and DNA-protein interaction

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...... denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed...... in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent...

  13. Coherent Protein Dynamics Explored at FELIX

    Austin, Robert

    2004-01-01

    We have discovered that there exists a very narrow (less than 0.02 microns) wide resonance in the amide I band of myoglobin and photoactive yellow protein that can be driven to greater than 30% saturation using very narrow linewidth pump-probe spectroscopy at FELIX. The extraordinary narrowness of this transition and the extraordinary ease of saturation inplies that this band is highly anharmonic and decoupled from the other oscillators in the amide I band. We will present detailed measurments on this discovery and implications for energy flow in proteins.

  14. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  15. Functional advantages of dynamic protein disorder.

    Berlow, Rebecca B; Dyson, H Jane; Wright, Peter E

    2015-09-14

    Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  16. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  17. Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

    Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

    2013-01-01

    We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

  18. Collective dynamics of protein hydration water by brillouin neutron spectroscopy.

    Orecchini, Andrea; Paciaroni, Alessandro; De Francesco, Alessio; Petrillo, Caterina; Sacchetti, Francesco

    2009-04-08

    By a detailed experimental study of THz dynamics in the ribonuclease protein, we could detect the propagation of coherent collective density fluctuations within the protein hydration shell. The emerging picture indicates the presence of both a dispersing mode, traveling with a speed greater than 3000 m/s, and a nondispersing one, characterized by an almost constant energy of 6-7 meV. In agreement with molecular dynamics simulations [Phys. Rev. Lett. 2002, 89, 275501], the features of the dispersion curves closely resemble those observed in pure liquid water [Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2004, 69, 061203]. On the contrary, the observed damping factors are much larger than in bulk water, with the dispersing mode becoming overdamped at Q = 0.6 A(-1) already. Such novel experimental findings are discussed as a dynamic signature of the disordering effect induced by the protein surface on the local structure of water.

  19. Hydration and temperature interdependence of protein picosecond dynamics.

    Lipps, Ferdinand; Levy, Seth; Markelz, A G

    2012-05-14

    We investigate the nature of the solvent motions giving rise to the rapid temperature dependence of protein picoseconds motions at 220 K, often referred to as the protein dynamical transition. The interdependence of picoseconds dynamics on hydration and temperature is examined using terahertz time domain spectroscopy to measure the complex permittivity in the 0.2-2.0 THz range for myoglobin. Both the real and imaginary parts of the permittivity over the frequency range measured have a strong temperature dependence at >0.27 h (g water per g protein), however the permittivity change is strongest for frequencies 1 THz, and 0.27 h for frequencies <1 THz. The data are consistent with the dynamical transition solvent fluctuations requiring only clusters of ~5 water molecules, whereas the enhancement of lowest frequency motions requires a fully spanning water network. This journal is © the Owner Societies 2012

  20. Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: Protein versus solvent environments

    Vengris, M.; Horst, M.A.; Zgrablic, G.; van Stokkum, I.H.M.; Haacke, S.; Chergui, M.; Hellingwerf, K.J.; van Grondelle, R.; Larsen, D.S.

    2004-01-01

    Wavelength- and time-resolved fluorescence experiments have been performed on the photoactive yellow protein, the E46Q mutant, the hybrids of these proteins containing a nonisomerizing "locked" chromophore, and the native and locked chromophores in aqueous solution. The ultrafast dynamics of these

  1. High-power Yb-fiber comb based on pre-chirped-management self-similar amplification

    Luo, Daping; Liu, Yang; Gu, Chenglin; Wang, Chao; Zhu, Zhiwei; Zhang, Wenchao; Deng, Zejiang; Zhou, Lian; Li, Wenxue; Zeng, Heping

    2018-02-01

    We report a fiber self-similar-amplification (SSA) comb system that delivers a 250-MHz, 109-W, 42-fs pulse train with a 10-dB spectral width of 85 nm at 1056 nm. A pair of grisms is employed to compensate the group velocity dispersion and third-order dispersion of pre-amplified pulses for facilitating a self-similar evolution and a self-phase modulation (SPM). Moreover, we analyze the stabilities and noise characteristics of both the locked carrier envelope phase and the repetition rate, verifying the stability of the generated high-power comb. The demonstration of the SSA comb at such high power proves the feasibility of the SPM-based low-noise ultrashort comb.

  2. General relativistic self-similar waves that induce an anomalous acceleration into the standard model of cosmology

    Smoller, Joel

    2012-01-01

    We prove that the Einstein equations in Standard Schwarzschild Coordinates close to form a system of three ordinary differential equations for a family of spherically symmetric, self-similar expansion waves, and the critical ($k=0$) Friedmann universe associated with the pure radiation phase of the Standard Model of Cosmology (FRW), is embedded as a single point in this family. Removing a scaling law and imposing regularity at the center, we prove that the family reduces to an implicitly defined one parameter family of distinct spacetimes determined by the value of a new {\\it acceleration parameter} $a$, such that $a=1$ corresponds to FRW. We prove that all self-similar spacetimes in the family are distinct from the non-critical $k\

  3. On the Isomorphism between Dissipative Systems, Fractal Self-Similarity and Electrodynamics. Toward an Integrated Vision of Nature

    Giuseppe Vitiello

    2014-05-01

    Full Text Available In electrodynamics there is a mutual exchange of energy and momentum between the matter field and the electromagnetic field and the total energy and momentum are conserved. For a constant magnetic field and harmonic scalar potential, electrodynamics is shown to be isomorph to a system of damped/amplified harmonic oscillators. These can be described by squeezed coherent states which in turn are isomorph to self-similar fractal structures. Under the said conditions of constant magnetic field and harmonic scalar potential, electrodynamics is thus isomorph to fractal self-similar structures and squeezed coherent states. At a quantum level, dissipation induces noncommutative geometry with the squeezing parameter playing a relevant role. Ubiquity of fractals in Nature and relevance of coherent states and electromagnetic interaction point to a unified, integrated vision of Nature.

  4. On the self-similar solution to the Euler equations for an incompressible fluid in three dimensions

    Pomeau, Yves

    2018-03-01

    The equations for a self-similar solution to an inviscid incompressible fluid are mapped into an integral equation that hopefully can be solved by iteration. It is argued that the exponents of the similarity are ruled by Kelvin's theorem of conservation of circulation. The end result is an iteration with a nonlinear term entering a kernel given by a 3D integral for a swirling flow, likely within reach of present-day computational power. Because of the slow decay of the similarity solution at large distances, its kinetic energy diverges, and some mathematical results excluding non-trivial solutions of the Euler equations in the self-similar case do not apply. xml:lang="fr"

  5. Time-resolved infrared studies of protein conformational dynamics

    Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)

    1994-12-01

    We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.

  6. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    Christian Mücksch

    Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  7. Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits

    Koseska, Aneta; Volkov, Evgenii; Kurths, Juergen

    2011-01-01

    Synthetic biology is a relatively new research discipline that combines standard biology approaches with the constructive nature of engineering. Thus, recent efforts in the field of synthetic biology have given a perspective to consider cells as 'programmable matter'. Here, we address the possibility of using synthetic circuits to control protein dynamics. In particular, we show how intercellular communication and stochasticity can be used to manipulate the dynamical behavior of a population of coupled synthetic units and, in this manner, finely tune the expression of specific proteins of interest, e.g. in large bioreactors.

  8. Dynamic organization of genetic recombination proteins and chromosomes

    Essers, J.; Van Cappellen, G.; Van Drunen, E.; Theil, A.; Jaspers, N.N.G.J.; Houtsmuller, A.B.; Vermeulen, W.; Kanaar, R.

    2003-01-01

    Homologous recombination requires the co-ordinated action of the RAD52 group proteins, including Rad51, Rad52 and Rad54. Upon treatment of mammalian cells with ionizing radiation, these proteins accumulate into foci at sites of DSB induction. We probed the nature of the DNA damage-induced foci in living cells with the use of photobleaching techniques. These foci are not static assemblies of DNA repair proteins. Instead, they are dynamic structures of which Rad51 is a stable core component, while Rad52 and Rad54 reversibly interact with the structure. Furthermore, even though the RAD52 group proteins colocalize in the DNA damage-induced foci, the majority of the proteins are not part of the same multi-protein complex in the absence of DNA damage. Executing DNA transactions through dynamic multi-protein complexes, rather than stable holo-complexes, allows greater flexibility during the transaction. In case of DNA repair, for example, it allows cross talk between different DNA repair pathways and coupling to other DNA transactions, such as replication. In addition to the behavior of proteins in living cells, we have tracked chromosomes during cell division. Our results suggest that the relative position of chromosomes in the mother cell is conserved in its daughter cells

  9. Solution structure and dynamics of melanoma inhibitory activity protein

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  10. Role of protein dynamics in transmembrane receptor signalling

    Wang, Yong; Bugge, Katrine Østergaard; Kragelund, Birthe Brandt

    2018-01-01

    Cells are dependent on transmembrane receptors to communicate and transform chemical and physical signals into intracellular responses. Because receptors transport 'information', conformational changes and protein dynamics play a key mechanistic role. We here review examples where experiment...... to function. Because the receptors function in a heterogeneous environment and need to be able to switch between distinct functional states, they may be particularly sensitive to small perturbations that complicate studies linking dynamics to function....

  11. A Study of Wavelet Analysis and Data Extraction from Second-Order Self-Similar Time Series

    Leopoldo Estrada Vargas

    2013-01-01

    Full Text Available Statistical analysis and synthesis of self-similar discrete time signals are presented. The analysis equation is formally defined through a special family of basis functions of which the simplest case matches the Haar wavelet. The original discrete time series is synthesized without loss by a linear combination of the basis functions after some scaling, displacement, and phase shift. The decomposition is then used to synthesize a new second-order self-similar signal with a different Hurst index than the original. The components are also used to describe the behavior of the estimated mean and variance of self-similar discrete time series. It is shown that the sample mean, although it is unbiased, provides less information about the process mean as its Hurst index is higher. It is also demonstrated that the classical variance estimator is biased and that the widely accepted aggregated variance-based estimator of the Hurst index results biased not due to its nature (which is being unbiased and has minimal variance but to flaws in its implementation. Using the proposed decomposition, the correct estimation of the Variance Plot is described, as well as its close association with the popular Logscale Diagram.

  12. Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.

    Eric A Yen

    2014-05-01

    Full Text Available Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and

  13. Evolutionary dynamics of protein domain architecture in plants

    Zhang Xue-Cheng

    2012-01-01

    Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

  14. Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2

    Laulumaa Saara

    2015-01-01

    Full Text Available Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.

  15. Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2

    Laulumaa, Saara; Kursula, Petri; Natali, Francesca

    2015-01-01

    Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.

  16. Progression of 3D Protein Structure and Dynamics Measurements

    Sato-Tomita, Ayana; Sekiguchi, Hiroshi; Sasaki, Yuji C.

    2018-06-01

    New measurement methodologies have begun to be proposed with the recent progress in the life sciences. Here, we introduce two new methodologies, X-ray fluorescence holography for protein structural analysis and diffracted X-ray tracking (DXT), to observe the dynamic behaviors of individual single molecules.

  17. Unveiling protein functions through the dynamics of the interaction network.

    Irene Sendiña-Nadal

    Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

  18. Protein electron transfer: is biology (thermo)dynamic?

    Matyushov, Dmitry V

    2015-01-01

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic

  19. Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces

    Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.

    2015-01-01

    We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces

  20. Two-halo term in stacked thermal Sunyaev-Zel'dovich measurements: Implications for self-similarity

    Hill, J. Colin; Baxter, Eric J.; Lidz, Adam; Greco, Johnny P.; Jain, Bhuvnesh

    2018-04-01

    The relation between the mass and integrated electron pressure of galaxy group and cluster halos can be probed by stacking maps of the thermal Sunyaev-Zel'dovich (tSZ) effect. Perhaps surprisingly, recent observational results have indicated that the scaling relation between integrated pressure and mass follows the prediction of simple, self-similar models down to halo masses as low as 1 012.5 M⊙ . Hydrodynamical simulations that incorporate energetic feedback processes suggest that gas should be depleted from such low-mass halos, thus decreasing their tSZ signal relative to self-similar predictions. Here, we build on the modeling of V. Vikram, A. Lidz, and B. Jain, Mon. Not. R. Astron. Soc. 467, 2315 (2017), 10.1093/mnras/stw3311 to evaluate the bias in the interpretation of stacked tSZ measurements due to the signal from correlated halos (the "two-halo" term), which has generally been neglected in the literature. We fit theoretical models to a measurement of the tSZ-galaxy group cross-correlation function, accounting explicitly for the one- and two-halo contributions. We find moderate evidence of a deviation from self-similarity in the pressure-mass relation, even after marginalizing over conservative miscentering effects. We explore pressure-mass models with a break at 1 014 M⊙, as well as other variants. We discuss and test for sources of uncertainty in our analysis, in particular a possible bias in the halo mass estimates and the coarse resolution of the Planck beam. We compare our findings with earlier analyses by exploring the extent to which halo isolation criteria can reduce the two-halo contribution. Finally, we show that ongoing third-generation cosmic microwave background experiments will explicitly resolve the one-halo term in low-mass groups; our methodology can be applied to these upcoming data sets to obtain a clear answer to the question of self-similarity and an improved understanding of hot gas in low-mass halos.

