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Sample records for all-atom normal mode

  1. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Twarock, Reidun

    2010-03-01

    Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.

  2. The effective degeneracy of protein normal modes

    NASA Astrophysics Data System (ADS)

    Na, Hyuntae; Song, Guang

    2016-06-01

    Normal modes are frequently computed and used to portray protein dynamics and interpret protein conformational changes. In this work, we investigate the nature of normal modes and find that the normal modes of proteins, especially those at the low frequency range (0–600 cm‑1), are highly susceptible to degeneracy. Two or more modes are degenerate if they have the same frequency and consequently any orthogonal transformation of them also is a valid representation of the mode subspace. Thus, degenerate modes can no longer characterize unique directions of motions as regular modes do. Though the normal modes of proteins are usually of different frequencies, the difference in frequency between neighboring modes is so small that, under even slight structural uncertainty that unavoidably exists in structure determination, it can easily vanish and as a result, a mode becomes effectively degenerate with its neighboring modes. This can be easily observed in that some modes seem to disappear and their matching modes cannot be found when the structure used to compute the modes is modified only slightly. We term this degeneracy the effective degeneracy of normal modes. This work is built upon our recent discovery that the vibrational spectrum of globular proteins is universal. The high density of modes observed in the vibrational frequency spectra of proteins renders their normal modes highly susceptible to degeneracy, under even the smallest structural uncertainty. Indeed, we find the degree of degeneracy of modes is proportional to the density of modes in the vibrational spectrum. This means that for modes at the same frequency, degeneracy is more severe for larger proteins. Degeneracy exists also in the modes of coarse-grained models, but to a much lesser extent than those of all-atom models. In closing, we discuss the implications of the effective degeneracy of normal modes: how it may significantly affect the ways in which normal modes are used in various normal modes

  3. The effective degeneracy of protein normal modes.

    PubMed

    Na, Hyuntae; Song, Guang

    2016-01-01

    Normal modes are frequently computed and used to portray protein dynamics and interpret protein conformational changes. In this work, we investigate the nature of normal modes and find that the normal modes of proteins, especially those at the low frequency range (0-600 cm(-1)), are highly susceptible to degeneracy. Two or more modes are degenerate if they have the same frequency and consequently any orthogonal transformation of them also is a valid representation of the mode subspace. Thus, degenerate modes can no longer characterize unique directions of motions as regular modes do. Though the normal modes of proteins are usually of different frequencies, the difference in frequency between neighboring modes is so small that, under even slight structural uncertainty that unavoidably exists in structure determination, it can easily vanish and as a result, a mode becomes effectively degenerate with its neighboring modes. This can be easily observed in that some modes seem to disappear and their matching modes cannot be found when the structure used to compute the modes is modified only slightly. We term this degeneracy the effective degeneracy of normal modes. This work is built upon our recent discovery that the vibrational spectrum of globular proteins is universal. The high density of modes observed in the vibrational frequency spectra of proteins renders their normal modes highly susceptible to degeneracy, under even the smallest structural uncertainty. Indeed, we find the degree of degeneracy of modes is proportional to the density of modes in the vibrational spectrum. This means that for modes at the same frequency, degeneracy is more severe for larger proteins. Degeneracy exists also in the modes of coarse-grained models, but to a much lesser extent than those of all-atom models. In closing, we discuss the implications of the effective degeneracy of normal modes: how it may significantly affect the ways in which normal modes are used in various normal modes

  4. Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Burri, Raghunadha Reddy; Ishikawa, Takeshi; Ishikura, Takakazu; Sakuraba, Shun; Matubayasi, Nobuyuki; Kuwata, Kazuo; Kitao, Akio

    2013-02-01

    We propose a method for calculating the binding free energy of protein-ligand complexes using all-atom molecular dynamics simulation combined with the solution theory in the energy representation. Four distinct modes for the binding of tri-N-acetyl-D-glucosamine (triNAG) to hen egg-white lysozyme were investigated, one from the crystal structure and three generated by docking predictions. The proposed method was demonstrated to be used to distinguish the most plausible binding mode (crystal model) as the lowest binding energy mode.

  5. TOPICAL REVIEW: Normal mode analysis and applications in biological physics

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Sankey, Otto F.

    2010-10-01

    Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.

  6. Terra is in NORMAL Mode

    Atmospheric Science Data Center

    2016-02-23

    ... 22, 2016.  TERRA has recovered from Safe Hold and is now in Normal mode. CERES will hold their CAM Wednesday morning and will ... . You can learn more about this mission at the Terra web site. The Flight Operations Team is working on resolving the issue as ...

  7. Normal modes and continuous spectra

    SciTech Connect

    Balmforth, N.J.; Morrison, P.J.

    1994-12-01

    The authors consider stability problems arising in fluids, plasmas and stellar systems that contain singularities resulting from wave-mean flow or wave-particle resonances. Such resonances lead to singularities in the differential equations determining the normal modes at the so-called critical points or layers. The locations of the singularities are determined by the eigenvalue of the problem, and as a result, the spectrum of eigenvalues forms a continuum. They outline a method to construct the singular eigenfunctions comprising the continuum for a variety of problems.

  8. Local and normal modes: A classical perspective

    NASA Astrophysics Data System (ADS)

    Jaffé, Charles; Brumer, Paul

    1980-12-01

    Normal and local mode behavior in molecular systems and the transition between them is explored using nonlinear mechanics techniques. Significant insight into this behavior and into the structure of phase space results from a generalized definition of local and normal modes and the associated identification of normal modes as a (1:1) resonance between local zeroth order oscillators. In addition to qualitative insight, this approach yields a simple formula [Eq. (28)] for the level of excitation at which local modes become possible. Applications to H2O and to the overtone spectroscopy of the dihalomethanes, benzene, and TMS are provided.

  9. Normal Modes of Black Hole Accretion Disks

    SciTech Connect

    Ortega-Rodriguez, Manuel; Silbergleit, Alexander S.; Wagoner, Robert V.; /Stanford U., Phys. Dept. /KIPAC, Menlo Park

    2006-11-07

    This paper studies the hydrodynamical problem of normal modes of small adiabatic oscillations of relativistic barotropic thin accretion disks around black holes (and compact weakly magnetic neutron stars). Employing WKB techniques, we obtain the eigen frequencies and eigenfunctions of the modes for different values of the mass and angular momentum of the central black hole. We discuss the properties of the various types of modes and examine the role of viscosity, as it appears to render some of the modes unstable to rapid growth.

  10. Normal modes of confined cold ionic systems

    SciTech Connect

    Schiffer, J.P.; Dubin, D.H.

    1995-08-01

    The normal modes of a cloud of confined ions forming a strongly-correlated plasma were investigated. The results of molecular-dynamics simulations were compared to predictions of a cold fluid mode. Mode frequencies are observed to shift slightly compared to the cold fluid predictions, and the modes are also observed to damp in time. Simulations also reveal a set of torsional oscillations which have no counterpart in cold fluid theory. The frequency shift, damping, and torsional effects are compared to a model that treats trapped plasmas as a visco-elastic spheroid. It may be possible to measure high-frequency bulk and shear moduli of a strongly-correlated plasma from mode excitation experiments on trapped non-neutral plasmas. An example of the results of the calculation is presented.

  11. A new method of normal mode calculation

    NASA Astrophysics Data System (ADS)

    Kobayashi, N.

    2004-12-01

    Numerical method of calculating normal modes of the Earth is classical problem in seismology and many methods have been developed, e.g. MINEOS, OBANI (Woodhouse 1989) and DISPER80 (Saito 1989). These methods are based on direct numerical integration of the governing differential equations (Runge-Kutta method). The methods are efficient for search for (real) eigenvalues of non dissipative cases but have some trouble to seek complex eigenvalues of dissipative or leaky oscillations. On the other hand, in solar seismology, the Henyey type relaxation method is used to calculate acoustic and gravity modes of the sun and stars (e.g. Unno et al. 1989). The latter method is generally more stable for eigenvalue problems of a self-gravitating gaseous body where the density and pressure vary exponentially near its surface. The efficiency of the method is, however, depends on initial guess of eigenvalues and eigenfunctions. Here we propose a new method to overcome the deficiency of the above methods. This method is formulated with the aid of the concept of the Henyey type relaxation method but does not needs initial guess of eigenfuctions and solves the problem more directly like the Runge-Hutta method. Some mumerical tests show good convergence of complex eigenvalues in our method. So the proposed method is effective to calculate solid modes, acoustic and gravity modes and ocean modes interfered with the other parts of the earth and planets.

  12. Electrostatic normal modes in nonneutral plasmas

    NASA Astrophysics Data System (ADS)

    Book, David L.

    1995-04-01

    A fluid description is employed to derive the dispersion relation for modes near the cyclotron frequency Ω in a nonuniform cylindrical nonneutral plasma of radius R with finite temperature confined by a uniform magnetic field B=B0ez. In contrast to the theory of Gould and LaPointe, the model includes the diamagnetic drift but omits finite-Larmor-radius effects. The eigenfrequencies for high-frequency electrostatic modes with wavevectors satisfying k ṡ B=0 (Bernstein modes) are found in the form ω=-Ω+Δω. Solutions are obtained and compared with experiment and the theory of Gould and LaPointe. The present theory predicts that at a given temperature modes with m≳1 propagate only when the density is less than a critical value that increases with m, and that Δω normalized by the diocotron frequency depends only on the ratio of the Debye length to the plasma radius and hence is independent of B and the particle mass.

  13. Electrostatic normal modes in nonneutral plasmas

    SciTech Connect

    Book, David L.

    1995-04-15

    A fluid description is employed to derive the dispersion relation for modes near the cyclotron frequency {omega} in a nonuniform cylindrical nonneutral plasma of radius R with finite temperature confined by a uniform magnetic field B=B0ez. In contrast to the theory of Gould and LaPointe, the model includes the diamagnetic drift but omits finite-Larmor-radius effects. The eigenfrequencies for high-frequency electrostatic modes with wavevectors satisfying k {center_dot} B=0 (Bernstein modes) are found in the form {omega}=-{omega}+{delta}{omega}. Solutions are obtained and compared with experiment and the theory of Gould and LaPointe. The present theory predicts that at a given temperature modes with m > or approx.1 propagate only when the density is less than a critical value that increases with m, and that {delta}{omega} normalized by the diocotron frequency depends only on the ratio of the Debye length to the plasma radius and hence is independent of B and the particle mass.

  14. A spectral characterization of nonlinear normal modes

    NASA Astrophysics Data System (ADS)

    Cirillo, G. I.; Mauroy, A.; Renson, L.; Kerschen, G.; Sepulchre, R.

    2016-09-01

    This paper explores the relationship that exists between nonlinear normal modes (NNMs) defined as invariant manifolds in phase space and the spectral expansion of the Koopman operator. Specifically, we demonstrate that NNMs correspond to zero level sets of specific eigenfunctions of the Koopman operator. Thanks to this direct connection, a new, global parametrization of the invariant manifolds is established. Unlike the classical parametrization using a pair of state-space variables, this parametrization remains valid whenever the invariant manifold undergoes folding, which extends the computation of NNMs to regimes of greater energy. The proposed ideas are illustrated using a two-degree-of-freedom system with cubic nonlinearity.

  15. A new method to calculate normal modes

    NASA Astrophysics Data System (ADS)

    Kobayashi, Naoki

    2007-01-01

    We developed a new method to calculate normal modes of the Earth and planets. It can treat anelasticity directly as imaginary parts of elastic constants and leaky modes due to the open boundary condition set at the upper atmosphere. The eigenvalue problem is described in complex numbers. It is formulated based on a similar treatment of the global matrix governing the system of oscillations to that in the Henyey-type relaxation method used in solar seismology. In our method, the complex eigenvalue problem of a large system is reduced to an eigenvalue problem of a quite small size matrix. The eigenvalue of the small problem is a correction of an assumed complex eigenfrequency and components of the eigenvector are values of eigenfunctions at the outer boundary. Starting from an arbitrary complex frequency around the eigenfrequency of a target mode, we can arrive there within, at most, a dozen of steps of iterative calculations. We compared the results of our method with those calculated by DISPER80, and found good agreement between them. The rate of convergence of the method depends on the linearity of the correction around the eigenfrequency. A numerical example shows good behaviour of them. Even for a model with an atmosphere in which the fundamental spheroidal mode 0S29 and the fundamental acoustic mode 0P29 nearly degenerate, we can easily reach the eigenfrequency of 0S29 and distinguish it from that of 0P29 without any confusion. And we found that the eigenfrequency of 0P29 calculated for a realistic atmospheric model which varies annually, most approaches the solid mode in August. The behaviour of 0P29 can be interpreted with the aid of an acoustic potential which characterizes vertical propagation of sound waves. In addition to the efficiency in the convergence to the eigenfrequencies, numerical tests show strong numerical stability of the method. It stems from the stability in the relaxation method because of the similarity in algebraic structure. For those

  16. Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach

    PubMed Central

    Zhou, Lei; Siegelbaum, Steven A.

    2008-01-01

    Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics. PMID:18212016

  17. Improving an all-atom force field.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-01

    Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516

  18. Wave Forced Normal Modes on Fringing Reefs

    NASA Astrophysics Data System (ADS)

    Pequignet, A. N.; Becker, J. M.; Merrifield, M. M.; Aucan, J.

    2008-12-01

    In an effort to assess wave-driven coastal inundation at the shoreline of fringing reefs, pressure and current observations were collected at reefs on Guam (Ipan) and Oahu, Hawaii (Mokuleia) as part of the PILOT (Pacific Island Land-Ocean Typhoon) experiment. Similar to dissipative sandy beaches, nearshore surface elevation at both reefs is dominated by energy in the infragravity frequency band. Coherent infragravity oscillations across the reef tend to occur at discrete frequencies and with standing wave cross-shore structures that are consistent with open basin resonant modes. The modes are forced by swell wave groups, similar to a time-dependent setup. The resonant modes are most apparent during energetic wave events, in part because wave setup over the reef increases the low mode resonant frequencies to a range that is conducive to wave group forcing. Evidence of the excitation of resonant modes during tropical storm Man-Yi at Ipan, Guam is presented.

  19. Atmospheric Excitation of Planetary Normal Modes

    NASA Technical Reports Server (NTRS)

    Tanimoto, Toshiro

    2001-01-01

    The objectives of this study were to: (1) understand the phenomenon of continuous free oscillations of the Earth and (2) examine the idea of using this phenomenon for planetary seismology. We first describe the results on (1) and present our evaluations of the idea (2) in the final section. In 1997, after almost forty years since the initial attempt by Benioff et al, continuous free oscillations of the Earth were discovered. Spheroidal fundamental modes between 2 and 7 millihertz are excited continuously with acceleration amplitudes of about 0.3-0.5 nanogals. The signal is now commonly found in virtually all data recorded by STS-1 type broadband seismometers at quiet sites. Seasonal variation in amplitude and the existence of two coupled modes between the atmosphere and the solid Earth support that these oscillations are excited by the atmosphere. Stochastic excitation due to atmospheric turbulence is a favored mechanism, providing a good match between theory and data. The atmosphere has ample energy to support this theory because excitation of these modes require only 500-10000 W whereas the atmosphere contains about 117 W of kinetic energy. An application of this phenomenon includes planetary seismology, because other planets may be oscillating due to atmospheric excitation. The interior structure of planets could be learned by determining the eigenfrequencies in the continuous free oscillations. It is especially attractive to pursue this idea for tectonically quiet planets, since quakes may be too infrequent to be recorded by seismic instruments.