  1. Self-similar and self-affine pionization in nuclear interactions at a few AgeV

    Ghosh, Dipak; Deb, Argha; Chattopadhyay, Keya Dutta; Sarkar, Rinku; Dutta, Ishita Sen

    2004-01-01

    Self-affine multiplicity scaling is investigated in the framework of two-dimensional factorial moment methodology using the concept of the Hurst exponent (H) considering different bins of the phase space. We have investigated the fluctuation pattern of emitted pions in 24 Mg-AgBr interactions at 4.5 AGeV and this study reveals that the fluctuation is self-similar in some bins, whereas it is self-affine in other bins, that is, the multiplicity scaling is bin-dependent. (author)

  2. Self-similarly evolving and minimally dissipated stable states of plasmas realized after relaxation and self-organization processes

    Kondoh, Yoshiomi; Hakoiwa, Toru; Okada, Akihito; Kobayashi, Naohiro; Takahashi, Toshiki

    2006-01-01

    A novel set of simultaneous eigenvalue equations having dissipative terms are derived to find self-similarly evolving and minimally dissipated stable states of plasmas realized after relaxation and self-organization processes. By numerically solving the set of eigenvalue equations in a cylindrical model, typical spatial profiles of plasma parameters, electric and magnetic fields and diffusion factors are presented, all of which determine self-consistently with each other by physical laws and mutual relations among them, just as in experimental plasmas. (author)

  3. Conformational dynamics of amyloid proteins at the aqueous interface

    Armbruster, Matthew; Horst, Nathan; Aoki, Brendy; Malik, Saad; Soto, Patricia

    2013-03-01

    Amyloid proteins is a class of proteins that exhibit distinct monomeric and oligomeric conformational states hallmark of deleterious neurological diseases for which there are not yet cures. Our goal is to examine the extent of which the aqueous/membrane interface modulates the folding energy landscape of amyloid proteins. To this end, we probe the dynamic conformational ensemble of amyloids (monomer prion protein and Alzheimer's Ab protofilaments) interacting with model bilayers. We will present the results of our coarse grain molecular modeling study in terms of the existence of preferential binding spots of the amyloid to the bilayer and the response of the bilayer to the interaction with the amyloid. NSF Nebraska EPSCoR First Award

  4. Dynamic gastric digestion of a commercial whey protein concentrate†.

    Miralles, Beatriz; Del Barrio, Roberto; Cueva, Carolina; Recio, Isidra; Amigo, Lourdes

    2018-03-01

    A dynamic gastrointestinal simulator, simgi ® , has been applied to assess the gastric digestion of a whey protein concentrate. Samples collected from the outlet of the stomach have been compared to those resulting from the static digestion protocol INFOGEST developed on the basis of physiologically inferred conditions. Progress of digestion was followed by SDS-PAGE and LC-MS/MS. By SDS-PAGE, serum albumin and α-lactalbumin were no longer detectable at 30 and 60 min, respectively. On the contrary, β-lactoglobulin was visible up to 120 min, although in decreasing concentrations in the dynamic model due to the gastric emptying and the addition of gastric fluids. Moreover, β-lactoglobulin was partly hydrolysed by pepsin probably due to the presence of heat-denatured forms and the peptides released using both digestion models were similar. Under dynamic conditions, a stepwise increase in number of peptides over time was observed, while the static protocol generated a high number of peptides from the beginning of digestion. Whey protein digestion products using a dynamic stomach are consistent with those generated with the static protocol but the kinetic behaviour of the peptide profile emphasises the effect of the sequential pepsin addition, peristaltic shaking, and gastric emptying on protein digestibility. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  5. Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein

    Michael T. Zimmermann

    2012-04-01

    Full Text Available We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure.

  6. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.

    Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin

    2016-01-01

    Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

  7. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

    Elise Delaforge

    2016-09-01

    Full Text Available Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

  8. Markov dynamic models for long-timescale protein motion.

    Chiang, Tsung-Han

    2010-06-01

    Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.

  9. Markov dynamic models for long-timescale protein motion.

    Chiang, Tsung-Han; Hsu, David; Latombe, Jean-Claude

    2010-01-01

    Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.

  10. The dynamics of plant plasma membrane proteins: PINs and beyond.

    Luschnig, Christian; Vert, Grégory

    2014-08-01

    Plants are permanently situated in a fixed location and thus are well adapted to sense and respond to environmental stimuli and developmental cues. At the cellular level, several of these responses require delicate adjustments that affect the activity and steady-state levels of plasma membrane proteins. These adjustments involve both vesicular transport to the plasma membrane and protein internalization via endocytic sorting. A substantial part of our current knowledge of plant plasma membrane protein sorting is based on studies of PIN-FORMED (PIN) auxin transport proteins, which are found at distinct plasma membrane domains and have been implicated in directional efflux of the plant hormone auxin. Here, we discuss the mechanisms involved in establishing such polar protein distributions, focusing on PINs and other key plant plasma membrane proteins, and we highlight the pathways that allow for dynamic adjustments in protein distribution and turnover, which together constitute a versatile framework that underlies the remarkable capabilities of plants to adjust growth and development in their ever-changing environment. © 2014. Published by The Company of Biologists Ltd.

  11. Studying pressure denaturation of a protein by molecular dynamics simulations.

    Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

    2010-05-15

    Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties

  12. Applications of Analytical Self-Similar Solutions of Reynolds-Averaged Models for Instability-Induced Turbulent Mixing

    Hartland, Tucker; Schilling, Oleg

    2017-11-01

    Analytical self-similar solutions to several families of single- and two-scale, eddy viscosity and Reynolds stress turbulence models are presented for Rayleigh-Taylor, Richtmyer-Meshkov, and Kelvin-Helmholtz instability-induced turbulent mixing. The use of algebraic relationships between model coefficients and physical observables (e.g., experimental growth rates) following from the self-similar solutions to calibrate a member of a given family of turbulence models is shown. It is demonstrated numerically that the algebraic relations accurately predict the value and variation of physical outputs of a Reynolds-averaged simulation in flow regimes that are consistent with the simplifying assumptions used to derive the solutions. The use of experimental and numerical simulation data on Reynolds stress anisotropy ratios to calibrate a Reynolds stress model is briefly illustrated. The implications of the analytical solutions for future Reynolds-averaged modeling of hydrodynamic instability-induced mixing are briefly discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  13. New self-similar radiation-hydrodynamics solutions in the high-energy density, equilibrium diffusion limit

    Lane, Taylor K; McClarren, Ryan G

    2013-01-01

    This work presents semi-analytic solutions to a radiation-hydrodynamics problem of a radiation source driving an initially cold medium. Our solutions are in the equilibrium diffusion limit, include material motion and allow for radiation-dominated situations where the radiation energy is comparable to (or greater than) the material internal energy density. As such, this work is a generalization of the classical Marshak wave problem that assumes no material motion and that the radiation energy is negligible. Including radiation energy density in the model serves to slow down the wave propagation. The solutions provide insight into the impact of radiation energy and material motion, as well as present a novel verification test for radiation transport packages. As a verification test, the solution exercises the radiation–matter coupling terms and their v/c treatment without needing a hydrodynamics solve. An example comparison between the self-similar solution and a numerical code is given. Tables of the self-similar solutions are also provided. (paper)

  14. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  15. Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria.

    Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong; Luo, Zhao-Qing; Shen, Xihui

    2014-05-20

    Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells

  16. Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

    Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

    2017-07-01

    To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

  17. Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy

    Adamczyk, Katrin; Candelaresi, Marco; Hunt, Neil T; Robb, Kirsty; Hoskisson, Paul A; Tucker, Nicholas P; Gumiero, Andrea; Walsh, Martin A; Parker, Anthony W

    2012-01-01

    Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms. (topical review)

  18. A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

    Schlecht, Ulrich; Liu, Zhimin; Blundell, Jamie R; St Onge, Robert P; Levy, Sasha F

    2017-05-25

    Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.

  19. Picosecond Fluorescence Dynamics of Tryptophan and 5-Fluorotryptophan in Monellin : Slow Water-Protein Relaxation Unmasked

    Xu, Jianhua; Chen, Binbin; Callis, Patrik Robert; Muiño, Pedro L; Rozeboom, Henriette J; Broos, Jaap; Toptygin, Dmitri; Brand, Ludwig; Knutson, Jay R

    2015-01-01

    Time Dependent Fluorescence Stokes (emission wavelength) Shifts (TDFSS) from tryptophan (Trp) following sub-picosecond excitation are increasingly used to investigate protein dynamics, most recently enabling active research interest into water dynamics near the surface of proteins. Unlike many

  20. ProteinAC: a frequency domain technique for analyzing protein dynamics

    Bozkurt Varolgunes, Yasemin; Demir, Alper

    2018-03-01

    It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.

  1. Gauge invariant perturbations of self-similar Lemaitre-Tolman-Bondi spacetime: Even parity modes with l≥2

    Waters, Thomas J.; Nolan, Brien C.

    2009-01-01

    In this paper we consider gauge invariant linear perturbations of the metric and matter tensors describing the self-similar Lemaitre-Tolman-Bondi (timelike dust) spacetime containing a naked singularity. We decompose the angular part of the perturbation in terms of spherical harmonics and perform a Mellin transform to reduce the perturbation equations to a set of ordinary differential equations with singular points. We fix initial data so the perturbation is finite on the axis and the past null cone of the singularity, and follow the perturbation modes up to the Cauchy horizon. There we argue that certain scalars formed from the modes of the perturbation remain finite, indicating linear stability of the Cauchy horizon.

  2. Probing multi-scale self-similarity of tissue structures using light scattering spectroscopy: prospects in pre-cancer detection

    Chatterjee, Subhasri; Das, Nandan K.; Kumar, Satish; Mohapatra, Sonali; Pradhan, Asima; Panigrahi, Prasanta K.; Ghosh, Nirmalya

    2013-02-01

    Multi-resolution analysis on the spatial refractive index inhomogeneities in the connective tissue regions of human cervix reveals clear signature of multifractality. We have thus developed an inverse analysis strategy for extraction and quantification of the multifractality of spatial refractive index fluctuations from the recorded light scattering signal. The method is based on Fourier domain pre-processing of light scattering data using Born approximation, and its subsequent analysis through Multifractal Detrended Fluctuation Analysis model. The method has been validated on several mono- and multi-fractal scattering objects whose self-similar properties are user controlled and known a-priori. Following successful validation, this approach has initially been explored for differentiating between different grades of precancerous human cervical tissues.

  3. Self-similar decay to the marginally stable ground state in a model for film flow over inclined wavy bottoms

    Tobias Hacker

    2012-04-01

    Full Text Available The integral boundary layer system (IBL with spatially periodic coefficients arises as a long wave approximation for the flow of a viscous incompressible fluid down a wavy inclined plane. The Nusselt-like stationary solution of the IBL is linearly at best marginally stable; i.e., it has essential spectrum at least up to the imaginary axis. Nevertheless, in this stable case we show that localized perturbations of the ground state decay in a self-similar way. The proof uses the renormalization group method in Bloch variables and the fact that in the stable case the Burgers equation is the amplitude equation for long waves of small amplitude in the IBL. It is the first time that such a proof is given for a quasilinear PDE with spatially periodic coefficients.

  4. Self-Similar Solutions of Rényi’s Entropy and the Concavity of Its Entropy Power

    Agapitos N. Hatzinikitas

    2015-08-01

    Full Text Available We study the class of self-similar probability density functions with finite mean and variance, which maximize Rényi’s entropy. The investigation is restricted in the Schwartz space S(Rd and in the space of l-differentiable compactly supported functions Clc (Rd. Interestingly, the solutions of this optimization problem do not coincide with the solutions of the usual porous medium equation with a Dirac point source, as occurs in the optimization of Shannon’s entropy. We also study the concavity of the entropy power in Rd with respect to time using two different methods. The first one takes advantage of the solutions determined earlier, while the second one is based on a setting that could be used for Riemannian manifolds.

  5. MAGIICAT III. Interpreting self-similarity of the circumgalactic medium with virial mass using Mg II absorption

    Churchill, Christopher W.; Trujillo-Gomez, Sebastian; Nielsen, Nikole M.; Kacprzak, Glenn G.

    2013-01-01

    In Churchill et al., we used halo abundance matching applied to 182 galaxies in the Mg II Absorber-Galaxy Catalog (MAGIICAT) and showed that the mean Mg II λ2796 equivalent width follows a tight inverse-square power law, W r (2796)∝(D/R vir ) –2 , with projected location relative to the galaxy virial radius and that the Mg II absorption covering fraction is effectively invariant with galaxy virial mass, M h , over the range 10.7 ≤ log M h /M ☉ ≤ 13.9. In this work, we explore multivariate relationships between W r (2796), virial mass, impact parameter, virial radius, and the theoretical cooling radius that further elucidate self-similarity in the cool/warm (T = 10 4 -10 4.5 K) circumgalactic medium (CGM) with virial mass. We show that virial mass determines the extent and strength of the Mg II absorbing gas such that the mean W r (2796) increases with virial mass at fixed distance while decreasing with galactocentric distance for fixed virial mass. The majority of the absorbing gas resides within D ≅ 0.3 R vir , independent of both virial mass and minimum absorption threshold; inside this region, and perhaps also in the region 0.3 < D/R vir ≤ 1, the mean W r (2796) is independent of virial mass. Contrary to absorber-galaxy cross-correlation studies, we show there is no anti-correlation between W r (2796) and virial mass. We discuss how simulations and theory constrained by observations support self-similarity of the cool/warm CGM via the physics governing star formation, gas-phase metal enrichment, recycling efficiency of galactic scale winds, filament and merger accretion, and overdensity of local environment as a function of virial mass.

  6. MAGIICAT III. Interpreting self-similarity of the circumgalactic medium with virial mass using Mg II absorption

    Churchill, Christopher W.; Trujillo-Gomez, Sebastian; Nielsen, Nikole M. [New Mexico State University, Las Cruces, NM 88003 (United States); Kacprzak, Glenn G. [Swinburne University of Technology, Victoria 3122 (Australia)

    2013-12-10

    In Churchill et al., we used halo abundance matching applied to 182 galaxies in the Mg II Absorber-Galaxy Catalog (MAGIICAT) and showed that the mean Mg II λ2796 equivalent width follows a tight inverse-square power law, W{sub r} (2796)∝(D/R {sub vir}){sup –2}, with projected location relative to the galaxy virial radius and that the Mg II absorption covering fraction is effectively invariant with galaxy virial mass, M {sub h}, over the range 10.7 ≤ log M {sub h}/M {sub ☉} ≤ 13.9. In this work, we explore multivariate relationships between W{sub r} (2796), virial mass, impact parameter, virial radius, and the theoretical cooling radius that further elucidate self-similarity in the cool/warm (T = 10{sup 4}-10{sup 4.5} K) circumgalactic medium (CGM) with virial mass. We show that virial mass determines the extent and strength of the Mg II absorbing gas such that the mean W{sub r} (2796) increases with virial mass at fixed distance while decreasing with galactocentric distance for fixed virial mass. The majority of the absorbing gas resides within D ≅ 0.3 R {sub vir}, independent of both virial mass and minimum absorption threshold; inside this region, and perhaps also in the region 0.3 < D/R {sub vir} ≤ 1, the mean W{sub r} (2796) is independent of virial mass. Contrary to absorber-galaxy cross-correlation studies, we show there is no anti-correlation between W{sub r} (2796) and virial mass. We discuss how simulations and theory constrained by observations support self-similarity of the cool/warm CGM via the physics governing star formation, gas-phase metal enrichment, recycling efficiency of galactic scale winds, filament and merger accretion, and overdensity of local environment as a function of virial mass.

  7. Using self-similarity compensation for improving inter-layer prediction in scalable 3D holoscopic video coding

    Conti, Caroline; Nunes, Paulo; Ducla Soares, Luís.

    2013-09-01

    Holoscopic imaging, also known as integral imaging, has been recently attracting the attention of the research community, as a promising glassless 3D technology due to its ability to create a more realistic depth illusion than the current stereoscopic or multiview solutions. However, in order to gradually introduce this technology into the consumer market and to efficiently deliver 3D holoscopic content to end-users, backward compatibility with legacy displays is essential. Consequently, to enable 3D holoscopic content to be delivered and presented on legacy displays, a display scalable 3D holoscopic coding approach is required. Hence, this paper presents a display scalable architecture for 3D holoscopic video coding with a three-layer approach, where each layer represents a different level of display scalability: Layer 0 - a single 2D view; Layer 1 - 3D stereo or multiview; and Layer 2 - the full 3D holoscopic content. In this context, a prediction method is proposed, which combines inter-layer prediction, aiming to exploit the existing redundancy between the multiview and the 3D holoscopic layers, with self-similarity compensated prediction (previously proposed by the authors for non-scalable 3D holoscopic video coding), aiming to exploit the spatial redundancy inherent to the 3D holoscopic enhancement layer. Experimental results show that the proposed combined prediction can improve significantly the rate-distortion performance of scalable 3D holoscopic video coding with respect to the authors' previously proposed solutions, where only inter-layer or only self-similarity prediction is used.

  8. Organizing membrane-curving proteins: the emerging dynamical picture.

    Simunovic, Mijo; Bassereau, Patricia; Voth, Gregory A

    2018-03-30

    Lipid membranes play key roles in cells, such as in trafficking, division, infection, remodeling of organelles, among others. The key step in all these processes is creating membrane curvature, typically under the control of many anchored, adhered or included proteins. However, it has become clear that the membrane itself can mediate the interactions among proteins to produce highly ordered assemblies. Computer simulations are ideally suited to investigate protein organization and the dynamics of membrane remodeling at near-micron scales, something that is extremely challenging to tackle experimentally. We review recent computational efforts in modeling protein-caused membrane deformation mechanisms, specifically focusing on coarse-grained simulations. We highlight work that exposed the membrane-mediated ordering of proteins into lines, meshwork, spirals and other assemblies, in what seems to be a very generic mechanism driven by a combination of short and long-ranged forces. Modulating the mechanical properties of membranes is an underexplored signaling mechanism in various processes deserving of more attention in the near future. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Fast dynamics perturbation analysis for prediction of protein functional sites

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  10. Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.

    Wako, Hiroshi; Endo, Shigeru

    2017-12-01

    Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo- and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

  11. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  12. Duplicate retention in signalling proteins and constraints from network dynamics.

    Soyer, O S; Creevey, C J

    2010-11-01

    Duplications are a major driving force behind evolution. Most duplicates are believed to fix through genetic drift, but it is not clear whether this process affects all duplications equally or whether there are certain gene families that are expected to show neutral expansions under certain circumstances. Here, we analyse the neutrality of duplications in different functional classes of signalling proteins based on their effects on response dynamics. We find that duplications involving intermediary proteins in a signalling network are neutral more often than those involving receptors. Although the fraction of neutral duplications in all functional classes increase with decreasing population size and selective pressure on dynamics, this effect is most pronounced for receptors, indicating a possible expansion of receptors in species with small population size. In line with such an expectation, we found a statistically significant increase in the number of receptors as a fraction of genome size in eukaryotes compared with prokaryotes. Although not confirmative, these results indicate that neutral processes can be a significant factor in shaping signalling networks and affect proteins from different functional classes differently. © 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology.

  13. Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

    A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

  14. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  15. Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein.

    Sharma, V K; Hayes, Douglas G; Urban, Volker S; O'Neill, Hugh M; Tyagi, M; Mamontov, E

    2017-07-19

    Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates that surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants' hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. This study

  16. Dynamics of proteins at low temperatures: fibrous vs. globular

    Foucat, L.; Renou, J.-P.; Tengroth, C.; Janssen, S.; Middendorf, H. D.

    We have measured quasielastic neutron scattering from H2O-hydrated collagen and haemoglobin at Tτ>10 ps. Relative to haemoglobin, the 200-K dynamic transition is shifted upward by 20-25 K in collagen, and the T-dependence of m.-sq. displacements derived from Sqe(Q;T) suggests that in triple-helical systems there are three rather than two regimes: one up to around 120K (probably purely harmonic), an intermediate quasiharmonic region with a linear dependence up to 240K, followed by a steeper nonlinear rise similar to that in globular proteins.

  17. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Klein, Heinrich C. R.; Schwarz, Ulrich S.

    2014-01-01

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

  18. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

    2014-05-14

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

  19. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  20. Reynolds stress structures in a self-similar adverse pressure gradient turbulent boundary layer at the verge of separation.

    Atkinson, C.; Sekimoto, A.; Jiménez, J.; Soria, J.

    2018-04-01

    Mean Reynolds stress profiles and instantaneous Reynolds stress structures are investigated in a self-similar adverse pressure gradient turbulent boundary layer (APG-TBL) at the verge of separation using data from direct numerical simulations. The use of a self-similar APG-TBL provides a flow domain in which the flow gradually approaches a constant non-dimensional pressure gradient, resulting in a flow in which the relative contribution of each term in the governing equations is independent of streamwise position over a domain larger than two boundary layer thickness. This allows the flow structures to undergo a development that is less dependent on the upstream flow history when compared to more rapidly decelerated boundary layers. This APG-TBL maintains an almost constant shape factor of H = 2.3 to 2.35 over a momentum thickness based Reynolds number range of Re δ 2 = 8420 to 12400. In the APG-TBL the production of turbulent kinetic energy is still mostly due to the correlation of streamwise and wall-normal fluctuations, 〈uv〉, however the contribution form the other components of the Reynolds stress tensor are no longer negligible. Statistical properties associated with the scale and location of sweeps and ejections in this APG-TBL are compared with those of a zero pressure gradient turbulent boundary layer developing from the same inlet profile, resulting in momentum thickness based range of Re δ 2 = 3400 to 3770. In the APG-TBL the peak in both the mean Reynolds stress and the production of turbulent kinetic energy move from the near wall region out to a point consistent with the displacement thickness height. This is associated with a narrower distribution of the Reynolds stress and a 1.6 times higher relative number of wall-detached negative uv structures. These structures occupy 5 times less of the boundary layer volume and show a similar reduction in their streamwise extent with respect to the boundary layer thickness. A significantly lower percentage

  1. Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex

    Lisa M. Tuttle

    2018-03-01

    Full Text Available Summary: Transcription activation domains (ADs are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. : Tuttle et al. report a “fuzzy free-for-all” interaction mechanism that explains how seemingly unrelated transcription activators converge on a limited number of coactivator targets. The mechanism provides a rationale for the observation that individually weak and low-specificity interactions can combine to produce biologically critical function without requiring highly ordered structure. Keywords: transcription activation, intrinsically disordered proteins, fuzzy binding

  2. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Aboul-Magd Mohammed O

    2009-07-01

    Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input

  3. A small world of weak ties provides optimal global integration of self-similar modules in functional brain networks.

    Gallos, Lazaros K; Makse, Hernán A; Sigman, Mariano

    2012-02-21

    The human brain is organized in functional modules. Such an organization presents a basic conundrum: Modules ought to be sufficiently independent to guarantee functional specialization and sufficiently connected to bind multiple processors for efficient information transfer. It is commonly accepted that small-world architecture of short paths and large local clustering may solve this problem. However, there is intrinsic tension between shortcuts generating small worlds and the persistence of modularity, a global property unrelated to local clustering. Here, we present a possible solution to this puzzle. We first show that a modified percolation theory can define a set of hierarchically organized modules made of strong links in functional brain networks. These modules are "large-world" self-similar structures and, therefore, are far from being small-world. However, incorporating weaker ties to the network converts it into a small world preserving an underlying backbone of well-defined modules. Remarkably, weak ties are precisely organized as predicted by theory maximizing information transfer with minimal wiring cost. This trade-off architecture is reminiscent of the "strength of weak ties" crucial concept of social networks. Such a design suggests a natural solution to the paradox of efficient information flow in the highly modular structure of the brain.

  4. From nucleotides to DNA analysis by a SERS substrate of a self similar chain of silver nanospheres

    Coluccio, M L

    2015-11-01

    In this work we realized a device of silver nanostructures designed so that they have a great ability to sustain the surface-enhanced Raman scattering effect. The nanostructures were silver self-similar chains of three nanospheres, having constant ratios between their diameters and between their reciprocal distances. They were realized by electron beam lithography, to write the pattern, and by silver electroless deposition technique, to fill it with the metal. The obtained device showed the capability to increase the Raman signal coming from the gap between the two smallest nanospheres (whose size is around 10 nm) and so it allows the detection of biomolecules fallen into this hot spot. In particular, oligonucleotides with 6 DNA bases, deposited on these devices with a drop coating method, gave a Raman spectrum characterized by a clear fingerprint coming from the hot spot and, with the help of a fitting method, also oligonucleotides of 9 bases, which are less than 3 nm long, were resolved. In conclusion the silver nanolens results in a SERS device able to measure all the molecules, or part of them, held into the hot spot of the nanolenses, and thus it could be a future instrument with which to analyze DNA portions.

  5. APPLICATION OF A SELF-SIMILAR PRESSURE PROFILE TO SUNYAEV-ZEL'DOVICH EFFECT DATA FROM GALAXY CLUSTERS

    Mroczkowski, Tony; Miller, Amber; Bonamente, Max; Carlstrom, John E.; Culverhouse, Thomas L.; Greer, Christopher; Hennessy, Ryan; Leitch, Erik M.; Loh, Michael; Marrone, Daniel P.; Pryke, Clem; Sharp, Matthew; Hawkins, David; Lamb, James W.; Woody, David; Joy, Marshall; Maughan, Ben; Muchovej, Stephen; Nagai, Daisuke

    2009-01-01

    We investigate the utility of a new, self-similar pressure profile for fitting Sunyaev-Zel'dovich (SZ) effect observations of galaxy clusters. Current SZ imaging instruments-such as the Sunyaev-Zel'dovich Array (SZA)-are capable of probing clusters over a large range in a physical scale. A model is therefore required that can accurately describe a cluster's pressure profile over a broad range of radii from the core of the cluster out to a significant fraction of the virial radius. In the analysis presented here, we fit a radial pressure profile derived from simulations and detailed X-ray analysis of relaxed clusters to SZA observations of three clusters with exceptionally high-quality X-ray data: A1835, A1914, and CL J1226.9+3332. From the joint analysis of the SZ and X-ray data, we derive physical properties such as gas mass, total mass, gas fraction and the intrinsic, integrated Compton y-parameter. We find that parameters derived from the joint fit to the SZ and X-ray data agree well with a detailed, independent X-ray-only analysis of the same clusters. In particular, we find that, when combined with X-ray imaging data, this new pressure profile yields an independent electron radial temperature profile that is in good agreement with spectroscopic X-ray measurements.

  6. Nonlinear theory for axisymmetric self-similar two-dimensional oscillations of electrons in cold plasma with constant proton background

    Osherovich, V. A.; Fainberg, J.

    2018-01-01

    We consider simultaneous oscillations of electrons moving both along the axis of symmetry and also in the direction perpendicular to the axis. We derive a system of three nonlinear ordinary differential equations which describe self-similar oscillations of cold electrons in a constant proton density background (np = n0 = constant). These three equations represent an exact class of solutions. For weak nonlinear conditions, the frequency spectra of electric field oscillations exhibit split frequency behavior at the Langmuir frequency ωp0 and its harmonics, as well as presence of difference frequencies at low spectral values. For strong nonlinear conditions, the spectra contain peaks at frequencies with values ωp0(n +m √{2 }) , where n and m are integer numbers (positive and negative). We predict that both spectral types (weak and strong) should be observed in plasmas where axial symmetry may exist. To illustrate possible applications of our theory, we present a spectrum of electric field oscillations observed in situ in the solar wind by the WAVES experiment on the Wind spacecraft during the passage of a type III solar radio burst.

  7. Effects of initial conditions on self-similarity in a co-flowing axi-symmetric round jet

    Uddin, M.; Pollard, A.

    2004-01-01

    The effect of initial conditions of a spatially developing coflowing jet is investigated using an LES at Re D = 7,300. A co-flow velocity to initial jet centerline velocity ratio of 1:11 and a co-flow to initial jet diameter ratio of 35:1 are used to match the flow cases of Reference 11. The 35D x 135D simulation volume is divided into 1024 x 256 x 128 control volumes in the longitudinal, radial and azimuthal directions respectively. Time averaged results of the effect of initial conditions on mean flow, the decay of jet centreline velocity, growth of the jet and the distribution of Reynolds stresses in the near, and far field of the shear layer is presented. These quantities show good agreement with the measurements of Reference 11. Our results suggest that the first order moments, e.g., decay of centreline velocity excess, the radial mean velocity profiles, have little dependence on the initial conditions. As well, the Reynolds shear stress appears to have lesser sensitivity to the variation of initial velocity profiles. However, initial conditions have pronounced effect on the self-similarity of normal stresses. Additionally, the computations indicate little Reynolds number dependency, which is consistent with Townsend's school of thought. (author)

  8. Characterizing multi-scale self-similar behavior and non-statistical properties of fluctuations in financial time series

    Ghosh, Sayantan; Manimaran, P.; Panigrahi, Prasanta K.