  20. Instantaneous normal modes and the protein glass transition.

    PubMed

    Schulz, Roland; Krishnan, Marimuthu; Daidone, Isabella; Smith, Jeremy C

    2009-01-01

    In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at approximately 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition. PMID:19167298

  1. Instantaneous Normal Modes and the Protein Glass Transition

    SciTech Connect

    Schultz, Roland; Krishnan, Marimuthu; Daidone, Isabella; Smith, Jeremy C

    2009-01-01

    In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.

  2. WEBnm@: a web application for normal mode analyses of proteins

    PubMed Central

    Hollup, Siv Midtun; Salensminde, Gisle; Reuter, Nathalie

    2005-01-01

    Background Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. Results We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on . We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. Conclusion We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains. PMID:15762993

  3. A Normal Mode Perspective of Intrinsic Ocean-Climate Variability

    NASA Astrophysics Data System (ADS)

    Dijkstra, Henk

    2016-01-01

    Observations of the sea surface temperature field over more than a century indicate that there is pronounced variability in the climate system. Understanding the mechanisms of this variability is crucial to determine the role of variations in ocean heat content in past and future climate changes. When a steady background state in an ocean-climate model is slightly perturbed, the long-time response is determined by the spatial patterns of the normal modes. Here, the type and patterns of normal modes for a range of different equilibrium states in a hierarchy of ocean-climate models are reviewed. The rather elegant organization of these normal modes is demonstrated, and prototype physical mechanisms explaining patterns of sea surface temperature variability based on these normal modes are provided.

  4. High-Frequency Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2009-01-01

    Acoustic measurements made using compressional-wave (P-wave) and shear-wave (S-wave) transducers in aluminum cylinders reveal waveform features with high amplitudes and with velocities that depend on the feature's dominant frequency. In a given waveform, high-frequency features generally arrive earlier than low-frequency features, typical for normal mode propagation. To analyze these waveforms, the elastic equation is solved in a cylindrical coordinate system for the high-frequency case in which the acoustic wavelength is small compared to the cylinder geometry, and the surrounding medium is air. Dispersive P- and S-wave normal mode propagations are predicted to exist, but owing to complex interference patterns inside a cylinder, the phase and group velocities are not smooth functions of frequency. To assess the normal mode group velocities and relative amplitudes, approximate dispersion relations are derived using Bessel functions. The utility of the normal mode theory and approximations from a theoretical and experimental standpoint are demonstrated by showing how the sequence of P- and S-wave normal mode arrivals can vary between samples of different size, and how fundamental normal modes can be mistaken for the faster, but significantly smaller amplitude, P- and S-body waves from which P- and S-wave speeds are calculated.

  5. Universal spectrum of normal modes in low-temperature glasses.

    PubMed

    Franz, Silvio; Parisi, Giorgio; Urbani, Pierfrancesco; Zamponi, Francesco

    2015-11-24

    We report an analytical study of the vibrational spectrum of the simplest model of jamming, the soft perceptron. We identify two distinct classes of soft modes. The first kind of modes are related to isostaticity and appear only in the close vicinity of the jamming transition. The second kind of modes instead are present everywhere in the glass phase and are related to the hierarchical structure of the potential energy landscape. Our results highlight the universality of the spectrum of normal modes in disordered systems, and open the way toward a detailed analytical understanding of the vibrational spectrum of low-temperature glasses. PMID:26561585

  6. Universal spectrum of normal modes in low-temperature glasses

    PubMed Central

    Franz, Silvio; Parisi, Giorgio; Urbani, Pierfrancesco; Zamponi, Francesco

    2015-01-01

    We report an analytical study of the vibrational spectrum of the simplest model of jamming, the soft perceptron. We identify two distinct classes of soft modes. The first kind of modes are related to isostaticity and appear only in the close vicinity of the jamming transition. The second kind of modes instead are present everywhere in the glass phase and are related to the hierarchical structure of the potential energy landscape. Our results highlight the universality of the spectrum of normal modes in disordered systems, and open the way toward a detailed analytical understanding of the vibrational spectrum of low-temperature glasses. PMID:26561585

  7. Normal modes of prion proteins: from native to infectious particle.

    PubMed

    Samson, Abraham O; Levitt, Michael

    2011-03-29

    Prion proteins (PrP) are the infectious agent in transmissible spongiform encephalopathies (i.e., mad cow disease). To be infectious, prion proteins must undergo a conformational change involving a decrease in α-helical content along with an increase in β-strand content. This conformational change was evaluated by means of elastic normal modes. Elastic normal modes show a diminution of two α-helices by one and two residues, as well as an extension of two β-strands by three residues each, which could instigate the conformational change. The conformational change occurs in a region that is compatible with immunological studies, and it is observed more frequently in mutant prions that are prone to conversion than in wild-type prions because of differences in their starting structures, which are amplified through normal modes. These findings are valuable for our comprehension of the conversion mechanism associated with the conformational change in prion proteins. PMID:21338080

  8. Refinement of protein dynamic structure: normal mode refinement.

    PubMed Central

    Kidera, A; Go, N

    1990-01-01

    An x-ray crystallographic refinement method, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the effective normal modes whose amplitudes and eigenvectors are experimentally determined by the crystallographic refinement. In contrast to the conventional method, the atomic motions are treated generally as anisotropic and concerted. This method is assessed by using the simulated x-ray data given by a Monte Carlo simulation of human lysozyme. In this article, we refine the dynamic structure by fixing the average static structure to exact coordinates. It is found that the normal mode refinement, using a smaller number of variables, gives a better R factor and more information on the dynamics (anisotropy and collectivity in the motion). Images PMID:2339115

  9. Normal Modes of Prion Proteins: From Native to Infectious particle◊

    PubMed Central

    Samson, Abraham O.; Levitt, Michael

    2011-01-01

    Prion proteins (PrP) are the infectious agent in transmissible spongiform encephalopathies (i.e. mad cow disease). To be infectious, prion proteins must undergo a conformational change involving a decrease of α-helical content along with an increase of β-strand structure. This conformational change was evaluated by means of elastic normal modes. Elastic normal modes show a diminution of two α-helices by one and two residues, as well as an extension of two β-strands by three residues each which could instigate the conformational change. The conformational change occurs in a region that is compatible with immunological studies, and it is observed more frequently in mutant prions which are prone to conversion, than in WT prions due to differences in their starting structures, which are amplified through normal modes. These findings are valuable for our comprehension of the conversion mechanism associated with the conformational change of prion proteins. PMID:21338080

  10. Mean flow generation mechanism by inertial waves and normal modes

    NASA Astrophysics Data System (ADS)

    Will, Andreas; Ghasemi, Abouzar

    2016-04-01

    The mean flow generation mechanism by nonlinearity of the inertial normal modes and inertial wave beams in a rotating annular cavity with longitudinally librating walls in stable regime is discussed. Inertial normal modes (standing waves) are excited when libration frequency matches eigenfrequencies of the system. Inertial wave beams are produced by Ekman pumping and suction in a rotating cylinder and form periodic orbits or periodic ray trajectories at selected frequencies. Inertial wave beams emerge as concentrated shear layers in a librating annular cavity, while normal modes appear as global recirculation cells. Both (inertial wave beam and mode) are helical and thus intrinsically non-linear flow structures. No second mode or wave is necessary for non-linearity. We considered the low order normal modes (1,1), (2,1) and (2,2) which are expected to be excited in the planetary objects and investigate the mean flow generation mechanism using two independent solutions: 1) analytical solution (Borcia 2012) and 2) the wave component of the flow (ω0 component) obtained from the direct numerical simulation (DNS). It is well known that a retrograde bulk mean flow is generated by the Ekman boundary layer and E1/4-Stewartson layer close to the outer cylinder side wall due to libration. At and around the normal mode resonant frequencies we found additionally a prograde azimuthal mean flow (Inertial Normal Mode Mean Flow: INMMF) in the bulk of the fluid. The fluid in the bulk is in geostrophic balance in the absence of the inertial normal modes. However, when INMMF is excited, we found that the geostrophic balance does not hold in the region occupied by INMMF. We hypothesize that INMMF is generated by the nonlinearity of the normal modes or by second order effects. Expanding the velocity {V}(u_r,u_θ,u_z) and pressure (p) in a power series in ɛ (libration amplitude), the Navier-Stokes equations are segregated into the linear and nonlinear parts at orders ɛ1 and ɛ^2

  11. Nonlinear normal modes modal interactions and isolated resonance curves

    DOE PAGESBeta

    Kuether, Robert J.; Renson, L.; Detroux, T.; Grappasonni, C.; Kerschen, G.; Allen, M. S.

    2015-05-21

    The objective of the present study is to explore the connection between the nonlinear normal modes of an undamped and unforced nonlinear system and the isolated resonance curves that may appear in the damped response of the forced system. To this end, an energy balance technique is used to predict the amplitude of the harmonic forcing that is necessary to excite a specific nonlinear normal mode. A cantilever beam with a nonlinear spring at its tip serves to illustrate the developments. Furthermore, the practical implications of isolated resonance curves are also discussed by computing the beam response to sine sweepmore » excitations of increasing amplitudes.« less

  12. Nonlinear normal modes modal interactions and isolated resonance curves

    SciTech Connect

    Kuether, Robert J.; Renson, L.; Detroux, T.; Grappasonni, C.; Kerschen, G.; Allen, M. S.

    2015-05-21

    The objective of the present study is to explore the connection between the nonlinear normal modes of an undamped and unforced nonlinear system and the isolated resonance curves that may appear in the damped response of the forced system. To this end, an energy balance technique is used to predict the amplitude of the harmonic forcing that is necessary to excite a specific nonlinear normal mode. A cantilever beam with a nonlinear spring at its tip serves to illustrate the developments. Furthermore, the practical implications of isolated resonance curves are also discussed by computing the beam response to sine sweep excitations of increasing amplitudes.

  13. Numerical computation of nonlinear normal modes in mechanical engineering

    NASA Astrophysics Data System (ADS)

    Renson, L.; Kerschen, G.; Cochelin, B.

    2016-03-01

    This paper reviews the recent advances in computational methods for nonlinear normal modes (NNMs). Different algorithms for the computation of undamped and damped NNMs are presented, and their respective advantages and limitations are discussed. The methods are illustrated using various applications ranging from low-dimensional weakly nonlinear systems to strongly nonlinear industrial structures.

  14. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  15. Nonlinear normal modes in electrodynamic systems: A nonperturbative approach

    NASA Astrophysics Data System (ADS)

    Kudrin, A. V.; Kudrina, O. A.; Petrov, E. Yu.

    2016-06-01

    We consider electromagnetic nonlinear normal modes in cylindrical cavity resonators filled with a nonlinear nondispersive medium. The key feature of the analysis is that exact analytic solutions of the nonlinear field equations are employed to study the mode properties in detail. Based on such a nonperturbative approach, we rigorously prove that the total energy of free nonlinear oscillations in a distributed conservative system, such as that considered in our work, can exactly coincide with the sum of energies of the normal modes of the system. This fact implies that the energy orthogonality property, which has so far been known to hold only for linear oscillations and fields, can also be observed in a nonlinear oscillatory system.

  16. User's manual for the coupled mode version of the normal modes rotor aeroelastic analysis computer program

    NASA Technical Reports Server (NTRS)

    Bergquist, R. R.; Carlson, R. G.; Landgrebe, A. J.; Egolf, T. A.

    1974-01-01

    This User's Manual was prepared to provide the engineer with the information required to run the coupled mode version of the Normal Modes Rotor Aeroelastic Analysis Computer Program. The manual provides a full set of instructions for running the program, including calculation of blade modes, calculations of variable induced velocity distribution and the calculation of the time history of the response for either a single blade or a complete rotor with an airframe (the latter with constant inflow).

  17. Dispersion correction and identification of ocean acoustic normal modes

    NASA Astrophysics Data System (ADS)

    Poplawski, James Edward

    1998-08-01

    The average temperature of the ocean can be determined by measuring the traveltimes of acoustic signals from a source to a receiver. In the temperate deep ocean, a narrow acoustic pulse transmitted from a source results in a reception at long ranges consisting of many (possibly overlapping) arrivals. One of the mathematical structures used to describe and interpret acoustic propagation in the ocean is normal mode theory. The identification of individual normal mode arrivals in a reception is difficult because modal arrivals are spread in time by geometric dispersion causing them to overlap and interfere with each other. Current signal processing methods aimed at identifying individual normal mode arrivals require the use of vertical arrays of receivers which are rare because they are very expensive to build and deploy. A new signal processing method using phase-only filters to compensate for the geometric dispersion of normal mode arrivals is presented. This compensation increases the peak signal to noise ratio of the individual modal arrivals while simultaneously compressing them in time, helping to isolate them and their arrival times from overlapping neighbors. The properties of the phase-only filters and their ability to help isolate and identify modal arrivals is investigated through the processing of computer simulated receptions. By processing a reception with a bank of phase-only filters characterized by different amounts of dispersion compensation, a plot dubbed the Dispersion Diagnostic (DD) Display is generated. The use of phase-only filters does not require vertical arrays of receivers because modal phase is constant across depth. DD Displays generated for a reception from a receiver at a single depth show compressed modes which are isolated from their neighbors and for which traveltimes can be determined. Thus, the dispersion processing opens up the use of horizontal arrays or single hydrophones in mode identification, broadening the capabilities of

  18. A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

    NASA Astrophysics Data System (ADS)

    Copperman, Jeremy; Romano, Pablo; Guenza, Marina

    2014-03-01

    We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

  19. S-Wave Normal Mode Propagation in Aluminum Cylinders

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2010-01-01

    Large amplitude waveform features have been identified in pulse-transmission shear-wave measurements through cylinders that are long relative to the acoustic wavelength. The arrival times and amplitudes of these features do not follow the predicted behavior of well-known bar waves, but instead they appear to propagate with group velocities that increase as the waveform feature's dominant frequency increases. To identify these anomalous features, the wave equation is solved in a cylindrical coordinate system using an infinitely long cylinder with a free surface boundary condition. The solution indicates that large amplitude normal-mode propagations exist. Using the high-frequency approximation of the Bessel function, an approximate dispersion relation is derived. The predicted amplitude and group velocities using the approximate dispersion relation qualitatively agree with measured values at high frequencies, but the exact dispersion relation should be used to analyze normal modes for full ranges of frequency of interest, particularly at lower frequencies.

  20. Normal-mode splitting with large collective cooperativity

    SciTech Connect

    Tuchman, A. K.; Long, R.; Vrijsen, G.; Boudet, J.; Lee, J.; Kasevich, M. A.

    2006-11-15

    We report the observation of normal-mode splitting of the atom-cavity dressed states in both the fluorescence and transmission spectra for large atom number and observe subnatural linewidths in this regime. We also implement a method of utilizing the normal-mode splitting to observe Rabi oscillations on the {sup 87}Rb ground state hyperfine clock transition. We demonstrate a large collective cooperativity, C=1.2x10{sup 4}, which, in combination with large atom number, N{approx}2x10{sup 5}, offers the potential to realize an absolute phase sensitivity better than that achieved by state-of-the-art atomic fountain clocks or inertial sensors operating near the quantum projection noise limit.

  1. A High Resolution Normal Mode Solution of Japan Sea

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Satake, K.