    2011-11-01

    We make use of wavelet transform to study the multi-scale, self-similar behavior and deviations thereof, in the stock prices of large companies, belonging to different economic sectors. The stock market returns exhibit multi-fractal characteristics, with some of the companies showing deviations at small and large scales. The fact that, the wavelets belonging to the Daubechies’ (Db) basis enables one to isolate local polynomial trends of different degrees, plays the key role in isolating fluctuations at different scales. One of the primary motivations of this work is to study the emergence of the k-3 behavior [X. Gabaix, P. Gopikrishnan, V. Plerou, H. Stanley, A theory of power law distributions in financial market fluctuations, Nature 423 (2003) 267-270] of the fluctuations starting with high frequency fluctuations. We make use of Db4 and Db6 basis sets to respectively isolate local linear and quadratic trends at different scales in order to study the statistical characteristics of these financial time series. The fluctuations reveal fat tail non-Gaussian behavior, unstable periodic modulations, at finer scales, from which the characteristic k-3 power law behavior emerges at sufficiently large scales. We further identify stable periodic behavior through the continuous Morlet wavelet.

  9. Stretchable human-machine interface based on skin-conformal sEMG electrodes with self-similar geometry

    Dong, Wentao; Zhu, Chen; Hu, Wei; Xiao, Lin; Huang, Yong'an

    2018-01-01

    Current stretchable surface electrodes have attracted increasing attention owing to their potential applications in biological signal monitoring, wearable human-machine interfaces (HMIs) and the Internet of Things. The paper proposed a stretchable HMI based on a surface electromyography (sEMG) electrode with a self-similar serpentine configuration. The sEMG electrode was transfer-printed onto the skin surface conformally to monitor biological signals, followed by signal classification and controlling of a mobile robot. Such electrodes can bear rather large deformation (such as >30%) under an appropriate areal coverage. The sEMG electrodes have been used to record electrophysiological signals from different parts of the body with sharp curvature, such as the index finger, back of the neck and face, and they exhibit great potential for HMI in the fields of robotics and healthcare. The electrodes placed onto the two wrists would generate two different signals with the fist clenched and loosened. It is classified to four kinds of signals with a combination of the gestures from the two wrists, that is, four control modes. Experiments demonstrated that the electrodes were successfully used as an HMI to control the motion of a mobile robot remotely. Project supported by the National Natural Science Foundation of China (Nos. 51635007, 91323303).

  10. Prediction of methyl-side Chain Dynamics in Proteins

    Ming Dengming; Brueschweiler, Rafael

    2004-01-01

    A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism

  11. Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity

    Digman, Michelle

    Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.

  12. Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.

    Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda; Luo, Jie; Ranish, Jeff; Hahn, Steven; Klevit, Rachel E

    2018-03-20

    Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Dynamics of proteins and of their hydration layer studied by neutron scattering and additional biophysical methods

    Gallat, Francois-Xavier

    2011-01-01

    This thesis work focused on the dynamics of proteins, surrounded by their hydration layer, a water shell around the protein vital for its biological function. Each of these components is accompanied by a specific dynamics which union reforms the complex energy landscape of the system. The joint implementation of selective deuteration, incoherent neutron scattering and tera-hertz spectroscopy allowed to explore the dynamics of proteins and that of the hydration shell. The influence of the folding state of protein on its dynamics has been studied by elastic neutron scattering. Globular proteins were less dynamic than its intrinsically disordered analogues. Themselves appear to be stiffer than non-physiological unfolded proteins. The oligomerization state and the consequences on the dynamics were investigated. Aggregates of a globular protein proved to be more flexible than the soluble form. In contrast, aggregates of a disordered protein showed lower average dynamics compared to the soluble form. These observations demonstrate the wide range of dynamics among the proteome. Incoherent neutron scattering experiences on the hydration layer of globular and disordered proteins have yielded information on the nature of water motion around these proteins. The measurements revealed the presence of translational motions concomitant with the onset of the transition dynamics of hydration layers, at 220 K. Measurements have also shown a stronger coupling between a disordered protein and its hydration water, compared to a globular protein and its hydration shell. The nature of the hydration layer and its influence on its dynamics has been explored with the use of polymers that mimic the water behavior and that act as a source of flexibility for the protein. Eventually, the dynamics of methyl groups involved in the dynamical changes observed at 150 and 220 K, was investigated. (author) [fr

  14. Protein-membrane interaction: effect of myelin basic protein on the dynamics of oriented lipids

    Natali, F.; Relini, A.; Gliozzi, A.; Rolandi, R.; Cavatorta, P.; Deriu, A.; Fasano, A.; Riccio, P

    2003-08-01

    We have studied the effect of physiological amounts of myelin basic protein (MBP) on pure dimyristoyl L-{alpha}-phosphatidic acid (DMPA) oriented membranes. The investigation has been carried out using several complementary experimental methods to provide a detailed characterization of the proteo-lipid complexes. In particular, taking advantage of the power of the quasi-elastic neutron scattering (QENS) technique as optimal probe in biology, a significant effect is suggested to be induced by MBP on the anisotropy of lipid dynamics across the liquid-gel phase transition. Thus, the enhancement of the spatially restricted, vertical translation motion of DMPA is suggested to be the main responsible for the increased contribution of the out of plane lipid dynamics observed at 340 K.

  15. Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin☆

    Roche, Camille J.; Dantsker, David; Heller, Elizabeth R.; Sabat, Joseph E.; Friedman, Joel M.

    2013-01-01

    Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to mani...

  16. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5

    Inger Lindin

    2014-03-01

    Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.

  17. Dissecting the dynamic conformations of the metamorphic protein lymphotactin.

    Harvey, Sophie R; Porrini, Massimiliano; Konijnenberg, Albert; Clarke, David J; Tyler, Robert C; Langridge-Smith, Patrick R R; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E

    2014-10-30

    A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.

  18. THE SELF-SIMILARITY OF THE CIRCUMGALACTIC MEDIUM WITH GALAXY VIRIAL MASS: IMPLICATIONS FOR COLD-MODE ACCRETION

    Churchill, Christopher W.; Nielsen, Nikole M.; Trujillo-Gomez, Sebastian [Department of Astronomy, New Mexico State University, Las Cruces, NM 88003 (United States); Kacprzak, Glenn G. [Center for Astrophysics and Supercomputing, Swinburne University of Technology, Victoria 3122 (Australia)

    2013-02-01

    We apply halo abundance matching to obtain galaxy virial masses, M{sub h}, and radii, R{sub vir}, for 183 'isolated' galaxies from the 'Mg II Absorber-Galaxy Catalog'. All galaxies have spectroscopic redshifts (0.07 {<=} z {<=} 1.12) and their circumgalactic medium (CGM) is probed in Mg II absorption within projected galactocentric distances D {<=} 200 kpc. We examine the behavior of equivalent width, W{sub r} (2796), and covering fraction, f{sub c} , as a function of D, D/R{sub vir}, and M{sub h}. Bifurcating the sample at the median mass log M{sub h}/M{sub Sun} = 12, we find (1) systematic segregation of M{sub h} on the W{sub r} (2796)-D plane (4.0{sigma}); high-mass halos are found at higher D with larger W{sub r} (2796) compared to low-mass halos. On the W{sub r} (2796)-D/R{sub vir} plane, mass segregation vanishes and we find W{sub r} (2796){proportional_to}(D/R{sub vir}){sup -2} (8.9{sigma}). (2) High-mass halos have larger f{sub c} at a given D, whereas f{sub c} is independent of M{sub h} at all D/R{sub vir}. (3) f{sub c} is constant with M{sub h} over the range 10.7 {<=} log M{sub h}/M{sub Sun} {<=} 13.9 within a given D or D/R{sub vir}. The combined results suggest the Mg II absorbing CGM is self-similar with halo mass, even above log M{sub h}/M{sub Sun} {approx_equal} 12, where cold mode accretion is predicted to be quenched. If theory is correct, either outflows or sub-halos must contribute to absorption in high-mass halos such that low- and high-mass halos are observationally indistinguishable using Mg II absorption strength once impact parameter is scaled by halo mass. Alternatively, the data may indicate predictions of a universal shut down of cold-mode accretion in high-mass halos may require revision.

  19. Self-similar bumps and wiggles: Isolating the evolution of the BAO peak with power-law initial conditions

    Orban, Chris; Weinberg, David H.

    2011-01-01

    Motivated by cosmological surveys that demand accurate theoretical modeling of the baryon acoustic oscillation (BAO) feature in galaxy clustering, we analyze N-body simulations in which a BAO-like Gaussian bump modulates the linear theory correlation function ξ L (r)=(r 0 /r) n+3 of an underlying self-similar model with initial power spectrum P(k)=Ak n . These simulations test physical and analytic descriptions of BAO evolution far beyond the range of most studies, since we consider a range of underlying power spectra (n=-0.5, -1, -1.5) and evolve simulations to large effective correlation amplitudes (equivalent to σ 8 =4-12 for r bao =100h -1 Mpc). In all cases, nonlinear evolution flattens and broadens the BAO bump in ξ(r) while approximately preserving its area. This evolution resembles a diffusion process in which the bump width σ bao is the quadrature sum of the linear theory width and a length proportional to the rms relative displacement Σ pair (r bao ) of particle pairs separated by r bao . For n=-0.5 and n=-1, we find no detectable shift of the location of the BAO peak, but the peak in the n=-1.5 model shifts steadily to smaller scales, following r peak /r bao =1-1.08(r 0 /r bao ) 1.5 . The perturbation theory scheme of McDonald (2007) [P. McDonald, Phys. Rev. D 75, 043514 (2007).] and, to a lesser extent, standard 1-loop perturbation theory are fairly successful at explaining the nonlinear evolution of the Fourier power spectrum of our models. Analytic models also explain why the ξ(r) peak shifts much more for n=-1.5 than for n≥-1, though no ab initio model we have examined reproduces all of our numerical results. Simulations with L box =10r bao and L box =20r bao yield consistent results for ξ(r) at the BAO scale, provided one corrects for the integral constraint imposed by the uniform density box.

  20. New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

    Yesylevskyy S. O.

    2010-04-01

    Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

  1. Discriminating males and unpredictable females: males differentiate self-similar facial cues more than females in the judgment of opposite-sex attractiveness.

    Jin-Ying Zhuang

    Full Text Available Attractiveness judgment in the context of mate preferences is thought to reflect an assessment of mate quality in relation to an absolute scale of genetic fitness and a relative scale of self-similarity. In this study, subjects judged the attractiveness and trustworthiness of faces in composite images that were manipulated to produce self-similar (self-resemblance and dissimilar (other-resemblance images. Males differentiated between self- and other-resemblance as well as among different degrees of self-resemblance in their attractiveness ratings; females did not. Specifically, in Experiment 1, using a morphing technique, we created previously unseen face images possessing different degrees (0%, 30%, 40%, or 50% of incorporation of the subject's images (different degrees of self-resemblance and found that males preferred images that were closer to average (0% rather than more self-similar, whereas females showed no preference for any degree of self-similarity. In Experiment 2, we added a pro-social question about trustworthiness. We replicated the Experiment 1 attractiveness rating results and further found that males differentiated between self- and other-resemblance for the same degree of composites; women did not. Both males and females showed a similar preference for self-resemblances when judging trustworthiness. In conclusion, only males factored self-resemblance into their attractiveness ratings of opposite-sex individuals in a manner consistent with cues of reproductive fitness, although both sexes favored self-resemblance when judging trustworthiness.

  2. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

    Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

    2014-12-11

    The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

  3. Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin

    Roche, Camille J.; Dantsker, David; Heller, Elizabeth R.; Sabat, Joseph E.; Friedman, Joel M.

    2013-08-01

    Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.

  4. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Asafi, M S; Tekpinar, M; Yildirim, A

    2016-01-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)

  5. Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.

    Yosef Y Kuttner

    2013-04-01

    Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

  6. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    . Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

  7. Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation

    Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.

    2012-08-01

    The conformational diversity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.

  8. Identification of hierarchy of dynamic domains in proteins: comparison of HDWA and HCCP techniques

    Yesylevskyy S. O.

    2010-07-01

    Full Text Available Aim. There are several techniques for the identification of hierarchy of dynamic domains in proteins. The goal of this work is to compare systematically two recently developed techniques, HCCP and HDWA,on a set of proteins from diverse structural classes. Methods. HDWA and HCCP techniques are used. The HDWA technique is designed to identify hierarchically organized dynamic domains in proteins using the Molecular Dynamics (MD trajectories, while HCCP utilizes the normal modes of simplified elastic network models. Results. It is shown that the dynamic domains found by HDWA are consistent with the domains identified by HCCP and other techniques. At the same time HDWA identifies flexible mobile loops of proteins correctly, which is hard to achieve with other model-based domain identification techniques. Conclusion. HDWA is shown to be a powerful method of analysis of MD trajectories, which can be used in various areas of protein science.

  9. Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.

    Xianjun Shen

    Full Text Available How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment. It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.

  10. Self-similar rupture implied by scaling properties of volcanic earthquakes occurring during the 2004-2008 eruption of Mount St. Helens, Washington

    Harrington, Rebecca M.; Kwiatek, Grzegorz; Moran, Seth C.

    2015-01-01

    We analyze a group of 6073 low-frequency earthquakes recorded during a week-long temporary deployment of broadband seismometers at distances of less than 3 km from the crater at Mount St. Helens in September of 2006. We estimate the seismic moment (M0) and spectral corner frequency (f0) using a spectral ratio approach for events with a high signal-to-noise (SNR) ratio that have a cross-correlation coefficient of 0.8 or greater with at least five other events. A cluster analysis of cross-correlation values indicates that the group of 421 events meeting the SNR and cross-correlation criteria forms eight event families that exhibit largely self-similar scaling. We estimate the M0 and f0 values of the 421 events and calculate their static stress drop and scaled energy (ER/M0) values. The estimated values suggest self-similar scaling within families, as well as between five of eight families (i.e.,  and  constant). We speculate that differences in scaled energy values for the two families with variable scaling may result from a lack of resolution in the velocity model. The observation of self-similar scaling is the first of its kind for such a large group of low-frequency volcanic tectonic events occurring during a single active dome extrusion eruption.

  11. Estimating serial correlation and self-similarity in financial time series-A diversification approach with applications to high frequency data

    Gerlich, Nikolas; Rostek, Stefan

    2015-09-01

    We derive a heuristic method to estimate the degree of self-similarity and serial correlation in financial time series. Especially, we propagate the use of a tailor-made selection of different estimation techniques that are used in various fields of time series analysis but until now have not consequently found their way into the finance literature. Following the idea of portfolio diversification, we show that considerable improvements with respect to robustness and unbiasedness can be achieved by using a basket of estimation methods. With this methodological toolbox at hand, we investigate real market data to show that noticeable deviations from the assumptions of constant self-similarity and absence of serial correlation occur during certain periods. On the one hand, this may shed a new light on seemingly ambiguous scientific findings concerning serial correlation of financial time series. On the other hand, a proven time-changing degree of self-similarity may help to explain high-volatility clusters of stock price indices.

  12. A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.

    Brittany Burton

    Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.

  13. Study of the interaction of potassium ion channel protein with micelle by molecular dynamics simulation

    Shantappa, Anil; Talukdar, Keka

    2018-04-01

    Ion channels are proteins forming pore inside the body of all living organisms. This potassium ion channel known as KcsA channel and it is found in the each cell and nervous system. Flow of various ions is regulated by the function of the ion channels. The nerve ion channel protein with protein data bank entry 1BL8, which is basically an ion channel protein in Streptomyces Lividans and which is taken up to form micelle-protein system and the system is analyzed by using molecular dynamics simulation. Firstly, ion channel pore is engineered by CHARMM potential and then Micelle-protein system is subjected to molecular dynamics simulation. For some specific micelle concentration, the protein unfolding is observed.

  14. Architecture and dynamics of proteins and aqueous solvation complexes

    Lotze, S.M.

    2015-01-01

    For this thesis, the molecular dynamics of water and biological (model) systems have been studied with advanced nonlinear optical techniques. In chapters 4-5, the technique of femtosecond mid-infrared pump probe spectroscopy has been used to study the energy transfer and the reorientational dynamics

  15. Initial photoinduced dynamics of the photoactive yellow protein

    Larsen, D.S.; van Grondelle, R.

    2005-01-01

    The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises

  16. Box-counting dimension revisited: presenting an efficient method of minimising quantisation error and an assessment of the self-similarity of structural root systems

    Martin eBouda

    2016-02-01

    Full Text Available Fractal dimension (FD, estimated by box-counting, is a metric used to characterise plant anatomical complexity or space-filling characteristic for a variety of purposes. The vast majority of published studies fail to evaluate the assumption of statistical self-similarity, which underpins the validity of the procedure. The box-counting procedure is also subject to error arising from arbitrary grid placement, known as quantisation error (QE, which is strictly positive and varies as a function of scale, making it problematic for the procedure's slope estimation step. Previous studies either ignore QE or employ inefficient brute-force grid translations to reduce it. The goals of this study were to characterise the effect of QE due to translation and rotation on FD estimates, to provide an efficient method of reducing QE, and to evaluate the assumption of statistical self-similarity of coarse root datasets typical of those used in recent trait studies. Coarse root systems of 36 shrubs were digitised in 3D and subjected to box-counts. A pattern search algorithm was used to minimise QE by optimising grid placement and its efficiency was compared to the brute force method. The degree of statistical self-similarity was evaluated using linear regression residuals and local slope estimates.QE due to both grid position and orientation was a significant source of error in FD estimates, but pattern search provided an efficient means of minimising it. Pattern search had higher initial computational cost but converged on lower error values more efficiently than the commonly employed brute force method. Our representations of coarse root system digitisations did not exhibit details over a sufficient range of scales to be considered statistically self-similar and informatively approximated as fractals, suggesting a lack of sufficient ramification of the coarse root systems for reiteration to be thought of as a dominant force in their development. FD estimates did

  17. Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

    Cheng, Chi-Yuan; Han, Songi

    2013-01-01

    Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

  18. Dynamics of domain coverage of the protein sequence universe

    2012-01-01

    Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its “dark matter”. Results Here we suggest that true size of “dark matter” is much larger than stated by current definitions. We propose an approach to reducing the size of “dark matter” by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of “dark matter”; however, its absolute size increases substantially with the growth of sequence data. PMID:23157439

  19. Dynamics of domain coverage of the protein sequence universe

    Rekapalli Bhanu

    2012-11-01

    Full Text Available Abstract Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its “dark matter”. Results Here we suggest that true size of “dark matter” is much larger than stated by current definitions. We propose an approach to reducing the size of “dark matter” by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of “dark matter”; however, its absolute size increases substantially with the growth of sequence data.

  20. Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain

    Coluccio, M. L.

    2015-09-04

    Control of the architecture and electromagnetic behavior of nanostructures offers the possibility of designing and fabricating sensors that, owing to their intrinsic behavior, provide solutions to new problems in various fields. We show detection of peptides in multicomponent mixtures derived from human samples for early diagnosis of breast cancer. The architecture of sensors is based on a matrix array where pixels constitute a plasmonic device showing a strong electric field enhancement localized in an area of a few square nanometers. The method allows detection of single point mutations in peptides composing the BRCA1 protein. The sensitivity demonstrated falls in the picomolar (10−12 M) range. The success of this approach is a result of accurate design and fabrication control. The residual roughness introduced by fabrication was taken into account in optical modeling and was a further contributing factor in plasmon localization, increasing the sensitivity and selectivity of the sensors. This methodology developed for breast cancer detection can be considered a general strategy that is applicable to various pathologies and other chemical analytical cases where complex mixtures have to be resolved in their constitutive components.

  1. Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain

    Coluccio, M. L.; Gentile, F.; Das, Gobind; Nicastri, A.; Perri, A. M.; Candeloro, P.; Perozziello, G.; Proietti Zaccaria, R.; Gongora, J. S. Totero; Alrasheed, Salma; Fratalocchi, Andrea; Limongi, Tania; Cuda, G.; Di Fabrizio, Enzo M.

    2015-01-01

    Control of the architecture and electromagnetic behavior of nanostructures offers the possibility of designing and fabricating sensors that, owing to their intrinsic behavior, provide solutions to new problems in various fields. We show detection of peptides in multicomponent mixtures derived from human samples for early diagnosis of breast cancer. The architecture of sensors is based on a matrix array where pixels constitute a plasmonic device showing a strong electric field enhancement localized in an area of a few square nanometers. The method allows detection of single point mutations in peptides composing the BRCA1 protein. The sensitivity demonstrated falls in the picomolar (10−12 M) range. The success of this approach is a result of accurate design and fabrication control. The residual roughness introduced by fabrication was taken into account in optical modeling and was a further contributing factor in plasmon localization, increasing the sensitivity and selectivity of the sensors. This methodology developed for breast cancer detection can be considered a general strategy that is applicable to various pathologies and other chemical analytical cases where complex mixtures have to be resolved in their constitutive components.

  2. Protein Availability and Satellite Cell Dynamics in Skeletal Muscle.

    Shamim, Baubak; Hawley, John A; Camera, Donny M

    2018-06-01

    Human skeletal muscle satellite cells are activated in response to both resistance and endurance exercise. It was initially proposed that satellite cell proliferation and differentiation were only required to support resistance exercise-induced hypertrophy. However, satellite cells may also play a role in muscle fibre remodelling after endurance-based exercise and extracellular matrix regulation. Given the importance of dietary protein, particularly branched chain amino acids, in supporting myofibrillar and mitochondrial adaptations to both resistance and endurance-based training, a greater understanding of how protein intake impacts satellite cell activity would provide further insight into the mechanisms governing skeletal muscle remodelling with exercise. While many studies have investigated the capacity for protein ingestion to increase post-exercise rates of muscle protein synthesis, few investigations have examined the role for protein ingestion to modulate satellite cell activity. Here we review the molecular mechanisms controlling the activation of satellite cells in response to mechanical stress and protein intake in both in vitro and in vivo models. We provide a mechanistic framework that describes how protein ingestion may enhance satellite activity and promote exercise adaptations in human skeletal muscle.

  3. Protein complexes and cholesterol in the control of late endosomal dynamicsCholesterol and multi-protein complexes in the control of late endosomal dynamics

    Kant, Rik Henricus Nicolaas van der

    2013-01-01

    Late endosomal transport is disrupted in several diseases such as Niemann-Pick type C, ARC syndrome and Alzheimer’s disease. This thesis describes the regulation of late endosomal dynamics by cholesterol and multi-protein complexes. We find that cholesterol acts as a cellular tomtom that steers the

  4. The consistency of large concerted motions in proteins in molecular dynamics simulations

    de Groot, B.L.; van Aalten, D.M.F.; Amadei, A; Berendsen, H.J.C.

    1996-01-01

    A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the

  5. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  6. Dynamic and bio-orthogonal protein assembly along a supramolecular polymer

    Petkau - Milroy, K.; Uhlenheuer, D.A.; Spiering, A.J.H.; Vekemans, J.A.J.M.; Brunsveld, L.

    2013-01-01

    Dynamic protein assembly along supramolecular columnar polymers has been achieved through the site-specific covalent attachment of different SNAP-tag fusion proteins to self-assembled benzylguanine-decorated discotics. The self-assembly of monovalent discotics into supramolecular polymers creates a

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

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

    2012-10-01

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

  8. msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks

    Yuan Zhang

    2014-01-01

    Full Text Available Dynamics of protein-protein interactions (PPIs reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process.

  9. Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. Ligand-induced changes in the protein motions

    Peters, Günther H. J.; Frimurer, T.M.; Andersen, J.N.

    1999-01-01

    Activity of enzymes, such as protein tyrosine phosphatases (PTPs), is often associated with structural changes in the enzyme, resulting in selective and stereospecific reactions with the substrate. To investigate the effect of a substrate on the motions occurring in PTPs, we have performed...... molecular dynamics simulations of PTP1B and PTP1B complexed with a high-affinity peptide DADEpYL, where pY stands for phosphorylated tyrosine. The peptide sequence is derived from the epidermal growth factor receptor (EGFR(988-993)). Simulations were performed in water for 1 ns, and the concerted motions...... in the protein were analyzed using the essential dynamics technique. Our results indicate that the predominately internal motions in PTP1B occur in a subspace of only a few degrees of freedom. Upon substrate binding, the flexibility of the protein is reduced by similar to 10%. The largest effect is found...

  10. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

    Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

    2005-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

  11. Non-interacting surface solvation and dynamics in protein-protein interactions

    Visscher, Koen M.; Kastritis, Panagiotis L.|info:eu-repo/dai/nl/315886668; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238

    2015-01-01

    Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo

  12. An experimental and computational framework to build a dynamic protein atlas of human cell division

    Kavur, Marina; Kavur, Marina; Kavur, Marina; Ellenberg, Jan; Peters, Jan-Michael; Ladurner, Rene; Martinic, Marina; Kueblbeck, Moritz; Nijmeijer, Bianca; Wachsmuth, Malte; Koch, Birgit; Walther, Nike; Politi, Antonio; Heriche, Jean-Karim; Hossain, M.

    2017-01-01

    Essential biological functions of human cells, such as division, require the tight coordination of the activity of hundreds of proteins in space and time. While live cell imaging is a powerful tool to study the distribution and dynamics of individual proteins after fluorescence tagging, it has not yet been used to map protein networks due to the lack of systematic and quantitative experimental and computational approaches. Using the cell and nuclear boundaries as landmarks, we generated a 4D ...

  13. Dynamic, electronically switchable surfaces for membrane protein microarrays.

    Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

    2006-02-01

    Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

  14. Dynamic protein S-palmitoylation mediates parasite life cycle progression and diverse mechanisms of virulence.

    Brown, Robert W B; Sharma, Aabha I; Engman, David M

    2017-04-01

    Eukaryotic parasites possess complex life cycles and utilize an assortment of molecular mechanisms to overcome physical barriers, suppress and/or bypass the host immune response, including invading host cells where they can replicate in a protected intracellular niche. Protein S-palmitoylation is a dynamic post-translational modification in which the fatty acid palmitate is covalently linked to cysteine residues on proteins by the enzyme palmitoyl acyltransferase (PAT) and can be removed by lysosomal palmitoyl-protein thioesterase (PPT) or cytosolic acyl-protein thioesterase (APT). In addition to anchoring proteins to intracellular membranes, functions of dynamic palmitoylation include - targeting proteins to specific intracellular compartments via trafficking pathways, regulating the cycling of proteins between membranes, modulating protein function and regulating protein stability. Recent studies in the eukaryotic parasites - Plasmodium falciparum, Toxoplasma gondii, Trypanosoma brucei, Cryptococcus neoformans and Giardia lamblia - have identified large families of PATs and palmitoylated proteins. Many palmitoylated proteins are important for diverse aspects of pathogenesis, including differentiation into infective life cycle stages, biogenesis and tethering of secretory organelles, assembling the machinery powering motility and targeting virulence factors to the plasma membrane. This review aims to summarize our current knowledge of palmitoylation in eukaryotic parasites, highlighting five exemplary mechanisms of parasite virulence dependent on palmitoylation.

  15. Structure and Dynamic Properties of Membrane Proteins using NMR

    Rösner, Heike; Kragelund, Birthe

    2012-01-01

    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  16. Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics

    Hirokawa, N.; Takemura, R.

    Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.

  17. Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

    Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

  18. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    Martinez, N.

    2016-09-06

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  19. High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

    Martinez, N.; Michoud, Gregoire; Cario, A.; Ollivier, J.; Franzetti, B.; Jebbar, M.; Oger, P.; Peters, J.

    2016-01-01

    Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.

  20. Molecular modeling of the conformational dynamics of the cellular prion protein

    Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

    2014-03-01

    Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

  1. Morphing methods to visualize coarse-grained protein dynamics.

    Weiss, Dahlia R; Koehl, Patrice

    2014-01-01

    Morphing was initially developed as a cinematic effect, where one image is seamlessly transformed into another image. The technique was widely adopted by biologists to visualize the transition between protein conformational states, generating an interpolated pathway from an initial to a final protein structure. Geometric morphing seeks to create visually suggestive movies that illustrate structural changes between conformations but do not necessarily represent a biologically relevant pathway, while minimum energy path (MEP) interpolations aim at describing the true transition state between the crystal structure minima in the energy landscape.

  2. A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.

    Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar

    2017-05-17

    Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.

  3. Is dynamic heterogeneity of water in presence of a protein ...

    Abstract. Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been inves- tigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutions.

  4. Static and dynamic properties of proteins adsorbed at liquid interfaces

    Benjamins, J.