    2014-12-01

    Normal mode calculation of a semi-closed or completely closed bay or ocean basin helps us to understand the oscillation characteristics including those excited by incoming tsunamis. In addition, tsunami propagation can be synthesized by superposition of normal modes. Japan Sea is an almost closed ocean basin where many large tsunamigenic earthquakes occurred (fig. 1). Satake and Shimazaki (1988) calculated the normal modes using a 20km grid (~10' or about 2,000 ocean grids), compared the observed and calculated normal modes from the 1964 Niigata and 1983 Japan Sea earthquakes, and discussed the their different excitation characteristics . Because of development of computer and numerical computation techniques, it is worthwhile to revisit this problem. Starting from Laplace's tidal equations and ignoring the rotation of the earth, Loomis (1975) discretized the problem into the eigenvalue problem of a symmetric sparse matrix, which was solved by Householder transformations. This method is used by Satake and Shimazaki (1988) for Japan Sea and Aida (1996) for Tokyo Bay. However, this method needs O(n^3) operation in time and O(n^2) in memory (n is the total number of water grid. e.g., for Japan Sea in 30 sec grid, n~10^6), which would require a super computer.To overcome this disadvantage, we first introduce a recent iteration method called Implicitly Restarted Arnoldi Method (Lehoucq et al., 1997), which itself speeds up the calculation a bit. Then after we develop a sparse version of matrix storage and multiplication, the operation count in time and memory reduced dramatically to O(n^1.5) (including about 0.5 for iteration process) and O(n) respectively, utilizing the special property of the matrix and the iteration method. This means any current computer can easily solve a large eigenvalue problem. Earthquakes.png

  2. Symmetry classification of the degenerate vibrational normal modes of ethane

    NASA Astrophysics Data System (ADS)

    Lattanzi, F.; di Lauro, C.; Legay-Sommaire, N.

    1992-11-01

    We determine the G36(EM) (usually called G 36†) symmetry species of all the degenerate vibrational normal modes of ethane unambiguously. We are able to do this as a result of observing the K-dependence of the sign of the energy separation between the torsionally split levels of ν4 + νy combination states, where ν4 is the torsion and νy ⊂ Eg of D3 d, and by observing the lack of any intrinsic torsional splitting or broadening in the νx fundamentals and hot ( ν4 + νx) - ν4 transitions ( νx ⊂ Eu of D3 d). It is found that in C 2H 6 all the Eu normal modes of D3 d correlate with E1 d of G36(EM) (and hence E' of D3 h), and all the Eg normal modes of D3 d correlate with E1 d of G36(EM) (and hence E″ of D3 h). High-resolution Q branches of ν8, ν4 + ν12, and ( ν4 + ν8) - ν4 of C 2H 6 are shown as illustrations.

  3. Normal Modes of Magnetized Finite Two-Dimensional Yukawa Crystals

    NASA Astrophysics Data System (ADS)

    Marleau, Gabriel-Dominique; Kaehlert, Hanno; Bonitz, Michael

    2009-11-01

    The normal modes of a finite two-dimensional dusty plasma in an isotropic parabolic confinement, including the simultaneous effects of friction and an external magnetic field, are studied. The ground states are found from molecular dynamics simulations with simulated annealing, and the influence of screening, friction, and magnetic field on the mode frequencies is investigated in detail. The two-particle problem is solved analytically and the limiting cases of weak and strong magnetic fields are discussed.[4pt] [1] C. Henning, H. K"ahlert, P. Ludwig, A. Melzer, and M.Bonitz. J. Phys. A 42, 214023 (2009)[2] B. Farokhi, M. Shahmansouri, and P. K. Shukla. Phys.Plasmas 16, 063703 (2009)[3] L. Cândido, J.-P. Rino, N. Studart, and F. M. Peeters. J. Phys.: Condens. Matter 10, 11627--11644 (1998)

  4. The normal modes of lattice vibrations of ice XI

    PubMed Central

    Zhang, Peng; Wang, Zhe; Lu, Ying-Bo; Ding, Zheng-Wen

    2016-01-01

    The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229 cm−1 and 310 cm−1 is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder. PMID:27375199

  5. The normal modes of lattice vibrations of ice XI

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Wang, Zhe; Lu, Ying-Bo; Ding, Zheng-Wen

    2016-07-01

    The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229 cm‑1 and 310 cm‑1 is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder.

  6. The normal modes of lattice vibrations of ice XI.

    PubMed

    Zhang, Peng; Wang, Zhe; Lu, Ying-Bo; Ding, Zheng-Wen

    2016-01-01

    The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229 cm(-1) and 310 cm(-1) is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder. PMID:27375199

  7. Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding

    SciTech Connect

    Mortisugu, Kei; Njunda, Brigitte; Smith, Jeremy C

    2009-12-01

    The change of protein vibrations on ligand binding is of functional and thermodynamic importance. Here, this process is characterized using a simple analytical 'ball-and-spring' model and all-atom normal-mode analysis (NMA) of the binding of the cancer drug, methotrexate (MTX) to its target, dihydrofolate reductase (DHFR). The analytical model predicts that the coupling between protein vibrations and ligand external motion generates entropy-rich, low-frequency vibrations in the complex. This is consistent with the atomistic NMA which reveals vibrational softening in forming the DHFR-MTX complex, a result also in qualitative agreement with neutron-scattering experiments. Energy minimization of the atomistic bound-state (B) structure while gradually decreasing the ligand interaction to zero allows the generation of a hypothetical 'intermediate' (I) state, without the ligand force field but with a structure similar to that of B. In going from I to B, it is found that the vibrational entropies of both the protein and MTX decrease while the complex structure becomes enthalpically stabilized. However, the relatively weak DHFR:MTX interaction energy results in the net entropy gain arising from coupling between the protein and MTX external motion being larger than the loss of vibrational entropy on complex formation. This, together with the I structure being more flexible than the unbound structure, results in the observed vibrational softening on ligand binding.

  8. DNA nanotube formation based on normal mode analysis

    NASA Astrophysics Data System (ADS)

    Qian, PengFei; Seo, Sangjae; Kim, Junghoon; Kim, Seungjae; Lim, Byeong Soo; Liu, Wing Kam; Kim, Bum Joon; LaBean, Thomas Henry; Park, Sung Ha; Kim, Moon Ki

    2012-03-01

    Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in the absence of which they roll up to form 3D nanotube structures. Here we present a theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices. Coarse-grained normal mode analysis of single and multiple cross tiles within the elastic network model was carried out to expound the vibration modes of the systems. While both single and multiple cross tile simulations produce results conducive to tube formations, the dominant modes of a unit of four cross tiles (one square cavity), termed a quadruplet, fully reflect the symmetries of the actual nanotubes found in experiments and firmly endorse circularization of an array of cross tiles.

  9. Antiport Mechanism for Cl−/H+ in ClC-ec1 from Normal-Mode Analysis

    PubMed Central

    Miloshevsky, Gennady V.; Hassanein, Ahmed; Jordan, Peter C.

    2010-01-01

    ClC chloride channels and transporters play major roles in cellular excitability, epithelial salt transport, volume, pH, and blood pressure regulation. One family member, ClC-ec1 from Escherichia coli, has been structurally resolved crystallographically and subjected to intensive mutagenetic, crystallographic, and electrophysiological studies. It functions as a Cl−/H+ antiporter, not a Cl− channel; however, the molecular mechanism for Cl−/H+ exchange is largely unknown. Using all-atom normal-mode analysis to explore possible mechanisms for this antiport, we propose that Cl−/H+ exchange involves a conformational cycle of alternating exposure of Cl− and H+ binding sites of both ClC pores to the two sides of the membrane. Both pores switch simultaneously from facing outward to facing inward, reminiscent of the standard alternating-access mechanism, which may have direct implications for eukaryotic Cl−/H+ transporters and Cl− channels. PMID:20303857

  10. [Raman, FTIR spectra and normal mode analysis of acetanilide].

    PubMed

    Liang, Hui-Qin; Tao, Ya-Ping; Han, Li-Gang; Han, Yun-Xia; Mo, Yu-Jun

    2012-10-01

    The Raman and FTIR spectra of acetanilide (ACN) were measured experimentally in the regions of 3 500-50 and 3 500-600 cm(-1) respectively. The equilibrium geometry and vibration frequencies of ACN were calculated based on density functional theory (DFT) method (B3LYP/6-311G(d, p)). The results showed that the theoretical calculation of molecular structure parameters are in good agreement with previous report and better than the ones calculated based on 6-31G(d), and the calculated frequencies agree well with the experimental ones. Potential energy distribution of each frequency was worked out by normal mode analysis, and based on this, a detailed and accurate vibration frequency assignment of ACN was obtained. PMID:23285870

  11. Generalized theory of helicon waves. I. Normal modes

    SciTech Connect

    Chen, F.F.; Arnush, D.

    1997-09-01

    The theory of helicon waves is extended to include finite electron mass. This introduces an additional branch to the dispersion relation that is essentially an electron cyclotron or Trivelpiece{endash}Gould (TG) wave with a short radial wavelength. The effect of the TG wave is expected to be important only for low dc magnetic fields and long parallel wavelengths. The normal modes at low fields are mixtures of the TG wave and the usual helicon wave and depend on the nature of the boundaries. Computations show, however, that since the TG waves are damped near the surface of the plasma, the helicon wave at high fields is almost exactly the same as is found when the electron mass is neglected. {copyright} {ital 1997 American Institute of Physics.}

  12. Instrumental evidence of normal mode rock slope vibration

    NASA Astrophysics Data System (ADS)

    Burjánek, Jan; Moore, Jeffrey R.; Yugsi Molina, Freddy X.; Fäh, Donat

    2012-02-01

    A unique field experiment was performed to constrain the seismic response of a large, potentially unstable rock slope in the southern Swiss Alps. Small-aperture seismic arrays were deployed to record ambient vibrations both inside and outside of the mapped instability boundary. The recordings were analysed by means of the high-resolution f-k method, site-to-reference spectral ratios and time-frequency dependent polarization analysis. All three methods indicated that the wavefield within the potentially unstable rock mass is dominated by normal mode motion (standing waves) rather than horizontal propagation of seismic waves. Both fundamental frequency and relative amplification could be recovered from ambient noise data. The observed amplification is strongly directional, and the maximum amplification is oriented perpendicular to open tension cracks mapped at the ground surface. Our results highlight site response characteristics relevant for analysis of earthquake-triggered rock slope failures.

  13. Vibrational dynamics of vocal folds using nonlinear normal modes.

    PubMed

    Pinheiro, Alan P; Kerschen, Gaëtan

    2013-08-01

    Many previous works involving physical models, excised and in vivo larynges have pointed out nonlinear vibration in vocal folds during voice production. Moreover, theoretical studies involving mechanical modeling of these folds have tried to gain a profound understanding of the observed nonlinear phenomena. In this context, the present work uses the nonlinear normal mode theory to investigate the nonlinear modal behavior of 16 subjects using a two-mass mechanical modeling of the vocal folds. The free response of the conservative system at different energy levels is considered to assess the impact of the structural nonlinearity of the vocal fold tissues. The results show very interesting and complex nonlinear phenomena including frequency-energy dependence, subharmonic regimes and, in some cases, modal interactions, entrainment and bifurcations. PMID:23218815

  14. iMODS: internal coordinates normal mode analysis server

    PubMed Central

    López-Blanco, José Ramón; Aliaga, José I.; Quintana-Ortí, Enrique S.; Chacón, Pablo

    2014-01-01

    Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. PMID:24771341

  15. Revealing short-period normal modes of the atmosphere

    NASA Astrophysics Data System (ADS)

    Shved, G. M.; Ermolenko, S. I.; Hoffmann, P.

    2015-09-01

    Barometer and seismometer measurements at Collm, Germany (51.3° N, 13.0° E) for all of 2002 are used to search for atmospheric normal modes (ANMs) in the frequency range 50-310 µHz. The measurements are spectrally analyzed using a 5-day window sliding along the 1-year series with a 1-day step. The subsequent analysis follows two procedures: (a) revealing features in the frequency distribution of the number of statistically significant spectral peaks in histograms built on the basis of these spectra and (b) calculating the multiplication spectra for the raw spectra. The two procedures yield the same result for the two instruments, i.e., reveal a periodicity in the clustering of atmospheric modes on the frequency axis with a period of ˜6 µHz. The fact that this period is close to 7 μHz, which is predicted by the crude theory of gravity—inertia ANMs [3] for their frequency distribution, suggests that ANMs are generated down to as small a period as ˜1 h.

  16. "Good Vibrations": A workshop on oscillations and normal modes

    NASA Astrophysics Data System (ADS)

    Barbieri, Sara; Carpineti, Marina; Giliberti, Marco; Rigon, Enrico; Stellato, Marco; Tamborini, Marina

    2016-05-01

    We describe some theatrical strategies adopted in a two hour workshop in order to show some meaningful experiments and the underlying useful ideas to describe a secondary school path on oscillations, that develops from harmonic motion to normal modes of oscillations, and makes extensive use of video analysis, data logging, slow motions and applet simulations. Theatre is an extremely useful tool to stimulate motivation starting from positive emotions. That is the reason why the theatrical approach to the presentation of physical themes has been explored by the group "Lo spettacolo della Fisica" (http://spettacolo.fisica.unimi.it) of the Physics Department of University of Milano for the last ten years (Carpineti et al., JCOM, 10 (2011) 1; Nuovo Cimento B, 121 (2006) 901) and has been inserted also in the European FP7 Project TEMI (Teaching Enquiry with Mysteries Incorporated, see http://teachingmysteries.eu/en) which involves 13 different partners coming from 11 European countries, among which the Italian (Milan) group. According to the TEMI guidelines, this workshop has a written script based on emotionally engaging activities of presenting mysteries to be solved while participants have been involved in nice experiments following the developed path.

  17. Antidepressants Normalize the Default Mode Network in Patients With Dysthymia

    PubMed Central

    Posner, Jonathan; Hellerstein, David J.; Gat, Inbal; Mechling, Anna; Klahr, Kristin; Wang, Zhishun; McGrath, Patrick J.; Stewart, Jonathan W.; Peterson, Bradley S.

    2014-01-01

    Importance The default mode network (DMN) is a collection of brain regions that reliably deactivate during goal-directed behaviors and is more active during a baseline, or so-called resting, condition. Coherence of neural activity, or functional connectivity, within the brain’s DMN is increased in major depressive disorder relative to healthy control (HC) subjects; however, whether similar abnormalities are present in persons with dysthymic disorder (DD) is unknown. Moreover, the effect of antidepressant medications on DMN connectivity in patients with DD is also unknown. Objective To use resting-state functional-connectivity magnetic resonance imaging (MRI) to study (1) the functional connectivity of the DMN in subjects with DD vs HC participants and (2) the effects of antidepressant therapy on DMN connectivity. Design After collecting baseline MRI scans from subjects with DD and HC participants, we enrolled the participants with DD into a 10-week prospective, double-blind, placebo-controlled trial of duloxetine and collected MRI scans again at the conclusion of the study. Enrollment occurred between 2007 and 2011. Setting University research institute. Participants Volunteer sample of 41 subjects with DD and 25 HC participants aged 18 to 53 years. Control subjects were group matched to patients with DD by age and sex. Main Outcome Measures We used resting-state functional-connectivity MRI to measure the functional connectivity of the brain’s DMN in persons with DD compared with HC subjects, and we examined the effects of treatment with duloxetine vs placebo on DMN connectivity. Results Of the 41 subjects with DD, 32 completed the clinical trial and MRI scans, along with the 25 HC participants. At baseline, we found that the coherence of neural activity within the brain’s DMN was greater in persons with DD compared with HC subjects. Following a 10-week clinical trial, we found that treatment with duloxetine, but not placebo, normalized DMN connectivity

  18. Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations.

    PubMed

    Nicolaï, Adrien; Senet, Patrick; Delarue, Patrice; Ripoll, Daniel R

    2010-08-10

    The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is known. Here, we report two models of human Hsp70, constructed by homology with Saccharomyces cerevisiae cochaperone protein Hsp110 (open model) and with Escherichia coli 70 kDa DnaK (closed model) and relaxed for several tens to hundreds of nanoseconds by using all-atom molecular dynamics simulations in explicit solvent. We obtain two stable states, Hsp70 with SBD open and SBD closed, which agree with experimental and structural information for ATP-Hsp70 and ADP-Hsp70, respectively. The dynamics of the transition from the open to closed states is investigated with a coarse-grained model and normal-mode analysis. The results show that the conformational change between the two states can be represented by a relatively small number of collective modes which involved major conformational changes in the two domains. These modes provide a mechanistic representation of the communication between NBD and SBD and allow us to identify subdomains and residues that appear to have a critical role in the conformational change mechanism that guides the chaperoning cycle of Hsp70. PMID:26613502

  19. A comparative study of the normal modes of various modern bells

    NASA Astrophysics Data System (ADS)

    Perrin, R.; Charnley, T.

    1987-09-01

    Finite element calculations of the normal modes of church, carillon, hand and fire-alarm bells have been made. Some of the results are presented and comparisons made which shed new light on mode classification.

  20. Confinement-induced differences between dielectric normal modes and segmental modes of an ion-conducting polymer.

    PubMed

    Kojio, K; Jeon, S; Granick, S

    2002-05-01

    Dielectric measurement in the range 0.1 Hz to 1 MHz were used to study the motions of polymers and ions in an ion-conducting polymer, polypropylene oxide containing small quantities (on the order of 1%) of lithium ions (LiClO(4)), confined as a sandwich of uniform thickness between parallel insulating mica surfaces. In the dielectric loss spectrum, we observed three peaks; they originated from the normal mode of the polymer, segmental mode of the polymer, and ion motions. With decreasing film thickness, the peak frequencies corresponding to the normal mode and ion motion shifted to lower frequencies, indicating retardation due to confinement above 30 nm. This was accompanied by diminished intensity of the dielectric normal-mode relaxation, suggesting that confinement diminished the fluctuations of the end-to-end vector of the chain dipole in the direction between the confining surfaces. On the contrary, the segmental mode was not affected at that thickness. Finally, significant retardation of the segmental mode was observed only for the thinnest film (14 nm). The different dynamical modes of the polymer (segmental and slowest normal modes) respond with different thickness and temperature dependence to confinement. PMID:15010966

  1. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  2. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    NASA Astrophysics Data System (ADS)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    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.

  3. Prufer Transformations for the Normal Modes in Ocean Acoustics

    SciTech Connect

    Baggeroer, Arthur B.

    2010-09-06

    In 1926 Prufer introduced a method of transforming the second order Sturm-Liouville (SL) equation into two nonlinear first order differential equations for the phase oe and ''magnitude'', |oe{sup 2}+oe{sup 2}| for a Poincare phase space representation, (oe,oe). The useful property is the phase equation decouples from the magnitude one which leads to a nonlinear, two point boundary value problem for the eigenvalues, or SL numbers. The transformation has been used both theoretically, e.g. Atkinson, [1960] to prove certain properties of SL equations as well as numerically e.g Bailey [1978]. This paper examines the utility of the Prufer transformation in the context of numerical solutions for modes of the ocean acoustic wave equation. (Its use is certainly not well known in the ocean acoustics community.) Equations for the phase, oe, and natural logarithm of the ''magnitude'', ln(|oe{sup 2}+oe{sup 2}|) lead to same decoupling and a fast and efficient numerical solution with the SL eigenvalues mapping to the horizontal wavenubers. The Prufer transformation has stabilty problems for low order modes at high frequecies, so a numerically stable method of integrating the phase equation is derived. This seems to be the first time the these stability issues have been highlighted to provide a robust algorthim for the modes.

  4. Prufer Transformations for the Normal Modes in Ocean Acoustics

    NASA Astrophysics Data System (ADS)

    Baggeroer, Arthur B.

    2010-09-01

    In 1926 Prufer introduced a method of transforming the second order Sturm-Liouville (SL) equation into two nonlinear first order differential equations for the phase o/ and "magnitude", |o/2+o/2| for a Poincare phase space representation, (o/,o/). The useful property is the phase equation decouples from the magnitude one which leads to a nonlinear, two point boundary value problem for the eigenvalues, or SL numbers. The transformation has been used both theoretically, e.g. Atkinson, [1960] to prove certain properties of SL equations as well as numerically e.g Bailey [1978]. This paper examines the utility of the Prufer transformation in the context of numerical solutions for modes of the ocean acoustic wave equation. (Its use is certainly not well known in the ocean acoustics community.) Equations for the phase, o/, and natural logarithm of the "magnitude", ln(|o/2+o/2|) lead to same decoupling and a fast and efficient numerical solution with the SL eigenvalues mapping to the horizontal wavenubers. The Prufer transformation has stabilty problems for low order modes at high frequecies, so a numerically stable method of integrating the phase equation is derived. This seems to be the first time the these stability issues have been highlighted to provide a robust algorthim for the modes.

  5. Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

    PubMed Central

    2013-01-01

    Background Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins. Methods This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics. Results Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path. Conclusions The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. PMID:24564964

  6. Electromagnetic fluctuations and normal modes of a drifting relativistic plasma

    SciTech Connect

    Ruyer, C.; Gremillet, L.; Bénisti, D.; Bonnaud, G.

    2013-11-15

    We present an exact calculation of the power spectrum of the electromagnetic fluctuations in a relativistic equilibrium plasma described by Maxwell-Jüttner distribution functions. We consider the cases of wave vectors parallel or normal to the plasma mean velocity. The relative contributions of the subluminal and supraluminal fluctuations are evaluated. Analytical expressions of the spatial fluctuation spectra are derived in each case. These theoretical results are compared to particle-in-cell simulations, showing a good reproduction of the subluminal fluctuation spectra.

  7. Echoes from anharmonic normal modes in model glasses.

    PubMed

    Burton, Justin C; Nagel, Sidney R

    2016-03-01

    Glasses display a wide array of nonlinear acoustic phenomena at temperatures T ≲ 1 K. This behavior has traditionally been explained by an ensemble of weakly coupled, two-level tunneling states, a theory that is also used to describe the thermodynamic properties of glasses at low temperatures. One of the most striking acoustic signatures in this regime is the existence of phonon echoes, a feature that has been associated with two-level systems with the same formalism as spin echoes in NMR. Here we report the existence of a distinctly different type of acoustic echo in classical models of glassy materials. Our simulations consist of finite-ranged, repulsive spheres and also particles with attractive forces using Lennard-Jones interactions. We show that these echoes are due to anharmonic, weakly coupled vibrational modes and perhaps provide an alternative explanation for the phonon echoes observed in glasses at low temperatures. PMID:27078434

  8. Normal force for static and steady shear mode in magnetorheological fluid

    NASA Astrophysics Data System (ADS)

    Liu, Xuhui; Ye, Dun; Gao, Xiaoli; Li, Fang; Sun, Meng; Zhang, Hui; Tu, Tiangang; Yu, Hao

    2016-01-01

    This paper presents the normal force phenomena for static and steady shear mode in magnetorheological (MR) fluid. The results of the study show that, in the static mode, with the magnetic flux density increasing, the normal force will increase until the maximum, and then reduce to a steady value, and during the increasing stage, it can be expressed as FN=4667*B2.48 approximately; however, in the steady shear mode, only when the magnetic flux density achieves a certain value, the normal force phenomena will be observed clearly, and with the increasing of magnetic field, the normal force reaches the maximum, and then also decreases to a steady value. Besides, by defining the time parameters of dynamic response, the dynamic response of normal force is studied. If the shear plate is stationary, from the magnetic field on to a stable normal force produced, the response time is about 25.11 ms.

  9. An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates.

    PubMed

    Sibaev, M; Crittenden, D L

    2016-06-01

    In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm(-1) in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/. PMID:27276945

  10. Computational aspects of the nonlinear normal mode initialization of the GLAS 4th order GCM

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S. C.; Takacs, L.

    1984-01-01

    Using the normal modes of the GLAS 4th Order Model, a Machenhauer nonlinear normal mode initialization (NLNMI) was carried out for the external vertical mode using the GLAS 4th Order shallow water equations model for an equivalent depth corresponding to that associated with the external vertical mode. A simple procedure was devised which was directed at identifying computational modes by following the rate of increase of BAL sub M, the partial (with respect to the zonal wavenumber m) sum of squares of the time change of the normal mode coefficients (for fixed vertical mode index) varying over the latitude index L of symmetric or antisymmetric gravity waves. A working algorithm is presented which speeds up the convergence of the iterative Machenhauer NLNMI. A 24 h integration using the NLNMI state was carried out using both Matsuno and leap-frog time-integration schemes; these runs were then compared to a 24 h integration starting from a non-initialized state. The maximal impact of the nonlinear normal mode initialization was found to occur 6-10 hours after the initial time.

  11. Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex.

    PubMed

    Téllez S, Claudio A; Costa, Anilton C; Mondragón, M A; Ferreira, Glaucio B; Versiane, O; Rangel, J L; Lima, G Müller; Martin, A A

    2016-12-01

    Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands. PMID:27344520

  12. An effective all-atom potential for proteins

    PubMed Central

    Irbäck, Anders; Mitternacht, Simon; Mohanty, Sandipan

    2009-01-01

    We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc PMID:19356242

  13. Normal modes in an overmoded circular waveguide coated with lossy material

    NASA Technical Reports Server (NTRS)

    Lee, C. S.; Lee, S. W.; Chuang, S. L.

    1985-01-01

    The normal modes in an overmoded waveguide coated with a lossy material are analyzed, particularly for their attenuation properties as a function of coating material, layer thickness, and frequency. When the coating material is not too lossy, the low-order modes are highly attenuated even with a thin layer of coating. This coated guide serves as a mode suppressor of the low-order modes, which can be particularly useful for reducing the radar cross section (RCS) of a cavity structure such as a jet inlet. When the coating material is very lossy, low-order modes fall into two distinct groups: highly and lowly attenuated modes. However, as a/lambda (a = radius of the cylinder; lambda = the free-space wavelength) increases, the separation between these two groups becomes less distinctive. The attenuation constants of most of the low-order modes become small, and decrease as a function of lambda sup 2/a sup 3.

  14. Normal forms for linear mode conversion and Landau-Zener transitions in one dimension

    SciTech Connect

    Flynn, W.G.; Littlejohn, R.G.

    1994-09-01

    Standard eikonal methods for the asymptotic analysis of coupled linear wave equations may fail when two eigenvalues of a matrix (the dispersion matrix) associated with the wave operator are both small in the same region of wave phase space. In this region the two eikonal modes associated with the two small eigenvalues are coupled, leading to a process called linear mode conversion or Landau-Zener coupling. A theory of linear mode conversion is presented in which geometric structure is emphasized. This theory is then used to identify the most generic type of mode conversion which occurs in one dimension. Finally, a general solution for this generic mode conversion problem is derived by transforming an arbitrary equation exhibiting generic mode conversion into an easily solvable normal form. This solution is given as a connection rule, with which one may continue standard eikonal wave solutions through mode conversion regions. 51 refs., 13 figs.

  15. Mode-locked dark pulse Kerr combs in normal-dispersion microresonators

    NASA Astrophysics Data System (ADS)

    Xue, Xiaoxiao; Xuan, Yi; Liu, Yang; Wang, Pei-Hsun; Chen, Steven; Wang, Jian; Leaird, Dan E.; Qi, Minghao; Weiner, Andrew M.

    2015-09-01

    The generation of Kerr frequency combs in a coherently driven nonlinear microresonator is now extensively investigated more generally by the research community as a potentially portable technology for a variety of applications. Here, we report experiments in which dark pulse combs are formed in normal-dispersion microresonators with mode-interaction-assisted excitation, and mode-locking transitions are observed in the normal-dispersion regime. The mode-interaction-aided excitation of dark pulses appears to occur through a deterministic pathway, in sharp contrast to the situation for bright pulses in the anomalous dispersion region. The ability to mode-lock in the normal-dispersion regime increases the freedom in the microresonator design and may make it possible to extend Kerr comb generation into the visible, where material dispersion is likely to dominate.

  16. Normal modes of the world's oceans: A numerical investigation using Proudman functions

    NASA Technical Reports Server (NTRS)

    Sanchez, Braulio V.; Morrow, Dennis

    1993-01-01

    The numerical modeling of the normal modes of the global oceans is addressed. The results of such modeling could be expected to serve as a guide in the analysis of observations and measurements intended to detect these modes. The numerical computation of normal modes of the global oceans is a field in which several investigations have obtained results during the past 15 years. The results seem to be model-dependent to an unsatisfactory extent. Some modeling areas, such as higher resolution of the bathymetry, inclusion of self-attraction and loading, the role of the Arctic Ocean, and systematic testing by means of diagnostic models are addressed. The results show that the present state of the art is such that a final solution to the normal mode problem still lies in the future. The numerical experiments show where some of the difficulties are and give some insight as to how to proceed in the future.

  17. Vertical normal modes of human ears: Individual variation and frequency estimation from pinna anthropometry.

    PubMed

    Mokhtari, Parham; Takemoto, Hironori; Nishimura, Ryouichi; Kato, Hiroaki

    2016-08-01

    Beyond the first peak of head-related transfer functions or pinna-related transfer functions (PRTFs) human pinnae are known to have two normal modes with "vertical" resonance patterns, involving two or three pressure anti-nodes in cavum, cymba, and fossa. However, little is known about individual variations in these modes, and there is no established model for estimating their center-frequencies from anthropometry. Here, with geometries of 38 pinnae measured, PRTFs were calculated and vertical modes visualized by numerical simulation. Most pinnae were found to have both Cavum-Fossa and Cavum-Cymba modes, with opposite-phase anti-nodes in cavum and either fossa or cymba, respectively. Nevertheless in both modes, fossa involvement varied substantially across pinnae, dependent on scaphoid fossa depth and cymba shallowness. Linear regression models were evaluated in mode frequency estimation, with 3322 measures derived from 31 pinna landmarks. The Cavum-Fossa normal mode frequency was best estimated [correlation coefficient r = 0.89, mean absolute error (MAE) = 257 Hz or 4.4%] by the distance from canal entrance to helix rim, and cymba horizontal depth. The Cavum-Cymba normal mode frequency was best estimated (r = 0.92, MAE = 247 Hz or 3.2%) by the sagittal-plane distance from concha floor to cymba anterior wall, and cavum horizontal depth. PMID:27586714

  18. Rossby normal modes in nonuniform background configurations. I Simple fields. II - Equinox and solstice conditions

    NASA Technical Reports Server (NTRS)

    Salby, M. L.