    2000-01-01

    The aim of the investigation described in this thesis was to increase the level of understanding of the role that proteins play in the preparation and subsequent stabilisation of foams and emulsions. One aspect of this role is facilitation of break-up, due to surface tension lowering. A

  5. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  6. Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

    Anfinrud, Philip

    2006-03-01

    Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

  7. Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

    Shubhada R Hegde

    2008-11-01

    Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.

  8. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)

    2015-08-18

    Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  9. Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

    Guimarães Katia S

    2006-04-01

    Full Text Available Abstract Background Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. Results We propose a new method for identifying and representing overlapping protein complexes (or larger units called functional groups within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. We illustrate the effectiveness of our method by applying it to TNFα/NF-κB and pheromone signaling pathways. Conclusion The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks.

  10. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

    Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

    2016-08-23

    Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. A self-similar solution of a curved shock wave and its time-dependent force variation for a starting flat plate airfoil in supersonic flow

    Zijun CHEN

    2018-02-01

    Full Text Available The problem of aeroelasticity and maneuvering of command surface and gust wing interaction involves a starting flow period which can be seen as the flow of an airfoil attaining suddenly an angle of attack. In the linear or nonlinear case, compressive Mach or shock waves are generated on the windward side and expansive Mach or rarefaction waves are generated on the leeward side. On each side, these waves are composed of an oblique steady state wave, a vertically-moving one-dimensional unsteady wave, and a secondary wave resulting from the interaction between the steady and unsteady ones. An analytical solution in the secondary wave has been obtained by Heaslet and Lomax in the linear case, and this linear solution has been borrowed to give an approximate solution by Bai and Wu for the nonlinear case. The structure of the secondary shock wave and the appearance of various force stages are two issues not yet considered in previous studies and has been studied in the present paper. A self-similar solution is obtained for the secondary shock wave, and the reason to have an initial force plateau as observed numerically is identified. Moreover, six theoretical characteristic time scales for pressure load variation are determined which explain the slope changes of the time-dependent force curve. Keywords: Force, Self-similar solution, Shock-shock interaction, Shock waves, Unsteady flow

  12. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding

    2008-07-11

    Nucleotide Base pairs Hydrogen bonds FIG. 1: Ladder structure of DNA showing the Watson - Crick bonding of the bases A, T, G, and C which are suspended by a...protected against unwanted action of chemicals and proteins. The three-dimensional structure of DNA is the famed Watson - Crick double-helix, the equilibrium...quantitative analysis [88]. [1] A. Kornberg and T. A. Baker, DNA Replication (W. H. Freeman, New York, 1992). [2] J. D. Watson and F. H. C. Crick

  13. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  14. Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

    Oyang Yen-Jen

    2010-10-01

    Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.

  15. Dynamical analysis of yeast protein interaction network during the sake brewing process.

    Mirzarezaee, Mitra; Sadeghi, Mehdi; Araabi, Babak N

    2011-12-01

    Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

  16. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

    Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

    2015-12-01

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  17. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  18. Conformational dynamics of a protein in the folded and the unfolded state

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  19. Dynamically polarized samples for neutron protein crystallography at the Spallation Neutron Source

    Zhao, Jinkui; Pierce, Josh; Robertson, J. L.; Herwig, Kenneth W.; Myles, Dean; Cuneo, Matt; Li, Le; Meilleur, Flora; Standaert, Bob

    2016-01-01

    To prepare for the next generation neutron scattering instruments for the planned second target station at the Spallation Neutron Source (SNS) and to broaden the scientific impact of neutron protein crystallography at the Oak Ridge National Laboratory, we have recently ramped up our efforts to develop a dynamically polarized target for neutron protein crystallography at the SNS. Proteins contain a large amount of hydrogen which contributes to incoherent diffraction background and limits the sensitivity of neutron protein crystallography. This incoherent background can be suppressed by using polarized neutron diffraction, which in the same time also improves the coherent diffraction signal. Our plan is to develop a custom Dynamic Nuclear Polarization (DNP) setup tailored to neutron protein diffraction instruments. Protein crystals will be polarized at a magnetic field of 5 T and temperatures of below 1 K. After the dynamic polarization process, the sample will be brought to a frozen-spin mode in a 0.5 T holding field and at temperatures below 100 mK. In a parallel effort, we are also investigating various ways of incorporating polarization agents needed for DNP, such as site specific spin labels, into protein crystals. (paper)

  20. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-08

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.

  1. MOLECULAR DOCKING AND DYNAMICS STUDIES ON THE PROTEIN-PROTEIN INTERACTIONS OF ELECTRICALLY ACTIVE PILIN NANOWIRES OF GEOBACTER SULFURREDUCENS.

    D. Jeya Sundara Sharmila1 *

    2017-06-01

    Full Text Available Molecular interactions are key aspects in biological recognitions applicable in nano/micro systems. Bacterial nanowires are pilus filament based structures that can conduct electrons. The transport of electron is proposed to be facilitated by filamentous fibers made up of polymeric assemblies of proteins called pilin. Geobacter sulfurreducens is capable of delivering electrons through extracellular electron transport (EET by employing conductive nanowires, which are pilin proteins composed of type IV subunit PilA. Protein-protein interactions play an important role in the stabilization of the pilin nanowire assembly complex and it contains transmembrane (TM domain. In current study, protein-protein docking and multiple molecular dynamic (MD simulations were performed to understand the binding mode of pilin nanowires. The MD result explains the conformational behavior and folding of pilin nanowires in water environment in different time scale duration 20, 5, 5, 10 and 20ns (total of 60ns. Direct hydrogen bonds and water mediated hydrogen bonds that play a crucial role during the simulation were investigated. The conformational state, folding, end-toend distance profile and hydrogen bonding behavior had indicated that the Geobacter sulfurreducens pilin nanowires have electrical conductivity properties.

  2. QM/MM Molecular Dynamics Studies of Metal Binding Proteins

    Pietro Vidossich

    2014-07-01

    Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

  3. Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations.

    Kundu, Mainak; He, Ting-Fang; Lu, Yangyi; Wang, Lijuan; Zhong, Dongping

    2018-05-03

    Short-range electron transfer (ET) in proteins is an ultrafast process on the similar timescales as local protein-solvent fluctuations thus the two dynamics are coupled. Here, we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with eleven mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical timescales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.

  4. Anisotropic biodegradable lipid coated particles for spatially dynamic protein presentation.

    Meyer, Randall A; Mathew, Mohit P; Ben-Akiva, Elana; Sunshine, Joel C; Shmueli, Ron B; Ren, Qiuyin; Yarema, Kevin J; Green, Jordan J

    2018-05-01

    There has been growing interest in the use of particles coated with lipids for applications ranging from drug delivery, gene delivery, and diagnostic imaging to immunoengineering. To date, almost all particles with lipid coatings have been spherical despite emerging evidence that non-spherical shapes can provide important advantages including reduced non-specific elimination and increased target-specific binding. We combine control of core particle geometry with control of particle surface functionality by developing anisotropic, biodegradable ellipsoidal particles with lipid coatings. We demonstrate that these lipid coated ellipsoidal particles maintain advantageous properties of lipid polymer hybrid particles, such as the ability for modular protein conjugation to the particle surface using versatile bioorthogonal ligation reactions. In addition, they exhibit biomimetic membrane fluidity and demonstrate lateral diffusive properties characteristic of natural membrane proteins. These ellipsoidal particles simultaneously provide benefits of non-spherical particles in terms of stability and resistance to non-specific phagocytosis by macrophages as well as enhanced targeted binding. These biomaterials provide a novel and flexible platform for numerous biomedical applications. The research reported here documents the ability of non-spherical polymeric particles to be coated with lipids to form anisotropic biomimetic particles. In addition, we demonstrate that these lipid-coated biodegradable polymeric particles can be conjugated to a wide variety of biological molecules in a "click-like" fashion. This is of interest due to the multiple types of cellular mimicry enabled by this biomaterial based technology. These features include mimicry of the highly anisotropic shape exhibited by cells, surface presentation of membrane bound protein mimetics, and lateral diffusivity of membrane bound substrates comparable to that of a plasma membrane. This platform is demonstrated to

  5. Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation*

    Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert

    2016-01-01

    trafficking, enhancement of metabolic activity, and Wnt signaling pathway during the steep phase of memory formation; and (3) cytoskeleton organization proteins. Taken together, this study clearly demonstrates dynamic assembly and disassembly of protein-protein interaction networks depending on the stage of memory formation engrams. PMID:26598641

  6. Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation.

    Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert; Michaelevski, Izhak

    2016-02-01

    trafficking, enhancement of metabolic activity, and Wnt signaling pathway during the steep phase of memory formation; and (3) cytoskeleton organization proteins. Taken together, this study clearly demonstrates dynamic assembly and disassembly of protein-protein interaction networks depending on the stage of memory formation engrams. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

    Miao, Yinglong [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hong, Liang [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yi, Zheng [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-07-16

    A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Furthermore, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.

  8. Exploration of Protein Conformational Change with PELE and Meta-Dynamics.

    Cossins, Benjamin P; Hosseini, Ali; Guallar, Victor

    2012-03-13

    Atomistic molecular simulation methods are now able to explore complex protein or protein-ligand dynamical space in a tractable way with methods such as meta-dynamics or adaptive biasing force. However, many of these methods either require a careful selection of reaction coordinates or the knowledge of an initial pathway of some kind. Thus, it is important that effective methods are developed to produce this pathway data in an efficient fashion. PELE, a proven protein-ligand sampling code, has been developed to provide rapid protein sampling in highly flexible cases, using a reduced network model eigen problem approach. The resulting method is able to rapidly sample configuration space with very general driving information. When applied to ubiquitin, PELE was able to reproduce RMSD and average force data found in molecular dynamics simulations. PELE was also applied to explore the opening/closing transition of T4 lysozyme. A meta-dynamics exploration using a low energy pathway validated that the configurations explored by PELE represent the most populated regions of phase space. PELE and meta-dynamics explorations also discovered a low free energy region where a large cross-domain helix of T4 lysozyme is broken in two. There is previous NMR evidence for the validity of this unfolded helix region.

  9. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Samuel Hertig

    2016-06-01

    Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  10. A dynamic study of protein secretion and aggregation in the secretory pathway.

    Mossuto, Maria Francesca; Sannino, Sara; Mazza, Davide; Fagioli, Claudio; Vitale, Milena; Yoboue, Edgar Djaha; Sitia, Roberto; Anelli, Tiziana

    2014-01-01

    Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.

  11. A dynamic study of protein secretion and aggregation in the secretory pathway.

    Maria Francesca Mossuto

    Full Text Available Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.

  12. Reaction dynamics of inflammation proteins and T lymphocytes during radon balneotherapy

    Peter, A.; Vulpe, B.

    1989-01-01

    During a three-week radon treatment with daily administration of baths a periodical course of reaction with antidromic dynamics of inflammation proteins and T lymphocytes could be shown. A conspicuous reaction of the organism (moment of the treatment reaction) is to be observed one week after the beginning of the treatment. At the end of the cure a decrease of the activity of inflammation as well as of individual acute-phase proteins and immunoglobulins it to be proved. (author)

  13. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

    Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

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

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

    2018-01-24

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

  15. Self-similarity of high-pT hadron production in cumulative processes and violation of discrete symmetries at small scales (suggestion for experiment)

    Tokarev, M.V.; Zborovsky, I.

    2009-01-01

    The hypothesis of self-similarity of hadron production in relativistic heavy ion collisions for search for phase transition in a nuclear matter is discussed. It is offered to use the established features of z-scaling for revealing signatures of new physics in cumulative region. It is noted that selection of events on centrality in cumulative region could help to localize a position of a critical point. Change of parameters of the theory (a specific heat and fractal dimensions) near to a critical point is considered as a signature of new physics. The relation of the power asymptotic of ψ(z) at high z, anisotropy of momentum space due to spontaneous symmetry breaking, and discrete (C, P, T) symmetries is emphasized

  16. Determination of Dynamics of Plant Plasma Membrane Proteins with Fluorescence Recovery and Raster Image Correlation Spectroscopy.

    Laňková, Martina; Humpolíčková, Jana; Vosolsobě, Stanislav; Cit, Zdeněk; Lacek, Jozef; Čovan, Martin; Čovanová, Milada; Hof, Martin; Petrášek, Jan

    2016-04-01

    A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.

  17. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.

    Gnanasekaran, Ramachandran; Xu, Yao; Leitner, David M

    2010-12-23

    Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.

  18. Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn.

    Yongbin Dong

    Full Text Available The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

  19. Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation

    Lan K. Nguyen

    2014-01-01

    Full Text Available Protein degradation via ubiquitination is a major proteolytic mechanism in cells. Once a protein is destined for degradation, it is tagged by multiple ubiquitin molecules. The synthesised polyubiquitin chains can be recognised by the 26S proteosome where proteins are degraded. These chains form through multiple ubiquitination cycles that are similar to multi-site phosphorylation cycles. As kinases and phosphatases, two opposing enzymes (E3 ligases and deubiquitinases DUBs catalyse (deubiquitination cycles. Although multi-ubiquitination cycles are fundamental mechanisms of controlling protein concentrations within a cell, their dynamics have never been explored. Here, we fill this knowledge gap. We show that under permissive physiological conditions, the formation of polyubiquitin chain of length greater than two and subsequent degradation of the ubiquitinated protein, which is balanced by protein synthesis, can display bistable, switch-like responses. Interestingly, the occurrence of bistability becomes pronounced, as the chain grows, giving rise to all-or-none regulation at the protein levels. We give predictions of protein distributions under bistable regime awaiting experimental verification. Importantly, we show for the first time that sustained oscillations can robustly arise in the process of formation of ubiquitin chain, largely due to the degradation of the target protein. This new feature is opposite to the properties of multi-site phosphorylation cycles, which are incapable of generating oscillation if the total abundance of interconverted protein forms is conserved. We derive structural and kinetic constraints for the emergence of oscillations, indicating that a competition between different substrate forms and the E3 and DUB is critical for oscillation. Our work provides the first detailed elucidation of the dynamical features brought about by different molecular setups of the polyubiquitin chain assembly process responsible for

  20. Effect of dynamic high pressure homogenization on the aggregation state of soy protein.

    Keerati-U-Rai, Maneephan; Corredig, Milena

    2009-05-13

    Although soy proteins are often employed as functional ingredients in oil-water emulsions, very little is known about the aggregation state of the proteins in solution and whether any changes occur to soy protein dispersions during homogenization. The effect of dynamic high pressure homogenization on the aggregation state of the proteins was investigated using microdifferential scanning calorimetry and high performance size exclusion chromatography coupled with multiangle laser light scattering. Soy protein isolates as well as glycinin and beta-conglycinin fractions were prepared from defatted soy flakes and redispersed in 50 mM sodium phosphate buffer at pH 7.4. The dispersions were then subjected to homogenization at two different pressures, 26 and 65 MPa. The results demonstrated that dynamic high pressure homogenization causes changes in the supramolecular structure of the soy proteins. Both beta-conglycinin and glycinin samples had an increased temperature of denaturation after homogenization. The chromatographic elution profile showed a reduction in the aggregate concentration with homogenization pressure for beta-conglycinin and an increase in the size of the soluble aggregates for glycinin and soy protein isolate.