    1981-01-01

    An investigation is conducted regarding the influence of mean field variations on the realization of planetary normal modes, taking into account the mode response and structure in the presence of simple background nonuniformities. It is found that mean field variations have the combined effect of depressing, shifting, and broadening the characteristic response of Rossby normal modes. While nonuniformities in both the mean wind and temperature fields contribute to the reduction in peak response, the former are primarily responsible for translation and spectral broadening. An investigation is conducted to determine which modes may be realized in actual atmospheric configurations and which may be identified. For both the equinox and solstice configurations, response peaks corresponding to all of the first four modes of wavenumbers 1, 2, and 3 are readily visible above the noise.

  19. Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water

    NASA Astrophysics Data System (ADS)

    Farag, Marwa H.; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

    2013-05-01

    Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ˜85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.

  20. All-atom simulations of crowding effects on ubiquitin dynamics

    NASA Astrophysics Data System (ADS)

    Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

  1. Isotope effect in normal-to-local transition of acetylene bending modes

    DOE PAGESBeta

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; Tyng, Vivian; Kellman, Michael E.

    2012-01-01

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helpsmore » to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.« less

  2. Isotope effect in normal-to-local transition of acetylene bending modes

    SciTech Connect

    Ma, Jianyi; Xu, Dingguo; Guo, Hua; Tyng, Vivian; Kellman, Michael E.

    2012-01-01

    The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helps to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.

  3. Normal incidence narrowband transmission filtering capabilities using symmetry-protected modes of a subwavelength, dielectric grating.

    PubMed

    Foley, Justin M; Phillips, Jamie D

    2015-06-01

    We computationally study a normal incidence narrowband transmission filter based on a subwavelength dielectric grating that operates through Fano interference between supported guided leaky modes of the system. We characterize the filtering capabilities as the cross section of the grating is manipulated and suggest techniques for experimental demonstration. Using group theory, we study the plane wave coupling to the supported modes that leads to broadband reflectance and narrowband transmittance responses for rectangular, pentagonal, rhomboidal, and right trapezoidal cross-sectional geometries. PMID:26030577

  4. Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

    DOE PAGESBeta

    Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; Allen, Matthew S.

    2015-09-15

    Several reduced-order modeling strategies have been developed to create low-order models of geometrically nonlinear structures from detailed finite element models, allowing one to compute the dynamic response of the structure at a dramatically reduced cost. But, the parameters of these reduced-order models are estimated by applying a series of static loads to the finite element model, and the quality of the reduced-order model can be highly sensitive to the amplitudes of the static load cases used and to the type/number of modes used in the basis. Our paper proposes to combine reduced-order modeling and numerical continuation to estimate the nonlinearmore » normal modes of geometrically nonlinear finite element models. Not only does this make it possible to compute the nonlinear normal modes far more quickly than existing approaches, but the nonlinear normal modes are also shown to be an excellent metric by which the quality of the reduced-order model can be assessed. Hence, the second contribution of this work is to demonstrate how nonlinear normal modes can be used as a metric by which nonlinear reduced-order models can be compared. Moreover, various reduced-order models with hardening nonlinearities are compared for two different structures to demonstrate these concepts: a clamped–clamped beam model, and a more complicated finite element model of an exhaust panel cover.« less

  5. Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

    SciTech Connect

    Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; Allen, Matthew S.

    2015-09-15

    Several reduced-order modeling strategies have been developed to create low-order models of geometrically nonlinear structures from detailed finite element models, allowing one to compute the dynamic response of the structure at a dramatically reduced cost. But, the parameters of these reduced-order models are estimated by applying a series of static loads to the finite element model, and the quality of the reduced-order model can be highly sensitive to the amplitudes of the static load cases used and to the type/number of modes used in the basis. Our paper proposes to combine reduced-order modeling and numerical continuation to estimate the nonlinear normal modes of geometrically nonlinear finite element models. Not only does this make it possible to compute the nonlinear normal modes far more quickly than existing approaches, but the nonlinear normal modes are also shown to be an excellent metric by which the quality of the reduced-order model can be assessed. Hence, the second contribution of this work is to demonstrate how nonlinear normal modes can be used as a metric by which nonlinear reduced-order models can be compared. Moreover, various reduced-order models with hardening nonlinearities are compared for two different structures to demonstrate these concepts: a clamped–clamped beam model, and a more complicated finite element model of an exhaust panel cover.

  6. The barotropic normal modes in certain shear flows and the traveling waves in the atmosphere

    NASA Technical Reports Server (NTRS)

    Chen, Ping

    1993-01-01

    It is shown analytically and numerically that in certain shear flows the linearized nondivergent barotropic vorticity equation has a limited number of neutral normal modes. The latitudinal structures of these shear flows can be expressed as polynomials of the sine of latitude. The first few such shear flows resemble the gross features of the zonal winds in the atmosphere of the earth at different times and altitudes. The spatial structures of the neutral normal modes in these shear flows are spherical harmonics, and, as a consequence, these modes are also the exact solutions of the fully nonlinear equation because the nonlinear interaction term vanishes identically. The spatial structures of the observed 5-, 4-, 2-, and 16-day free traveling waves in the atmosphere are often identified with the spherical harmonics with indices of (m, n) = ( 1, 2), (2, 3), (3, 3), and ( 1, 4), which are known previously as the neutral normal modes of the nondivergent barotropic vorticity equation in a motionless background state. Our results could explain why these free traveling waves can survive the shearing effects of zonal flows that are far different from rest because these spherical harmonics are also normal modes in certain shear flows that resemble the observations of the atmosphere.

  7. Majorana modes and transport across junctions of superconductors and normal metals

    NASA Astrophysics Data System (ADS)

    Sen, Diptiman; Thakurathi, Manisha; Deb, Oindrila

    2015-03-01

    We study Majorana modes and transport in one-dimensional systems with junctions of p-wave superconductors (SCs) and normal metal (NM) leads. For a system with a SC lying between two NM leads, it is known that there is a Majorana mode at the junction between the SC and each NM. If an impurity is present or the p-wave pairing amplitude changes sign at some point in the superconductor, two additional Majorana modes appear near that point. We study the effects of all these modes on the normal and Cooper pair conductances. The main effect is to shift the conductance peaks away from zero bias due to hybridization between the Majoranas; the shift oscillates and also decays exponentially as the length of the SC is increased. Using bosonization and the renormalization group (RG) method, we study the effect of interactions between the electrons on the Majorana modes and the conductances. We then consider a system with a junction of three SC regions connected to NM leads. The junction is parameterized by a scattering matrix. Depending on the relative signs of the pairing amplitudes in the three SCs, there may be one or three Majorana modes at the junction. We study the effect of interactions on these modes using an RG analysis which is valid for weak interactions. We thank DST, India and CSIR, India for financial support.

  8. Photoelectron spectra of dihalomethyl anions: Testing the limits of normal mode analysis

    NASA Astrophysics Data System (ADS)

    Vogelhuber, Kristen M.; Wren, Scott W.; McCoy, Anne B.; Ervin, Kent M.; Lineberger, W. Carl

    2011-05-01

    We report the 364-nm negative ion photoelectron spectra of CHX2- and CDX2-, where X = Cl, Br, and I. The pyramidal dihalomethyl anions undergo a large geometry change upon electron photodetachment to become nearly planar, resulting in multiple extended vibrational progressions in the photoelectron spectra. The normal mode analysis that successfully models photoelectron spectra when geometry changes are modest is unable to reproduce qualitatively the experimental data using physically reasonable parameters. Specifically, the harmonic normal mode analysis using Cartesian displacement coordinates results in much more C-H stretch excitation than is observed, leading to a simulated photoelectron spectrum that is much broader than that which is seen experimentally. A (2 + 1)-dimensional anharmonic coupled-mode analysis much better reproduces the observed vibrational structure. We obtain an estimate of the adiabatic electron affinity of each dihalomethyl radical studied. The electron affinity of CHCl2 and CDCl2 is 1.3(2) eV, of CHBr2 and CDBr2 is 1.9(2) eV, and of CHI2 and CDI2 is 1.9(2) eV. Analysis of the experimental spectra illustrates the limits of the conventional normal mode approach and shows the type of analysis required for substantial geometry changes when multiple modes are active upon photodetachment.

  9. IMAGING AND CHARACTERIZING THE WASTE MATERIALS INSIDE AN UNDERGROUND STORAGE TANK USING SEISMIC NORMAL MODES

    EPA Science Inventory

    The objective of this study is to develop and test a seismic method to image and characterize waste materials contained in tanks using complete seismic response including the normal modes, or "free oscillations." The method will be developed with the ultimate application to image...

  10. Time-frequency characterization of nonlinear normal modes and challenges in nonlinearity identification of dynamical systems

    NASA Astrophysics Data System (ADS)

    Pai, P. Frank

    2011-10-01

    Presented here is a new time-frequency signal processing methodology based on Hilbert-Huang transform (HHT) and a new conjugate-pair decomposition (CPD) method for characterization of nonlinear normal modes and parametric identification of nonlinear multiple-degree-of-freedom dynamical systems. Different from short-time Fourier transform and wavelet transform, HHT uses the apparent time scales revealed by the signal's local maxima and minima to sequentially sift components of different time scales. Because HHT does not use pre-determined basis functions and function orthogonality for component extraction, it provides more accurate time-varying amplitudes and frequencies of extracted components for accurate estimation of system characteristics and nonlinearities. CPD uses adaptive local harmonics and function orthogonality to extract and track time-localized nonlinearity-distorted harmonics without the end effect that destroys the accuracy of HHT at the two data ends. For parametric identification, the method only needs to process one steady-state response (a free undamped modal vibration or a steady-state response to a harmonic excitation) and uses amplitude-dependent dynamic characteristics derived from perturbation analysis to determine the type and order of nonlinearity and system parameters. A nonlinear two-degree-of-freedom system is used to illustrate the concepts and characterization of nonlinear normal modes, vibration localization, and nonlinear modal coupling. Numerical simulations show that the proposed method can provide accurate time-frequency characterization of nonlinear normal modes and parametric identification of nonlinear dynamical systems. Moreover, results show that nonlinear modal coupling makes it impossible to decompose a general nonlinear response of a highly nonlinear system into nonlinear normal modes even if nonlinear normal modes exist in the system.

  11. The effect of truncating the normal mode coupling equations on synthetic spectra

    NASA Astrophysics Data System (ADS)

    Akbarashrafi, F.; Valentine, A. P.; Al-Attar, D.; Trampert, J.

    2015-12-01

    The free oscillations, or normal modes, of the Earth provide important constraints on the long-wavelength structure of our planet. Calculations using normal modes are also necessary if the effects of gravity are to be fully modeled in seismic waveforms, which becomes important at low frequencies. To implement these calculations, we typically initially compute the normal modes (eigenfunctions) of a spherically-symmetric model such as PREM. These form a complete set of basis functions, which may then be used to describe the seismic response of laterally heterogeneous models. This procedure is known as 'mode coupling'. In order to implement the calculation, it is necessary to select a finite subset of modes (invariably defined by a frequency range) to be considered. This truncation of the infinite-dimensional equations necessarily introduces an error into the results. Here, we consider the fundamental question: if we wish to calculate synthetic spectra in a given frequency range, how many modes must we couple for the resulting spectra to be sufficiently accurate? To investigate this question, we compute spectra in the 3D model S20RTS up to 2mHz, but allowing coupling with all modes up to 5mHz. We then explore how the spectra change as we reduce the upper frequency used in the coupling. We compare this to the effects introduced by altering the 3D density structure of the model. Clearly, if we wish to image Earth's density structure accurately, it is important that the truncation error is small compared to this signal.

  12. Mode-Locked Ultrashort Pulse Generation from On-Chip Normal Dispersion Microresonators

    NASA Astrophysics Data System (ADS)

    Huang, S.-W.; Zhou, H.; Yang, J.; McMillan, J. F.; Matsko, A.; Yu, M.; Kwong, D.-L.; Maleki, L.; Wong, C. W.

    2015-02-01

    We describe generation of stable mode-locked pulse trains from on-chip normal dispersion microresonators. The excitation of hyperparametric oscillation is facilitated by the local dispersion disruptions induced by mode interactions. The system is then driven from hyperparametric oscillation to the mode-locked state with over 200 nm spectral width by controlled pump power and detuning. With the continuous-wave-driven nonlinearity, the pulses sit on a pedestal, akin to a cavity soliton. We identify the importance of pump detuning and wavelength-dependent quality factors in stabilizing and shaping the pulse structure, to achieve a single pulse inside the cavity. We examine the mode-locking dynamics by numerically solving the master equation and provide analytic solutions under appropriate approximations.

  13. Ocean surface maps from blending disparate data through normal mode analysis

    NASA Astrophysics Data System (ADS)

    Schulz, William John, Jr.

    Rapid environmental assessment is conducted using disparate data sources in the northwestern Gulf of Mexico. An overview of significant physical features in the Gulf highlights the complexities of the large and meso-scale circulations. Spectral analysis of high resolution current meter and drifter data reveals the significant forcing features detectable by readily available observing techniques. These observations are combined with boundary data extracted from the U.S. Navy's Modular Ocean Data Assimilation System (MODAS) through Normal Mode Analysis (NMA). The NMA blending process is described, and surface maps of velocity and convergence are produced. Using statistical and qualitative techniques, the NMA generated "nowcasts" are analyzed to determine the significant modes applicable to varying oceanographic situations. Fundamental guidance for choosing the number and type of modes in an REA scenario are noted. The NMA method proves to be a useful tool in constructing analytic surface maps when the component modes are wisely chosen.

  14. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264

  15. Normal and anomalous plasmonic lattice modes of gold nanodisk arrays in inhomogeneous media

    NASA Astrophysics Data System (ADS)

    Sadeghi, S. M.; Wing, W. J.; Campbell, Q.

    2016-03-01

    We study plasmonic lattice modes in two dimensional arrays of large metallic nanodisks in strongly inhomogeneous environments with controlled dielectric asymmetries. This is done within the two limits of positive (air/substrate) and negative (Si/substrate) asymmetries. In the former, the nanodisks are exposed to air, while in the latter, they are fully embedded in a dielectric material with a refractive index much higher than that of the glass substrate (Si). Our results show that in the air/substrate limit, the arrays can mainly support two distinct visible and infrared peaks associated with the optical coupling of multipolar plasmonic resonances of nanodisks in air and substrate (normal modes). As the nanodisks are gradually embedded in Si, i.e., going from the positive to negative asymmetry limit, the visible peak undergoes more than 200 nm red shift without significant mode degradation. Our results show that as this transition happens, a third peak (anomalous mode) becomes dominant. The amplitude and wavelength of this peak increase quadratically with the thickness of the Si layer, indicating formation of a unique collective mode. We study the impact of this mode on the emission semiconductor quantum dots, demonstrating they become much brighter as the result of the long-reach plasmonic fields of the nanodisks when the arrays are in this mode.

  16. Numerical Modeling of Normal-Mode Oscillations in Planetary Atmospheres: Application to Saturn and Titan

    NASA Astrophysics Data System (ADS)

    Friedson, Andrew James; Ding, Leon

    2015-11-01

    We have developed a numerical model to calculate the frequencies and eigenfunctions of adiabatic, non-radial normal-mode oscillations in the gas giants and Titan. The model solves the linearized momentum, energy, and continuity equations for the perturbation displacement, pressure, and density fields and solves Poisson’s equation for the perturbation gravitational potential. The response to effects associated with planetary rotation, including the Coriolis force, centrifugal force, and deformation of the equilibrium structure, is calculated numerically. This provides the capability to accurately compute the influence of rotation on the modes, even in the limit where mode frequency approaches the rotation rate, when analytical estimates based on functional perturbation analysis become inaccurate. This aspect of the model makes it ideal for studying the potential role of low-frequency modes for driving spiral density waves in the C ring that possess relatively low pattern speeds (Hedman, M.M and P.D. Nicholson, MNRAS 444, 1369-1388). In addition, the model can be used to explore the effect of internal differential rotation on the eigenfrequencies. We will (1) present examples of applying the model to calculate the properties of normal modes in Saturn and their relationship to observed spiral density waves in the C ring, and (2) discuss how the model is used to examine the response of the superrotating atmosphere of Titan to the gravitational tide exerted by Saturn. This research was supported by a grant from the NASA Planetary Atmosphere Program.

  17. Free and forced Rossby normal modes in a rectangular gulf of arbitrary orientation

    NASA Astrophysics Data System (ADS)

    Graef, Federico

    2016-09-01

    A free Rossby normal mode in a rectangular gulf of arbitrary orientation is constructed by considering the reflection of a Rossby mode in a channel at the head of the gulf. Therefore, it is the superposition of four Rossby waves in an otherwise unbounded ocean with the same frequency and wavenumbers perpendicular to the gulf axis whose difference is equal to 2mπ/W, where m is a positive integer and W the gulf's width. The lower (or higher) modes with small m (or large m) are oscillatory (evanescent) in the coordinate along the gulf; these are elucidated geometrically. However for oceanographically realistic parameter values, most of the modes are evanescent. When the gulf is forced at the mouth with a single Fourier component, the response is in general an infinite sum of modes that are needed to match the value of the streamfunction at the gulf's entrance. The dominant mode of the response is the resonant one, which corresponds to forcing with a frequency ω and wavenumber normal to the gulf axis η appropriate to a gulf mode: η =- β sin α/(2ω) ± Mπ/W, where α is the angle between the gulf's axis and the eastern direction (+ve clockwise) and M the resonant's mode number. For zonal gulfs ω drops out of the resonance condition. For the special cases η = 0 in which the free surface goes up and down at the mouth with no flow through it, or a flow with a sinusoidal profile, resonant modes can get excited for very specific frequencies (only for non-zonal gulfs in the η = 0 case). The resonant mode is around the annual frequency for a wide range of gulf orientations α ∈ [40°, 130°] or α ∈ [220°, 310°] and gulf widths between 150 and 200 km; these include the Gulf of California and the Adriatic Sea. If η is imaginary, i.e. a flow with an exponential profile, there is no resonance. In general less modes get excited if the gulf is zonally oriented.

  18. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

    PubMed Central

    Qin, Feng

    2015-01-01

    The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

  19. New insight into the structure of dispersed titania by combining normal-mode analysis with experiment

    NASA Astrophysics Data System (ADS)

    Nitsche, David; Hess, Christian

    2014-11-01

    Normal-mode analysis has been combined with experiment to gain new insight into the vibrational structure of dispersed titania. For the calculations, double- and tri-grafted hydroxylated titania species have been adapted to a model silica support based on polyhedral oligomeric silsesquioxane (POSS). The choice of hydroxylated models was validated by IR detection of the Osbnd H stretching band of dispersed titania (0.7 Ti/nm2). UV resonance Raman experiments have identified three titania-related vibrational features within the spectral region 900-1100 cm-1 due to Tisbnd Osbnd Si interphase, Tisbnd Osbnd Si in-phase and out-of-phase stretching vibrations. This behaviour is fully consistent with the results obtained by the normal-mode analysis.

  20. High-frequency Born synthetic seismograms based on coupled normal modes

    USGS Publications Warehouse

    Pollitz, Fred F.

    2011-01-01

    High-frequency and full waveform synthetic seismograms on a 3-D laterally heterogeneous earth model are simulated using the theory of coupled normal modes. The set of coupled integral equations that describe the 3-D response are simplified into a set of uncoupled integral equations by using the Born approximation to calculate scattered wavefields and the pure-path approximation to modulate the phase of incident and scattered wavefields. This depends upon a decomposition of the aspherical structure into smooth and rough components. The uncoupled integral equations are discretized and solved in the frequency domain, and time domain results are obtained by inverse Fourier transform. Examples show the utility of the normal mode approach to synthesize the seismic wavefields resulting from interaction with a combination of rough and smooth structural heterogeneities. This approach is applied to an ∼4 Hz shallow crustal wave propagation around the site of the San Andreas Fault Observatory at Depth (SAFOD).

  1. Charge transfer mobility of naphthodithiophenediimide derivative: Normal-mode and bond length relaxation analysis

    NASA Astrophysics Data System (ADS)

    Liu, Xiaoyan; Liu, Yujuan; Zheng, Yujun

    2016-02-01

    In this letter, the charge transfer mobility of naphthalenediimide (NDTI) derivative is investigated. By employing the normal-mode analysis and bond length relaxation analysis, the influences of chemical elements on reorganization energies and intermolecular electronic couplings are investigated in NDTI derivative. The results show that the introduction of atom O would decrease reorganization energy in hole-hopping process and increase electronic coupling. This analysis encourages the molecular and material design in organic semiconductors.

  2. A brief study of quasi-normal modes in relativistic stars using algebraic computation

    SciTech Connect

    Campos, M. de

    2010-11-12

    The damped oscillations in relativistic stars generate gravitational waves that in the literature appear under the general denomination of quasi-normal modes. In this brief note we want offer some information about the use of algebraic computation to obtain the field equations and the perturbed version of them, in the context of general relativity theory, that is the framework to study gravitational waves in this work.

  3. Normal modes and time evolution of a holographic superconductor after a quantum quench

    NASA Astrophysics Data System (ADS)

    Gao, Xin; García-García, Antonio M.; Zeng, Hua Bi; Zhang, Hai-Qing

    2014-06-01

    We employ holographic techniques to investigate the dynamics of the order parameter of a strongly coupled superconductor after a perturbation that drives the system out of equilibrium. The gravity dual that we employ is the AdS5 Soliton background at zero temperature. We first analyze the normal modes associated to the superconducting order parameter which are purely real since the background has no horizon. We then study the full time evolution of the order parameter after a quench. For sufficiently a weak and slow perturbation we show that the order parameter undergoes simple undamped oscillations in time with a frequency that agrees with the lowest normal model computed previously. This is expected as the soliton background has no horizon and therefore, at least in the probe and large N limits considered, the system will never return to equilibrium. For stronger and more abrupt perturbations higher normal modes are excited and the pattern of oscillations becomes increasingly intricate. We identify a range of parameters for which the time evolution of the order parameter become quasi chaotic. The details of the chaotic evolution depend on the type of perturbation used. Therefore it is plausible to expect that it is possible to engineer a perturbation that leads to the almost complete destruction of the oscillating pattern and consequently to quasi equilibration induced by superposition of modes with different frequencies.

  4. Finite-time normal mode disturbances and error growth during Southern Hemisphere blocking

    NASA Astrophysics Data System (ADS)

    Wei, Mozheng; Frederiksen, Jorgen S.

    2005-01-01

    The structural organization of initially random errors evolving in a barotropic tangent linear model, with time-dependent basic states taken from analyses, is examined for cases of block development, maturation and decay in the Southern Hemisphere atmosphere during April, November, and December 1989. The statistics of 100 evolved errors are studied for six-day periods and compared with the growth and structures of fast growing normal modes and finite-time normal modes (FTNMs). The amplification factors of most initially random errors are slightly less than those of the fastest growing FTNM for the same time interval. During their evolution, the standard deviations of the error fields become concentrated in the regions of rapid dynamical development, particularly associated with developing and decaying blocks. We have calculated probability distributions and the mean and standard deviations of pattern correlations between each of the 100 evolved error fields and the five fastest growing FTNMs for the same time interval. The mean of the largest pattern correlation, taken over the five fastest growing FTNMs, increases with increasing time interval to a value close to 0.6 or larger after six days. FTNM 1 generally, but not always, gives the largest mean pattern correlation with error fields. Corresponding pattern correlations with the fast growing normal modes of the instantaneous basic state flow are significant but lower than with FTNMs. Mean pattern correlations with fast growing FTNMs increase further when the time interval is increased beyond six days.

  5. Skin pigmentation and texture changes after hair removal with the normal-mode ruby laser.

    PubMed

    Haedersdal, M; Egekvist, H; Efsen, J; Bjerring, P

    1999-11-01

    Promising clinical results have been obtained with the normal mode ruby laser for removal of unwanted hair. Melanin within the hair follicles is thought to act as target for the ruby laser pulses, whereas epidermal melanin is thought to be a competitive chromophore, responsible for potential side effects. This study aimed (i) to objectify postoperative changes in skin pigmentation and texture and (ii) to evaluate the importance of variations in preoperative skin pigmentation for the development of side effects 12 weeks after 1 treatment with the normal-mode ruby laser. A total of 17 volunteers (skin types I-IV) were laser-treated in the hairy pubic region (n = 51 test areas). A shaved test area served as control. Skin reflectance spectroscopical measurements, 3-dimensional surface contour analysis and ultrasonography objectified postoperative changes in skin pigmentation and texture. Blinded clinical assessments revealed postoperative hyperpigmentation (2% of test areas) and hypopigmentation (10%), whereas no textural changes were seen. Reflectance spectroscopically-determined pigmentary changes depended on the degree of preoperative skin pigmentation, fairly pigmented skin types experiencing subclinical hyperpigmentation and darkly pigmented skin types experiencing subclinical hypopigmentation. Three-dimensional surface profilometry documented similar pre- and postoperative surface contour parameters, indicating that the skin surface texture is preserved after laser exposure. Ultrasonography revealed similar skin thicknesses in laser-exposed and untreated control areas. It is concluded that normal-mode ruby laser treatment is safe for hair removal in skin types I-IV. PMID:10598763

  6. Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes.

    PubMed

    Hanson-Heine, Magnus W D; Husseini, Fouad S; Hirst, Jonathan D; Besley, Nicholas A

    2016-04-12

    Nonlinear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides and hexapeptide Z-Aib-L-Leu-(Aib)2-Gly-Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode approach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parametrization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local-mode approach provides a convenient platform for the development of site frequency and coupling maps. PMID:26913672

  7. Normal force of magnetorheological fluids with foam metal under oscillatory shear modes

    NASA Astrophysics Data System (ADS)

    Yao, Xingan; Liu, Chuanwen; Liang, Huang; Qin, Huafeng; Yu, Qibing; Li, Chuan

    2016-04-01

    The normal force of magnetorheological (MR) fluids in porous foam metal was investigated in this paper. The dynamic repulsive normal force was studied using an advanced commercial rheometer under oscillatory shear modes. In the presence of magnetic fields, the influences of time, strain amplitude, frequency and shear rate on the normal force of MR fluids drawn from the porous foam metal were systematically analysed. The experimental results indicated that the magnetic field had the greatest effect on the normal force, and the effect increased incrementally with the magnetic field. Increasing the magnetic field produced a step-wise increase in the shear gap. However, other factors in the presence of a constant magnetic field only had weak effects on the normal force. This behaviour can be regarded as a magnetic field-enhanced normal force, as increases in the magnetic field resulted in more MR fluids being released from the porous foam metal, and the chain-like magnetic particles in the MR fluids becoming more elongated with aggregates spanning the gap between the shear plates.

  8. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540

  9. Normal mode calculation for triple helical DNA, stability and hydration effects

    NASA Astrophysics Data System (ADS)

    Dadarlat, Voichita Maria

    The effective field model for the dynamics of the triple helix d(T)n - d(A)n - d(T)n DNA polymer in solution has been applied to determine the vibrational normal modes of the system for both A and B conformation. The effect of site-bound counterions as compared to the area-bound counterions has been considered specifically by explicitly introducing degrees of freedom for the three counterions associated with a unit cell and coupling these to the DNA degrees of freedom via appropriate interactions. Stability of the system for all vibrational modes (positive eigenvalues for the solution of the dynamics problem) was used as a criterion to find possible equilibrium positions of the site-bound counterions in specific conditions of weak covalent bonding between the counterions and the phosphate free oxygens and distance dependent dielectric constants. Normal mode calculation for the A conformation shows that this type of triple helix is not stable in aqueous solutions unless the counterions are site-bound in certain positions close to the phosphate groups. The equilibrium domains for the positions of the counterions in both conformations have been determined. Free energy calculations for the two triple helices show that the B conformation is more stable than the A conformation. Our calculated normal modes match reasonably well with the experimental IR spectra. The effect of adding structural waters to the triplex DNA in the B conformation have been studied. The results clearly show that there is an inverse proportional relationship between the degree of boundness of the water molecules to the atoms in the triple helix and the relative humidity (RH) of the samples.

  10. Accretion onto magnetized neutron stars - Normal mode analysis of the interchange instability at the magnetopause

    NASA Technical Reports Server (NTRS)

    Arons, J.; Lea, S. M.

    1976-01-01

    Results are reported for a linearized hydromagnetic stability analysis of the magnetopause of an accreting neutron star. The magnetosphere is assumed to be slowly rotating, and the plasma just outside the magnetopause is assumed to be weakly magnetized. The plasma layer is assumed to be bounded above by a shock wave and to be thin compared with the radius of the magnetosphere. Under these circumstances, the growing modes are shown to be localized in the direction parallel to the zero-order magnetic field, but the structure of the modes is still similar to the flute mode. An expression for the growth rate at each magnetic latitude is obtained in terms of the magnitude of the gravitational acceleration normal to the surface, the azimuthal mode number, the radius of the magnetosphere, the height of the shock above the magnetopause, and the effective Atwood number which embodies the stabilizing effects of favorable curvature and magnetic tension. The effective Atwood number is calculated, and the stabilizing effects of viscosity and aligned flow parallel to the magnetopause are discussed.

  11. Polymorphic Ab protofilaments exhibit distinct conformational dynamics as calculated by normal mode analysis

    NASA Astrophysics Data System (ADS)

    Armbruster, Matthew; Soto, Patricia

    2012-02-01

    This project proposes to test the hypothesis that the physicochemical milieu modulates the conformational dynamics of synthetic Alzheimer's Ab protofilament structures, the main component of Alzheimer's senile plaques. To this end, 3D solid-state NMR structures of Ab protofilaments were used as initial structures for molecular dynamics simulations in explicit water and a water/hexane environment. The initial structures of the simulations and representative structures from the simulation-generated trajectories were taken to perform computational normal mode analysis. We developed a code in python with a graphical user-friendly interface. The program incorporated the ProDy (0.7.1) package. With the application, we examined cross-correlation plots of Ca positions of the 2-fold Ab protofilaments along the most collective mode and the slowest mode. The protofilament structures were highly correlated in the water environment. We hypothesized the protofilament would move as one in water because of the viscosity. The square fluctuation of Ca positions was calculated for the slowest mode for the hexane model and the MD generated ensemble. The two plots match up until midway through the structure. At the midway point a phase shift emerged between the two structures most likely where the surrounding changes. The in-house developed code made it easy to perform analysis and will be used by other students in the research group.