  1. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

    Moye Wang

    2016-04-01

    Full Text Available As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

  2. Direct observation of TALE protein dynamics reveals a two-state search mechanism.

    Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M

    2015-06-01

    Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process-a search state and a recognition state-facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state.

  3. Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.

    Visone, Valeria; Vettone, Antonella; Serpe, Mario; Valenti, Anna; Perugino, Giuseppe; Rossi, Mosè; Ciaramella, Maria

    2014-09-25

    In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  4. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  5. Coevolving residues of (beta/alpha)(8)-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics.

    Shen, Hongbo; Xu, Feng; Hu, Hairong; Wang, Feifei; Wu, Qi; Huang, Qiang; Wang, Honghai

    2008-12-01

    Indole-3-glycerol phosphate synthase (IGPS) is a representative of (beta/alpha)(8)-barrel proteins-the most common enzyme fold in nature. To better understand how the constituent amino-acids work together to define the structure and to facilitate the function, we investigated the evolutionary and dynamical coupling of IGPS residues by combining statistical coupling analysis (SCA) and molecular dynamics (MD) simulations. The coevolving residues identified by the SCA were found to form a network which encloses the active site completely. The MD simulations showed that these coevolving residues are involved in the correlated and anti-correlated motions. The correlated residues are within van der Waals contact and appear to maintain the active site architecture; the anti-correlated residues are mainly distributed on opposite sides of the catalytic cavity and coordinate the motions likely required for the substrate entry and product release. Our findings might have broad implications for proteins with the highly conserved (betaalpha)(8)-barrel in assessing the roles of amino-acids that are moderately conserved and not directly involved in the active site of the (beta/alpha)(8)-barrel. The results of this study could also provide useful information for further exploring the specific residue motions for the catalysis and protein design based on the (beta/alpha)(8)-barrel scaffold.

  6. Structure and dynamics of interfacial water. Role of hydratation water in the globular proteins dynamics

    Zanotti, J.M.

    1997-01-01

    This memoir includes five chapters. In the first chapter, are given the elements of the neutrons scattering theory that is used in this study. the second chapter is devoted to a general presentation of the interaction between biological macro molecule and water. The third part is dedicated to the study of the structure and the dynamics of interfacial water in the neighbouring of model systems, the vycor and the amorphous carbon. The results presented in this part are compared with these one relative to water dynamics at the C-phycocyanin surface. This study makes the object of the fourth chapter. Then, in the fifth and last chapter are discussed the results relative to the role of hydratation on the parv-albumin dynamics for which have been combined the neutron quasi elastic incoherent scattering and the nuclear magnetic resonance of the carbon 13 solid in natural abundance

  7. Getting the ion-protein interactions right in molecular dynamics simulations

    Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel

    2017-01-01

    Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics

  8. Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering.

    Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel

    2015-10-01

    A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).

  9. Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

    Choy, Meng S; Li, Yang; Machado, Luciana E S F; Kunze, Micha B A; Connors, Christopher R; Wei, Xingyu; Lindorff-Larsen, Kresten; Page, Rebecca; Peti, Wolfgang

    2017-02-16

    Protein function originates from a cooperation of structural rigidity, dynamics at different timescales, and allostery. However, how these three pillars of protein function are integrated is still only poorly understood. Here we show how these pillars are connected in Protein Tyrosine Phosphatase 1B (PTP1B), a drug target for diabetes and cancer that catalyzes the dephosphorylation of numerous substrates in essential signaling pathways. By combining new experimental and computational data on WT-PTP1B and ≥10 PTP1B variants in multiple states, we discovered a fundamental and evolutionarily conserved CH/π switch that is critical for positioning the catalytically important WPD loop. Furthermore, our data show that PTP1B uses conformational and dynamic allostery to regulate its activity. This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

    Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

    2007-01-01

    The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ

  11. Multicompartment lipid cubic nanoparticles with high protein upload: millisecond dynamics of formation

    Angelov, Borislav; Angelova, A.; Filippov, Sergey K.; Drechsler, M.; Štěpánek, Petr; Lesieur, S.

    2014-01-01

    Roč. 8, č. 5 (2014), s. 5216-5226 ISSN 1936-0851 R&D Projects: GA ČR GAP208/10/1600 Institutional support: RVO:61389013 Keywords : lipid- protein nanoassembly * dynamic membrane curvature * amphiphile nanoarchitectonics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 12.881, year: 2014

  12. The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

    Wassenaar, T.A.; Mark, A.E.

    The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard

  13. Changes in the anisotropy of oriented membrane dynamics induced by myelin basic protein

    Natali, F. [OGG-INFM, Grenoble (France); Gliozzi, A.; Rolandi, R.; Relini, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Genova (Italy); Cavatorta, P.; Deriu, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Parma (Italy); Fasano, A. [Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari (Italy); Riccio, P. [Dipartimento di Biologia D.B.A.F., Universita della Basilicata, Potenza (Italy)

    2002-07-01

    We report recent results showing the evidence of the effect induced by physiological amounts of myelin basic protein (MBP) on the dynamics of dimyristoyl L-a-phosphatidic acid (DMPA) membranes. Incoherent elastic neutron scattering scans, performed over a wide temperature range, have shown that the anisotropy of motions in oriented membranes is significantly enhanced by the presence of MBP. (orig.)

  14. Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies

    Krutika Bavishi

    2014-11-01

    Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

  15. A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.

    Saha, Tanumoy; Rathmann, Isabel; Galic, Milos

    2017-07-11

    Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

  16. A general theory of non-equilibrium dynamics of lipid-protein fluid membranes

    Lomholt, Michael Andersen; Hansen, Per Lyngs; Miao, L.

    2005-01-01

    We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of statistical physics and designed to be a meso...

  17. Dynamic strength of the interaction between lung surfactant protein D (SP-D) and saccharide ligands

    Thormann, Esben; Dreyer, Jakob K; Simonsen, Adam C

    2007-01-01

    In order to investigate the dynamic strength of the interaction between lung surfactant protein D (SP-D) and different sugars, maltose, mannose, glucose, and galactose, we have used an atomic force microscope to monitor the interaction on a single molecule scale. The experiment is performed...

  18. Pyrenebutanoate as a dynamic protein modifier for fluorometric detection in capillary zone electrophoresis

    Horká, Marie; Šlais, Karel

    2002-01-01

    Roč. 23, 7-8 (2002), s. 1090-1095 ISSN 0173-0835 R&D Projects: GA AV ČR IAA4031901 Institutional research plan: CEZ:AV0Z4031919 Keywords : pyrenebutanoate * dynamic protein modifier * CZE Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.325, year: 2002

  19. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  20. Molecular Dynamics Simulations of a Flexible Polyethylene: A Protein-Like Behaviour in a Water Solvent

    Kretov, D A

    2005-01-01

    We used molecular dynamics (MD) simulations to study the density and the temperature behaviour of a flexible polyethylene (PE) subjected to various heating conditions and to investigate the PE chain conformational changes in a water solvent. First, we have considered the influence of the heating process on the final state of the polymeric system and the sensitivity of its thermodynamic characteristics (density, energy, etc.) for different heating regimes. For this purpose three different simulations were performed: fast, moderate, and slow heating. Second, we have investigated the PE chain conformational dynamics in water solvent for various simulation conditions and various configurations of the environment. From the obtained results we have got the pictures of the PE dynamical motions in water. We have observed a protein-like behaviour of the PE chain, like that of the DNA and the proteins in water, and have also estimated the rates of the conformational changes. For the MD simulations we used the optimized...

  1. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

    Juan A. González-Vera

    2015-11-01

    Full Text Available Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.

  2. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

    Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

    2016-02-26

    G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle

    Grabon, Aby; Orłowski, Adam; Tripathi, Ashutosh

    2017-01-01

    . However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical...... analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability......Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling...

  4. The dynamic mechanism of presenilin-function: Sensitive gate dynamics and loop unplugging control protein access

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2016-01-01

    There is no molecular explanation for the many presenilin 1 (PSEN1) mutations causing Alzheimer's disease, but both gain of function relating to amyloid production and loss of isolated PSEN1 function have been implied. We report here the first detailed dynamic all-atom model of mature PSEN1 from ...

  5. Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

    Chun, Chan; Haohua, Wen; Lanyuan, Lu; Jun, Fan

    2016-01-01

    Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs (BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics (MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins. Project supported by the National Natural Science Foundation of China (Grant No. 21403182) and the Research Grants Council of Hong Kong, China (Grant No. CityU 21300014).

  6. Differential dynamic microscopy of weakly scattering and polydisperse protein-rich clusters

    Safari, Mohammad S.; Vorontsova, Maria A.; Poling-Skutvik, Ryan; Vekilov, Peter G.; Conrad, Jacinta C.

    2015-10-01

    Nanoparticle dynamics impact a wide range of biological transport processes and applications in nanomedicine and natural resource engineering. Differential dynamic microscopy (DDM) was recently developed to quantify the dynamics of submicron particles in solutions from fluctuations of intensity in optical micrographs. Differential dynamic microscopy is well established for monodisperse particle populations, but has not been applied to solutions containing weakly scattering polydisperse biological nanoparticles. Here we use bright-field DDM (BDDM) to measure the dynamics of protein-rich liquid clusters, whose size ranges from tens to hundreds of nanometers and whose total volume fraction is less than 10-5. With solutions of two proteins, hemoglobin A and lysozyme, we evaluate the cluster diffusion coefficients from the dependence of the diffusive relaxation time on the scattering wave vector. We establish that for weakly scattering populations, an optimal thickness of the sample chamber exists at which the BDDM signal is maximized at the smallest sample volume. The average cluster diffusion coefficient measured using BDDM is consistently lower than that obtained from dynamic light scattering at a scattering angle of 90∘. This apparent discrepancy is due to Mie scattering from the polydisperse cluster population, in which larger clusters preferentially scatter more light in the forward direction.

  7. Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells.

    Tan, Chris Soon Heng; Go, Ka Diam; Bisteau, Xavier; Dai, Lingyun; Yong, Chern Han; Prabhu, Nayana; Ozturk, Mert Burak; Lim, Yan Ting; Sreekumar, Lekshmy; Lengqvist, Johan; Tergaonkar, Vinay; Kaldis, Philipp; Sobota, Radoslaw M; Nordlund, Pär

    2018-03-09

    Proteins differentially interact with each other across cellular states and conditions, but an efficient proteome-wide strategy to monitor them is lacking. We report the application of thermal proximity coaggregation (TPCA) for high-throughput intracellular monitoring of protein complex dynamics. Significant TPCA signatures observed among well-validated protein-protein interactions correlate positively with interaction stoichiometry and are statistically observable in more than 350 annotated human protein complexes. Using TPCA, we identified many complexes without detectable differential protein expression, including chromatin-associated complexes, modulated in S phase of the cell cycle. Comparison of six cell lines by TPCA revealed cell-specific interactions even in fundamental cellular processes. TPCA constitutes an approach for system-wide studies of protein complexes in nonengineered cells and tissues and might be used to identify protein complexes that are modulated in diseases. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  8. Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

    Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

    2012-10-09

    NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.

  9. Conformational Dynamics of the Receptor Protein Galactose/Glucose Binding Protein

    Messina, Troy; Talaga, David

    2006-03-01

    We have performed time-correlated single photon counting (TCSPC) anisotropy and Stokes Shift measurements on bulk solutions of galactose/glucose binding protein. Site-directed mutagenesis was used to provide a single cysteine amino acid near the sugar-binding center of the protein (glutamine 26 to cysteine -- Q26C). The cysteine was covalently labeled with the environmentally-sensitive fluorophore acrylodan, and a long-lived ruthenium complex was covalently attached to the N-terminus to provide a fluorescent reference. The TCSPC data were analyzed using global convolute-and-compare fitting routines over the entire glucose titration and temperature range to provide minimal reduced chi-squared values and the highest time resolution possible. Using a standard ligand-binding model, the resulting distributions show that the closed (ligand-bound) conformation exists even at zero glucose concentration. At 20^oC, the relative abundance of this conformation is as high as 40%. The temperature dependence of this conformational study will be discussed and related to the ligand-binding free energy surface.

  10. GPI-anchored protein organization and dynamics at the cell surface.

    Saha, Suvrajit; Anilkumar, Anupama Ambika; Mayor, Satyajit

    2016-02-01

    The surface of eukaryotic cells is a multi-component fluid bilayer in which glycosylphosphatidylinositol (GPI)-anchored proteins are an abundant constituent. In this review, we discuss the complex nature of the organization and dynamics of GPI-anchored proteins at multiple spatial and temporal scales. Different biophysical techniques have been utilized for understanding this organization, including fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single particle tracking, and a number of super resolution methods. Major insights into the organization and dynamics have also come from exploring the short-range interactions of GPI-anchored proteins by fluorescence (or Förster) resonance energy transfer microscopy. Based on the nanometer to micron scale organization, at the microsecond to the second time scale dynamics, a picture of the membrane bilayer emerges where the lipid bilayer appears inextricably intertwined with the underlying dynamic cytoskeleton. These observations have prompted a revision of the current models of plasma membrane organization, and suggest an active actin-membrane composite. Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.

  11. Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

    Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

    2015-01-01

    Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

  12. Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

    Våge, Selina; Thingstad, T. Frede

    2015-01-01

    Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales. PMID:26648929

  13. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. © 2015 The Protein Society.