  12. On Quasi-Normal Modes, Area Quantization and Bohr Correspondence Principle

    NASA Astrophysics Data System (ADS)

    Corda, Christian

    2015-10-01

    In (Int. Journ. Mod. Phys. D 14, 181 2005), the author Khriplovich verbatim claims that "the correspondence principle does not dictate any relation between the asymptotics of quasinormal modes and the spectrum of quantized black holes" and that "this belief is in conflict with simple physical arguments". In this paper we analyze Khriplovich's criticisms and realize that they work only for the original proposal by Hod, while they do not work for the improvements suggested by Maggiore and recently finalized by the author and collaborators through a connection between Hawking radiation and black hole (BH) quasi-normal modes (QNMs). This is a model of quantum BH somewhat similar to the historical semi-classical model of the structure of a hydrogen atom introduced by Bohr in 1913. Thus, QNMs can be really interpreted as BH quantum levels (the "electrons" of the "Bohr-like BH model").Our results have also important implications on the BH information puzzle.

  13. Cavity quantum optomechanics of ultracold atoms in an optical lattice: Normal-mode splitting

    SciTech Connect

    Bhattacherjee, Aranya B.

    2009-10-15

    We consider the dynamics of a movable mirror (cantilever) of a cavity coupled through radiation pressure to the light scattered from ultracold atoms in an optical lattice. Scattering from different atomic quantum states creates different quantum states of the scattered light, which can be distinguished by measurements of the displacement spectrum of the cantilever. We show that for large pump intensities the steady-state displacement of the cantilever shows bistable behavior. Due to atomic back action, the displacement spectrum of the cantilever is modified and depends on the position of the condensate in the Brillouin zone. We further analyze the occurrence of splitting of the normal mode into three modes due to mixing of the mechanical motion with the fluctuations of the cavity field and the fluctuations of the condensate with finite atomic two-body interaction.

  14. Parameter identification of structural systems possessing one or two nonlinear normal modes

    NASA Astrophysics Data System (ADS)

    Fahey, Sean O'flaherty

    2000-09-01

    In this Dissertation, we develop, and provide proof of principle for, parameter identification techniques for structural systems that can be described in terms of one or two nonlinear normal modes. We model the dynamics of these modes by second-order ordinary-differential equations based on the principles of mechanics, past experience, and engineering judgment. We perform a number of separate experiments on a two-mass structure using several different types of excitation. For the linear tests, the theoretical system response is known in closed-form. For the nonlinear test, we use the method of multiple scales to determine second-order uniform expansions of the model equations and hence determine the approximations to responses of the structure. Then, we estimate the linear and nonlinear parameters by regressive fits between the theoretically and experimentally obtained response relations. We report deviations and agreements between model and experiment.

  15. An instrument for direct observations of seismic and normal-mode rotational oscillations of the Earth

    PubMed Central

    Cowsik, R.

    2007-01-01

    The rotations around the vertical axis associated with the normal mode oscillations of the Earth and those induced by the seismic and other disturbances have been very difficult to observe directly. Such observations will provide additional information for 3D modeling of the Earth and for understanding earthquakes and other underground explosions. In this paper, we describe the design of an instrument capable of measuring the rotational motions associated with the seismic oscillations of the Earth, including the lowest frequency normal mode at ν ≈ 3.7 × 10−4 Hz. The instrument consists of a torsion balance with a natural frequency of ν0 ≈ 1.6 × 10−4 Hz, which is observed by an autocollimating optical lever of high angular resolution and dynamic range. Thermal noise limits the sensitivity of the apparatus to amplitudes of ≈ 1.5 × 10−9 rad at the lowest frequency normal mode and the sensitivity improves as ν−3/2 with increasing frequency. Further improvements in sensitivity by about two orders of magnitude may be achieved by operating the balance at cryogenic temperatures. Alternatively, the instrument can be made more robust with a reduced sensitivity by increasing ν0 to ≈10−2 Hz. This instrument thus complements the ongoing effort by Igel and others to study rotational motions using ring laser gyroscopes and constitutes a positive response to the clarion call for developments in rotation seismology by Igel, Lee, and Todorovska [H. Igel, W.H.K. Lee and M.I. Todorovska, AGU Fall Meeting 2006, Rotational Seismology Sessions: S22A,S23B, Inauguration of the International Working Group on Rotational Seismology (IWGoRS)]. PMID:17438268

  16. Twist-radial normal mode analysis in double-stranded DNA chains

    NASA Astrophysics Data System (ADS)

    Torrellas, Germán; Maciá, Enrique

    2012-10-01

    We study the normal modes of a duplex DNA chain at low temperatures. We consider the coupling between the hydrogen-bond radial oscillations and the twisting motion of each base pair within the Peyrard-Bishop-Dauxois model. The coupling is mediated by the stacking interaction between adjacent base pairs along the helix. We explicitly consider different mass values for different nucleotides, extending previous works. We disclose several resonance conditions of interest, determined by the fine-tuning of certain model parameters. The role of these dynamical effects on the DNA chain charge transport properties is discussed.

  17. Normal mode solutions for seismo-acoustic propagation resulting from shear and combined wave point sources.

    PubMed

    Nealy, Jennifer L; Collis, Jon M; Frank, Scott D

    2016-04-01

    Normal mode solutions to range-independent seismo-acoustic problems are benchmarked against elastic parabolic equation solutions and then used to benchmark the shear elastic parabolic equation self-starter [Frank, Odom, and Collis, J. Acoust. Soc. Am. 133, 1358-1367 (2013)]. The Pekeris waveguide with an elastic seafloor is considered for a point source located in the ocean emitting compressional waves, or in the seafloor, emitting both compressional and shear waves. Accurate solutions are obtained when the source is in the seafloor, and when the source is at the interface between the fluid and elastic layers. PMID:27106346

  18. Identification of nonlinear normal modes of engineering structures under broadband forcing

    NASA Astrophysics Data System (ADS)

    Noël, Jean-Philippe; Renson, L.; Grappasonni, C.; Kerschen, G.

    2016-06-01

    The objective of the present paper is to develop a two-step methodology integrating system identification and numerical continuation for the experimental extraction of nonlinear normal modes (NNMs) under broadband forcing. The first step processes acquired input and output data to derive an experimental state-space model of the structure. The second step converts this state-space model into a model in modal space from which NNMs are computed using shooting and pseudo-arclength continuation. The method is demonstrated using noisy synthetic data simulated on a cantilever beam with a hardening-softening nonlinearity at its free end.

  19. Supercontinuum generation by noise-like pulses transmitted through normally dispersive standard single-mode fibers.

    PubMed

    Zaytsev, Alexey; Lin, Chih-Hsuan; You, Yi-Jing; Chung, Chia-Chun; Wang, Chi-Luen; Pan, Ci-Ling

    2013-07-01

    We report generation of broadband supercontinuum (SC) by noise-like pulses (NLPs) with a central wavelength of 1070 nm propagating through a long piece of standard single-mode fibers (~100 meters) in normal dispersion region far from the zero-dispersion point. Theoretical simulations indicate that the physical mechanism of SC generation is due to nonlinear effects in fibers. The cascaded Raman scattering is responsible for significant spectral broadening in the longer wavelength regions whereas the Kerr effect results in smoothing of SC generated spectrum. The SC exhibits low threshold (43 nJ) and a flat spectrum over 1050-1250 nm. PMID:23842392

  20. Experimental and numerical studies of mode-locked fiber laser with large normal and anomalous dispersion.

    PubMed

    Zhang, Lei; El-Damak, A R; Feng, Yan; Gu, Xijia

    2013-05-20

    An ytterbium-doped mode-locked fiber laser was demonstrated with a chirped fiber Bragg grating for dispersion management. The cavity net dispersion could be changed from large normal dispersion (2.4 ps(2)) to large anomalous dispersion (-2.0 ps(2)), depending on the direction of the chirped Bragg grating in laser cavity. The proposed fiber lasers with large normal dispersion generated stable pulses with a pulse width of <1.1 ns and a pulse energy of 1.5 nJ. The laser with large anomalous dispersion generated wavelength-tunable soliton with a pulse width of 2.7 ps and pulse energy of 0.13 nJ. A theoretical model was established and used to verify the experimental observations. PMID:23736423

  1. Nonlinear normal vibration modes in the dynamics of nonlinear elastic systems

    NASA Astrophysics Data System (ADS)

    Mikhlin, Yu V.; Perepelkin, N. V.; Klimenko, A. A.; Harutyunyan, E.

    2012-08-01

    Nonlinear normal modes (NNMs) are a generalization of the linear normal vibrations. By the Kauderer-Rosenberg concept in the regime of the NNM all position coordinates are single-values functions of some selected position coordinate. By the Shaw-Pierre concept, the NNM is such a regime when all generalized coordinates and velocities are univalent functions of a couple of dominant (active) phase variables. The NNMs approach is used in some applied problems. In particular, the Kauderer-Rosenberg NNMs are analyzed in the dynamics of some pendulum systems. The NNMs of forced vibrations are investigated in a rotor system with an isotropic-elastic shaft. A combination of the Shaw-Pierre NNMs and the Rauscher method is used to construct the forced NNMs and the frequency responses in the rotor dynamics.

  2. Variability in Diaphragm Motion During Normal Breathing, Assessed With B-Mode Ultrasound

    PubMed Central

    Harper, Caitlin J; Shahgholi, Leili; Cieslak, Kathryn; Hellyer, Nathan J.; Strommen, Jeffrey A.; Boon, Andrea J.

    2014-01-01

    STUDY DESIGN Clinical measurement, cross-sectional. OBJECTIVES To establish a set of normal values for diaphragm thickening with tidal breathing in healthy subjects. BACKGROUND Normal values for diaphragm contractility, as imaged sonographically, have not been described, despite the known role of the diaphragm in contributing to spinal stability. If the normal range of diaphragm contractility can be defined in a reliable manner, ultrasound has the potential to be used clinically and in research as a biofeedback tool to enhance diaphragm activation/contractility. METHODS B-mode ultrasound was performed on 150 healthy subjects to visualize and measure hemi-diaphragm thickness on each side at resting inspiration and expiration. Primary outcome measures were hemi-diaphragm thickness and thickening ratio, stratified for age, gender, and body mass index. Interrater and intrarater reliability were also measured. RESULTS Normal thickness of the diaphragm at rest ranged from 0.12 to 1.18 cm, with slightly greater thickness in men but no effect of age. Average ± SD change in thickness from resting expiration to resting inspiration was 20.0% ± 15.5% on the right and 23.5% ± 24.4% on the left; however, almost one third of healthy subjects had no to minimal diaphragm thickening with tidal breathing. CONCLUSION There is wide variability in the degree of diaphragm contractility during quiet breathing. B-mode ultrasound appears to be a reliable means of determining the contractility of the diaphragm, an important muscle in spinal stability. Further studies are needed to validate this imaging modality as a clinical tool in the neuromuscular re-education of the diaphragm to improve spinal stability in both healthy subjects and in patients with low back pain. PMID:24175600

  3. Numerical investigations with a hybrid isentropic-sigma model. I - Normal-mode characteristics. II - The inclusion of moist processes

    NASA Technical Reports Server (NTRS)

    Pierce, R. B.; Johnson, Donald R.; Reames, Fred M.; Zapotocny, Tom H.; Wolf, Bart J.

    1991-01-01

    The normal-mode characteristics of baroclinically amplifying disturbances were numerically investigated in a series of adiabatic simulations by a hybrid isentropic-sigma model, demonstrating the effect of coupling an isentropic-coordinate free atmospheric domain with a sigma-coordinate PBL on the normal-mode characteristics. Next, the normal-mode model was modified by including a transport equation for water vapor and adiabatic heating by condensation. Simulations with and without a hydrological component showed that the overall effect of latent heat release is to markedly enhance cyclogenesis and frontogenesis.

  4. A new general normal mode approach to dynamic tides in rotating stars with realistic structure and its applications

    NASA Astrophysics Data System (ADS)

    Ivanov, P. B.; Papaloizou, J. C. B.; Chernov, S. V.

    We review our recent results on a unified normal model approach to dynamic tides proposed recently in Ivanov, Papaloizou & Chernov (2013) and Chernov, Papaloizou & Ivanov (2013). Our formalism can be used whenever the tidal interactions are mainly determined by normal modes of a star with identifiable regular spectrum of low frequency modes. We provide in the text basic expressions for tidal energy and angular momentum transfer valid both for periodic and parabolic orbits, and different assumptions about effciency of normal mode damping due to viscosity and/or non- linear effects and discuss applications to binary stars and close orbiting extrasolar planets.

  5. Classification of ground states and normal modes for phase-frustrated multicomponent superconductors

    NASA Astrophysics Data System (ADS)

    Weston, Daniel; Babaev, Egor

    2013-12-01

    We classify ground states and normal modes for n-component superconductors with frustrated intercomponent Josephson couplings, focusing on n=4. The results should be relevant not only to multiband superconductors, but also to Josephson-coupled multilayers and Josephson-junction arrays. It was recently discussed that three-component superconductors can break time-reversal symmetry as a consequence of phase frustration. We discuss how to classify frustrated superconductors with an arbitrary number of components. Although already for the four-component case there are a large number of different combinations of phase-locking and phase-antilocking Josephson couplings, we establish that there are a much smaller number of equivalence classes where properties of frustrated multicomponent superconductors can be mapped to each other. This classification is related to the graph-theoretical concept of Seidel switching. Numerically, we calculate ground states, normal modes, and characteristic length scales for the four-component case. We report conditions of appearance of new accidental continuous ground-state degeneracies.

  6. Coherent reverberation model based on adiabatic normal mode theory in a range dependent shallow water environment

    NASA Astrophysics Data System (ADS)

    Li, Zhenglin; Zhang, Renhe; Li, Fenghua

    2010-09-01

    Ocean reverberation in shallow water is often the predominant background interference in active sonar applications. It is still an open problem in underwater acoustics. In recent years, an oscillation phenomenon of the reverberation intensity, due to the interference of the normal modes, has been observed in many experiments. A coherent reverberation theory has been developed and used to explain this oscillation phenomenon [F. Li et al., Journal of Sound and Vibration, 252(3), 457-468, 2002]. However, the published coherent reverberation theory is for the range independent environment. Following the derivations by F. Li and Ellis [D. D. Ellis, J. Acoust. Soc. Am., 97(5), 2804-2814, 1995], a general reverberation model based on the adiabatic normal mode theory in a range dependent shallow water environment is presented. From this theory the coherent or incoherent reverberation field caused by sediment inhomogeneity and surface roughness can be predicted. Observations of reverberation from the 2001 Asian Sea International Acoustic Experiment (ASIAEX) in the East China Sea are used to test the model. Model/data comparison shows that the coherent reverberation model can predict the experimental oscillation phenomenon of reverberation intensity and the vertical correlation of reverberation very well.

  7. DNA-triplex conformation from normal mode and hydrogen bond stability calculations.

    NASA Astrophysics Data System (ADS)

    Chen, Y. Z.; Prohofsky, E. W.; Powell, J. W.; White, A. P.

    1996-03-01

    Triple-stranded DNAs are of potential applications in genome mapping and in the treatment of genetic disorders with little side-effect. Despite significant interests, structural information of DNA triplexes is limited and sometimes conflicting. For instance, two structural models with different conformation have been proposed for a DNA-triplex Poly(dA)\\cdot2Poly(dT). We propose that the sensitivity of normal modes and hydrogen-bond stability on conformation can be used to determine the structure of biomolecules difficult to access by other methods. The structural model representative of the true conformation should have normal modes in agreement with observations, and have most stable hydrogen bonds which melt at observed temperatures. We carried out calculations on the two models of Poly(dA)\\cdot2Poly(dT) and found that one model is consistent with observations at high humidity and thus most likely a good approximation to the true conformation in that environment. Our method has potential application in structural prediction for other biomolecules.