  14. Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

    Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

    2016-08-01

    Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.

  15. How does the antagonism between capping and anti-capping proteins affect actin network dynamics?

    Hu Longhua; Papoian, Garegin A

    2011-01-01

    Actin-based cell motility is essential to many biological processes. We built a simplified, three-dimensional computational model and subsequently performed stochastic simulations to study the growth dynamics of lamellipodia-like branched networks. In this work, we shed light on the antagonism between capping and anti-capping proteins in regulating actin dynamics in the filamentous network. We discuss detailed mechanisms by which capping and anti-capping proteins affect the protrusion speed of the actin network and the rate of nucleation of filaments. We computed a phase diagram showing the regimes of motility enhancement and inhibition by these proteins. Our work shows that the effects of capping and anti-capping proteins are mainly transmitted by modulation of the filamentous network density and local availability of monomeric actin. We discovered that the combination of the capping/anti-capping regulatory network with nucleation-promoting proteins introduces robustness and redundancy in cell motility machinery, allowing the cell to easily achieve maximal protrusion speeds under a broader set of conditions. Finally, we discuss distributions of filament lengths under various conditions and speculate on their potential implication for the emergence of filopodia from the lamellipodial network.

  16. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

    Allen Holder

    2013-11-01

    Full Text Available Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs is robust against both parametric and structural variation.

  18. Local dynamics of proteins and DNA evaluated from crystallographic B factors

    Schneider, Bohdan; Gelly, Jean-Christophe; Brevern, Alexandre G. de; Černý, Jiří

    2014-01-01

    Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

  19. Local dynamics of proteins and DNA evaluated from crystallographic B factors

    Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic); Gelly, Jean-Christophe; Brevern, Alexandre G. de [INSERM, U1134, DSIMB, 75739 Paris (France); Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris (France); Institut National de la Transfusion Sanguine (INTS), 75739 Paris (France); Laboratoire d’Excellence GR-Ex, 75739 Paris (France); Černý, Jiří [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)

    2014-09-01

    Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

  20. A comparative molecular dynamics study on thermostability of human and chicken prion proteins

    Ji, Hong-Fang; Zhang, Hong-Yu

    2007-01-01

    To compare the thermostabilities of human and chicken normal cellular prion proteins (HuPrP C and CkPrP C ), molecular dynamics (MD) simulations were performed for both proteins at an ensemble level (10 parallel simulations at 400 K and 5 parallel simulations at 300 K as a control). It is found that the thermostability of HuPrP C is comparable with that of CkPrP C , which implicates that the non-occurrence of prion diseases in non-mammals cannot be completely attributed to the thermodynamic properties of non-mammalian PrP C

  1. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

    Dong, Zheng; Zhou, Hongyu; Tao, Peng

    2018-02-01

    PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

  2. Dynamics of protein aggregation and oligomer formation governed by secondary nucleation

    Michaels, Thomas C. T., E-mail: tctm3@cam.ac.uk; Lazell, Hamish W.; Arosio, Paolo; Knowles, Tuomas P. J., E-mail: tpjk2@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

    2015-08-07

    The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.

  3. Protein dynamics during presynaptic complex assembly on individual ssDNA molecules

    Gibb, Bryan; Ye, Ling F.; Kwon, YoungHo; Niu, Hengyao; Sung, Patrick; Greene, Eric C.

    2014-01-01

    Homologous recombination is a conserved pathway for repairing double?stranded breaks, which are processed to yield single?stranded DNA overhangs that serve as platforms for presynaptic complex assembly. Here we use single?molecule imaging to reveal the interplay between Saccharomyce cerevisiae RPA, Rad52, and Rad51 during presynaptic complex assembly. We show that Rad52 binds RPA?ssDNA and suppresses RPA turnover, highlighting an unanticipated regulatory influence on protein dynamics. Rad51 b...

  4. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-04-01

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  5. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-01-01

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc 1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins

  6. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

    Martin, Daniel R.; Matyushov, Dmitry V., E-mail: dmitrym@asu.edu [Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287 (United States)

    2015-04-28

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  7. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

  8. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.

    Kehl, Catherine; Simms, Andrew M; Toofanny, Rudesh D; Daggett, Valerie

    2008-06-01

    The Dynameomics project is our effort to characterize the native-state dynamics and folding/unfolding pathways of representatives of all known protein folds by way of molecular dynamics simulations, as described by Beck et al. (in Protein Eng. Des. Select., the first paper in this series). The data produced by these simulations are highly multidimensional in structure and multi-terabytes in size. Both of these features present significant challenges for storage, retrieval and analysis. For optimal data modeling and flexibility, we needed a platform that supported both multidimensional indices and hierarchical relationships between related types of data and that could be integrated within our data warehouse, as described in the accompanying paper directly preceding this one. For these reasons, we have chosen On-line Analytical Processing (OLAP), a multi-dimensional analysis optimized database, as an analytical platform for these data. OLAP is a mature technology in the financial sector, but it has not been used extensively for scientific analysis. Our project is further more unusual for its focus on the multidimensional and analytical capabilities of OLAP rather than its aggregation capacities. The dimensional data model and hierarchies are very flexible. The query language is concise for complex analysis and rapid data retrieval. OLAP shows great promise for the dynamic protein analysis for bioengineering and biomedical applications. In addition, OLAP may have similar potential for other scientific and engineering applications involving large and complex datasets.

  9. ESTABLISHING A STEREOSCOPIC TECHNIQUE FOR DETERMINING THE KINEMATIC PROPERTIES OF SOLAR WIND TRANSIENTS BASED ON A GENERALIZED SELF-SIMILARLY EXPANDING CIRCULAR GEOMETRY

    Davies, J. A.; Perry, C. H.; Harrison, R. A.; Trines, R. M. G. M.; Lugaz, N.; Möstl, C.; Liu, Y. D.; Steed, K.

    2013-01-01

    The twin-spacecraft STEREO mission has enabled simultaneous white-light imaging of the solar corona and inner heliosphere from multiple vantage points. This has led to the development of numerous stereoscopic techniques to investigate the three-dimensional structure and kinematics of solar wind transients such as coronal mass ejections (CMEs). Two such methods—triangulation and the tangent to a sphere—can be used to determine time profiles of the propagation direction and radial distance (and thereby radial speed) of a solar wind transient as it travels through the inner heliosphere, based on its time-elongation profile viewed by two observers. These techniques are founded on the assumption that the transient can be characterized as a point source (fixed φ, FP, approximation) or a circle attached to Sun-center (harmonic mean, HM, approximation), respectively. These geometries constitute extreme descriptions of solar wind transients, in terms of their cross-sectional extent. Here, we present the stereoscopic expressions necessary to derive propagation direction and radial distance/speed profiles of such transients based on the more generalized self-similar expansion (SSE) geometry, for which the FP and HM geometries form the limiting cases; our implementation of these equations is termed the stereoscopic SSE method. We apply the technique to two Earth-directed CMEs from different phases of the STEREO mission, the well-studied event of 2008 December and a more recent event from 2012 March. The latter CME was fast, with an initial speed exceeding 2000 km s –1 , and highly geoeffective, in stark contrast to the slow and ineffectual 2008 December CME

  10. Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

    Balsara, Dinshaw S.; Nkonga, Boniface

    2017-10-01

    Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

  11. Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response.

    Li, Yang; Roberts, Julie; AkhavanAghdam, Zohreh; Hao, Nan

    2017-12-15

    In the yeast Saccharomyces cerevisiae , the exposure to mating pheromone activates a prototypic mitogen-activated protein kinase (MAPK) cascade and triggers a dose-dependent differentiation response. Whereas a high pheromone dose induces growth arrest and formation of a shmoo-like morphology in yeast cells, lower pheromone doses elicit elongated cell growth. Previous population-level analysis has revealed that the MAPK Fus3 plays an important role in mediating this differentiation switch. To further investigate how Fus3 controls the fate decision process at the single-cell level, we developed a specific translocation-based reporter for monitoring Fus3 activity in individual live cells. Using this reporter, we observed strikingly different dynamic patterns of Fus3 activation in single cells differentiated into distinct fates. Cells committed to growth arrest and shmoo formation exhibited sustained Fus3 activation. In contrast, most cells undergoing elongated growth showed either a delayed gradual increase or pulsatile dynamics of Fus3 activity. Furthermore, we found that chemically perturbing Fus3 dynamics with a specific inhibitor could effectively redirect the mating differentiation, confirming the causative role of Fus3 dynamics in driving cell fate decisions. MAPKs mediate proliferation and differentiation signals in mammals and are therapeutic targets in many cancers. Our results highlight the importance of MAPK dynamics in regulating single-cell responses and open up the possibility that MAPK signaling dynamics could be a pharmacological target in therapeutic interventions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore

    Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.

    2017-08-01

    We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

  13. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

    Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

    2017-05-01

    The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

  14. Variable-angle epifluorescence microscopy characterizes protein dynamics in the vicinity of plasma membrane in plant cells.

    Chen, Tong; Ji, Dongchao; Tian, Shiping

    2018-03-14

    The assembly of protein complexes and compositional lipid patterning act together to endow cells with the plasticity required to maintain compositional heterogeneity with respect to individual proteins. Hence, the applications for imaging protein localization and dynamics require high accuracy, particularly at high spatio-temporal level. We provided experimental data for the applications of Variable-Angle Epifluorescence Microscopy (VAEM) in dissecting protein dynamics in plant cells. The VAEM-based co-localization analysis took penetration depth and incident angle into consideration. Besides direct overlap of dual-color fluorescence signals, the co-localization analysis was carried out quantitatively in combination with the methodology for calculating puncta distance and protein proximity index. Besides, simultaneous VAEM tracking of cytoskeletal dynamics provided more insights into coordinated responses of actin filaments and microtubules. Moreover, lateral motility of membrane proteins was analyzed by calculating diffusion coefficients and kymograph analysis, which represented an alternative method for examining protein motility. The present study presented experimental evidence on illustrating the use of VAEM in tracking and dissecting protein dynamics, dissecting endosomal dynamics, cell structure assembly along with membrane microdomain and protein motility in intact plant cells.

  15. Real-Time G-Protein-Coupled Receptor Imaging to Understand and Quantify Receptor Dynamics

    María S. Aymerich

    2011-01-01

    Full Text Available Understanding the trafficking of G-protein-coupled receptors (GPCRs and their regulation by agonists and antagonists is fundamental to develop more effective drugs. Optical methods using fluorescent-tagged receptors and spinning disk confocal microscopy are useful tools to investigate membrane receptor dynamics in living cells. The aim of this study was to develop a method to characterize receptor dynamics using this system which offers the advantage of very fast image acquisition with minimal cell perturbation. However, in short-term assays photobleaching was still a problem. Thus, we developed a procedure to perform a photobleaching-corrected image analysis. A study of short-term dynamics of the long isoform of the dopamine type 2 receptor revealed an agonist-induced increase in the mobile fraction of receptors with a rate of movement of 0.08 μm/s For long-term assays, the ratio between the relative fluorescence intensity at the cell surface versus that in the intracellular compartment indicated that receptor internalization only occurred in cells co-expressing G protein-coupled receptor kinase 2. These results indicate that the lateral movement of receptors and receptor internalization are not directly coupled. Thus, we believe that live imaging of GPCRs using spinning disk confocal image analysis constitutes a powerful tool to study of receptor dynamics.

  16. Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

    Cheng, Ryan R.; Hawk, Alexander T.; Makarov, Dmitrii E.

    2013-02-01

    Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often adequately described by simple polymer models. In particular, the Rouse model with internal friction (RIF) captures internal friction effects as observed in single-molecule fluorescence correlation spectroscopy (FCS) studies of a number of proteins. Here we use RIF, and its non-free draining analog, Zimm model with internal friction, to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain. Unlike the reconfiguration times inferred from FCS experiments, which depend linearly on the solvent viscosity, the first passage times to form intramolecular contacts are shown to display a more complex viscosity dependence. We further describe scaling relationships obeyed by contact formation times in the limits of high and low internal friction. Our findings provide experimentally testable predictions that can serve as a framework for the analysis of future studies of contact formation in proteins.

  17. A customized light sheet microscope to measure spatio-temporal protein dynamics in small model organisms.

    Matthias Rieckher

    Full Text Available We describe a customizable and cost-effective light sheet microscopy (LSM platform for rapid three-dimensional imaging of protein dynamics in small model organisms. The system is designed for high acquisition speeds and enables extended time-lapse in vivo experiments when using fluorescently labeled specimens. We demonstrate the capability of the setup to monitor gene expression and protein localization during ageing and upon starvation stress in longitudinal studies in individual or small groups of adult Caenorhabditis elegans nematodes. The system is equipped to readily perform fluorescence recovery after photobleaching (FRAP, which allows monitoring protein recovery and distribution under low photobleaching conditions. Our imaging platform is designed to easily switch between light sheet microscopy and optical projection tomography (OPT modalities. The setup permits monitoring of spatio-temporal expression and localization of ageing biomarkers of subcellular size and can be conveniently adapted to image a wide range of small model organisms and tissue samples.

  18. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  19. Impact of transamination reactions and protein turnover on labeling dynamics in C-13-labeling experiments

    Grotkjær, Thomas; Åkesson, M.; Christensen, Bjarke

    2004-01-01

    A dynamic model describing carbon atom transitions in the central metabolism of Saccharomyces cerevisiae is used to investigate the influence of transamination reactions and protein turnover on the transient behavior of C-13-labeling chemostat experiments. The simulations performed suggest...... that carbon exchange due to transamination and protein turnover can significantly increase the required time needed for metabolites in the TCA cycle to reach isotopic steady state, which is in agreement with published experimental observations. On the other hand, transamination and protein turnover will speed...... behavior until after three residence times. These observations suggest that greater caution should be used while also pointing to new opportunities in the design and interpretation of C-13-labeling experiments....

  20. Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

    de Oliveira dos Santos Soares, Ricardo; Oliveira Bortot, Leandro; van der Spoel, David; Caliri, Antonio

    2017-12-01

    Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the dengue virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process. In silico mutagenesis of two charged residues of the anchor helices of the envelope proteins of DENV shows that Arg-471 and Arg-60 are fundamental to produce bending stress on the membrane. The fine-tuning between the size of the EM3 unit and its specific bending action suggests this protein unit is an important factor in determining the viral particle size.