  8. Application of Normal Mode Expansion to AE Waves in Finite Plates

    NASA Technical Reports Server (NTRS)

    Gorman, M. R.; Prosser, W. H.

    1997-01-01

    Breckenridge et al. (1975), Hsu (1985) and Pao (1978) adapted approaches from seismology to calculate the response at the surface of an infinite half-space and an infinite plate. These approaches have found use in calibrating acoustic emission (AE) transducers. However, it is difficult to extend this theoretical approach to AE testing of practical structures. Weaver and Pao (1982) considered a normal mode solution to the Lamb equations. Hutchinson (1983) pointed out the potential relevance of Mindlin's plate theory (1951) to AE. Pao (1982) reviewed Medick s (1961) classical plate theory for a point source, but rejected it as useful for AE and no one seems to have investigated its relevance to AE any further. Herein, a normal mode solution to the classical plate bending equation was investigated for its applicability to AE. The same source-time function chosen by Weaver and Pao is considered. However, arbitrary source and receiver positions are chosen relative to the boundaries of the plate. This is another advantage of the plate theory treatment in addition to its simplicity. The source does not have to be at the center of the plate as in the axisymmetric treatment. The plate is allowed to remain finite and reflections are predicted. The importance of this theory to AE is that it can handle finite plates, realistic boundary conditions, and can be extended to composite materials.

  9. An approach to detect afterslips in giant earthquakes in the normal-mode frequency band

    NASA Astrophysics Data System (ADS)

    Tanimoto, Toshiro; Ji, Chen; Igarashi, Mitsutsugu

    2012-08-01

    An approach to detect afterslips in the source process of giant earthquakes is presented in the normal-mode frequency band (0.3-2.0 mHz). The method is designed to avoid a potential systematic bias problem in the determination of earthquake moment by a typical normal-mode approach. The source of bias is the uncertainties in Q (modal attenuation parameter) which varies by up to about ±10 per cent among published studies. A choice of Q values within this range affects amplitudes in synthetic seismograms significantly if a long time-series of about 5-7 d is used for analysis. We present an alternative time-domain approach that can reduce this problem by focusing on a shorter time span with a length of about 1 d. Application of this technique to four recent giant earthquakes is presented: (1) the Tohoku, Japan, earthquake of 2011 March 11, (2) the 2010 Maule, Chile earthquake, (3) the 2004 Sumatra-Andaman earthquake and (4) the Solomon earthquake of 2007 April 1. The Global Centroid Moment Tensor (GCMT) solution for the Tohoku earthquake explains the normal-mode frequency band quite well. The analysis for the 2010 Chile earthquake indicates that the moment is about 7-10 per cent higher than the moment determined by its GCMT solution but further analysis shows that there is little evidence of afterslip; the deviation in moment can be explained by an increase of the dip angle from 18° in the GCMT solution to 19°. This may be a simple trade-off problem between the moment and dip angle but it may also be due to a deeper centroid in the normal-mode frequency band data, as a deeper source could have steeper dip angle due to changes in geometry of the Benioff zone. For the 2004 Sumatra-Andaman earthquake, the five point-source solution by Tsai et al. explains most of the signals but a sixth point-source with long duration improves the fit to the normal-mode frequency band data. The 2007 Solomon earthquake shows that the high-frequency part of our analysis (above 1 mHz) is

  10. Estimation of splitting functions from Earth's normal mode spectra using the neighbourhood algorithm

    NASA Astrophysics Data System (ADS)

    Pachhai, Surya; Tkalčić, Hrvoje; Masters, Guy

    2016-01-01

    The inverse problem for Earth structure from normal mode data is strongly non-linear and can be inherently non-unique. Traditionally, the inversion is linearized by taking partial derivatives of the complex spectra with respect to the model parameters (i.e. structure coefficients), and solved in an iterative fashion. This method requires that the earthquake source model is known. However, the release of energy in large earthquakes used for the analysis of Earth's normal modes is not simple. A point source approximation is often inadequate, and a more complete account of energy release at the source is required. In addition, many earthquakes are required for the solution to be insensitive to the initial constraints and regularization. In contrast to an iterative approach, the autoregressive linear inversion technique conveniently avoids the need for earthquake source parameters, but it also requires a number of events to achieve full convergence when a single event does not excite all singlets well. To build on previous improvements, we develop a technique to estimate structure coefficients (and consequently, the splitting functions) using a derivative-free parameter search, known as neighbourhood algorithm (NA). We implement an efficient forward method derived using the autoregresssion of receiver strips, and this allows us to search over a multiplicity of structure coefficients in a relatively short time. After demonstrating feasibility of the use of NA in synthetic cases, we apply it to observations of the inner core sensitive mode 13S2. The splitting function of this mode is dominated by spherical harmonic degree 2 axisymmetric structure and is consistent with the results obtained from the autoregressive linear inversion. The sensitivity analysis of multiple events confirms the importance of the Bolivia, 1994 earthquake. When this event is used in the analysis, as little as two events are sufficient to constrain the splitting functions of 13S2 mode. Apart from

  11. Source models of great earthquakes from ultra low-frequency normal mode data

    NASA Astrophysics Data System (ADS)

    Lentas, Konstantinos; Ferreira, Ana; Clévédé, Eric

    2014-05-01

    We present a new earthquake source inversion technique based on normal mode data for the simultaneous determination of the rupture duration, length and moment tensor of large earthquakes with unilateral rupture. We use ultra low-frequency (f < 1 mHz) normal mode spheroidal multiplets and the phases of split free oscillations, which are modelled using Higher Order Perturbation Theory (HOPT), taking into account the Earth's rotation, ellipticity and lateral heterogeneities. A Monte Carlo exploration of the model space is carried out, enabling the assessment of source parameter tradeoffs and uncertainties. We carry out synthetic tests for four different realistic artificial earthquakes with different faulting mechanisms and magnitudes (Mw 8.1-9.3) to investigate errors in the source inversions due to: (i) unmodelled 3-D Earth structure; (ii) noise in the data; (iii) uncertainties in spatio-temporal earthquake location; and, (iv) neglecting the source finiteness in point source moment tensor inversions. We find that unmodelled 3-D structure is the most serious source of errors for rupture duration and length determinations especially for the lowest magnitude artificial events. The errors in moment magnitude and fault mechanism are generally small, with the rake angle showing systematically larger errors (up to 20 degrees). We then carry out source inversions of five giant thrust earthquakes (Mw ≥ 8.5): (i) the 26 December 2004 Sumatra-Andaman earthquake; (ii) the 28 March 2005 Nias, Sumatra earthquake; (iii) the 12 September 2007 Bengkulu earthquake; (iv) the Tohoku, Japan earthquake of 11 March 2011; (v) the Maule, Chile earthquake of 27 February 2010; and (vi) the recent 24 May 2013 Mw 8.3 Okhotsk Sea, Russia, deep (607 km) earthquake. While finite source inversions for rupture length, duration, magnitude and fault mechanism are possible for the Sumatra-Andaman and Tohoku events, for all the other events their lower magnitudes do not allow stable inversions of mode

  12. Protein Normal Modes: Calculations of Amide Band Positions and Infrared Intensities for Helical Polypeptides and Proteins

    NASA Astrophysics Data System (ADS)

    Reisdorf, William Charles, Jr.

    To understand protein function requires input from a wide variety of techniques. The ability of diffraction and magnetic resonance studies to provide structural models with high atomic resolution are particularly crucial. Increasingly, information on protein dynamics is also sought. Vibrational spectroscopy can contribute information on the conformations of peptides and proteins, but the complexity of proteins makes interpretation of their spectra difficult. For this reason, computational models of protein vibrational modes are expected to play a major role in aiding our comprehension of protein dynamics. A set of FORTRAN programs referred to as 'POLYPEP' has been designed for computing the frequencies (eigenvalues) and normal modes (eigenvectors) of polypeptides of any structure. Model structures can be generated by specifying the backbone dihedral angles and using standard peptide group geometry. Alternatively one can use cartesian coordinates from experimental structures as input. The side chains are modeled as point masses, except for cysteine residues which may participate in disulfide linkages. Hydrogen bonding interactions between backbone groups are also included. The force fields adopted have been developed and refined to accurately reproduce the vibrational modes of alpha-helical and beta -sheet conformations of poly-L-alanine. Preliminary attempts have also been made for modifying selected force constants according to variations in hydrogen bond strength. Dipole derivatives for the peptide group are taken from an ab initio study of hydrogen-bonded N-methylacetamide. Those values, in combination with the calculated eigenvectors and frequencies, allow determination of infrared intensities for selected spectral regions, and the use of transition dipole coupling theory to obtain better frequencies. The present work involves application of this model to studies of model helical polypeptides and proteins. For the model structures (alpha-helix, 3 _{10}-helix

  13. Source models of great earthquakes from ultra low-frequency normal mode data

    NASA Astrophysics Data System (ADS)

    Lentas, K.; Ferreira, A. M. G.; Clévédé, E.; Roch, J.

    2014-08-01

    We present a new earthquake source inversion technique based on normal mode data for the simultaneous determination of the rupture duration, length and moment tensor of large earthquakes with unilateral rupture. We use ultra low-frequency (f <1 mHz) mode singlets and multiplets which are modelled using Higher Order Perturbation Theory (HOPT), taking into account the Earth’s rotation, ellipticity and lateral heterogeneities. A Monte Carlo exploration of the model space is carried out, enabling the assessment of source parameter tradeoffs and uncertainties. We carry out synthetic tests to investigate errors in the source inversions due to: (i) unmodelled 3-D Earth structure; (ii) noise in the data; (iii) uncertainties in spatio-temporal earthquake location; and, (iv) neglecting the source finiteness in point source inversions. We find that unmodelled 3-D structure is the most serious source of errors for rupture duration and length determinations especially for the lowest magnitude events. The errors in moment magnitude and fault mechanism are generally small, with the rake angle showing systematically larger errors (up to 20°). We then investigate five real thrust earthquakes (Mw⩾8.5): (i) Sumatra-Andaman (26th December 2004); (ii) Nias, Sumatra (28th March 2005); (iii) Bengkulu (12th September 2007); (iv) Tohoku, Japan (11th March 2011); (v) Maule, Chile (27th February 2010); and, (vi) the 24 May 2013 Mw 8.3 Okhotsk Sea, Russia, deep (607 km) event. While finite source inversions for rupture length, duration, magnitude and fault mechanism are possible for the Sumatra-Andaman and Tohoku events, for all the other events their lower magnitudes only allow stable point source inversions of mode multiplets. We obtain the first normal mode finite source model for the 2011 Tohoku earthquake, which yields a fault length of 461 km, a rupture duration of 151 s, and hence an average rupture velocity of 3.05 km/s, giving an independent confirmation of the compact nature of

  14. Possibility of observation of polaron normal modes at the far-infrared spectrum of acetanilide and related organics

    NASA Astrophysics Data System (ADS)

    Kalosakas, G.; Aubry, S.; Tsironis, G. P.

    1998-10-01

    We use a stationary and normal mode analysis of the semiclassical Holstein model in order to connect the low-frequency linear polaron modes to low-lying far-infrared lines of the acetanilide spectrum and through parameter fitting we comment on the validity of the polaron results in this system.

  15. Computational modes and the Machenauer N.L.N.M.I. of the GLAS 4th order model. [NonLinear Normal Mode Initialization in numerical weather forecasting

    NASA Technical Reports Server (NTRS)

    Navon, I. M.; Bloom, S.; Takacs, L. L.

    1985-01-01

    An attempt was made to use the GLAS global 4th order shallow water equations to perform a Machenhauer nonlinear normal mode initialization (NLNMI) for the external vertical mode. A new algorithm was defined for identifying and filtering out computational modes which affect the convergence of the Machenhauer iterative procedure. The computational modes and zonal waves were linearly initialized and gravitational modes were nonlinearly initialized. The Machenhauer NLNMI was insensitive to the absence of high zonal wave numbers. The effects of the Machenhauer scheme were evaluated by performing 24 hr integrations with nondissipative and dissipative explicit time integration models. The NLNMI was found to be inferior to the Rasch (1984) pseudo-secant technique for obtaining convergence when the time scales of nonlinear forcing were much smaller than the time scales expected from the natural frequency of the mode.

  16. On the sensitivity of protein data bank normal mode analysis: an application to GH10 xylanases

    NASA Astrophysics Data System (ADS)

    Tirion, Monique M.

    2015-12-01

    Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing the results on one class of glycosidases: family 10 xylanases. A conserved tryptophan that appears to affect access to the active site can be in one of two conformations according to x-ray crystallographic electron density data. The two alternate orientations of this active site tryptophan lead to distinct flexibility spectra, with one orientation thwarting the oscillations seen in the other. The particular orientation of this sidechain furthermore affects the appearance of the motility of a distant, C terminal region we term the mallet. The mallet region is known to separate members of this family of enzymes into two classes.

  17. On the sensitivity of protein data bank normal mode analysis: an application to GH10 xylanases.

    PubMed

    Tirion, Monique M

    2015-01-01

    Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing the results on one class of glycosidases: family 10 xylanases. A conserved tryptophan that appears to affect access to the active site can be in one of two conformations according to x-ray crystallographic electron density data. The two alternate orientations of this active site tryptophan lead to distinct flexibility spectra, with one orientation thwarting the oscillations seen in the other. The particular orientation of this sidechain furthermore affects the appearance of the motility of a distant, C terminal region we term the mallet. The mallet region is known to separate members of this family of enzymes into two classes. PMID:26599799

  18. Rotational normal modes of triaxial two-layered anelastic Earth model

    NASA Astrophysics Data System (ADS)

    Yang, Zhuo; Shen, WenBin

    2016-04-01

    This study focuses on providing rotational normal modes of a triaxial two-layered anelastic Earth model with considering the electromagnetic coupling. We formulate the rotation equation of the triaxial two-layered anelastic Earth model and then provide solution of that equation. We obtain four mathematically possible solutions which might exist in reality. Based on present choice of the conventional reference systems, only two of these four solutions correspond to the real existing prograde Chandler wobble (CW) and the retrograde free core nutation (FCN). We provide the periods of CW and FCN as well as their quality factors based on various experiments and observations. This study is supported by National 973 Project China (grant No. 2013CB733305) and NSFC (grant Nos. 41174011, 41210006, 41429401).

  19. Streaky noise in seismic normal mode band observed at Syowa Station, Antarctica

    NASA Astrophysics Data System (ADS)

    Hayakawa, H.; Shibuya, K.; Doi, K.; Aoyama, Y.

    2010-12-01

    Background free oscillations are known as continuous and global signals on noise level in seismic normal mode band. These were found from record of superconducting gravimeter (SG) at Syowa Station, Antarctica in 1998 [Nawa et al. 1998], and then were confirmed at various sites. Other unknown slightly broad spectrum peaks were also found as streak on spectrogram of Syowa SG data in seismic normal mode band. But the feature is not found in gravimeter and seismometer records from any other sites, including IDA gravimeter record at SPA station, Antarctica. New SG (SG058), that is the third generation at Syowa Station, has started to observe since January 2010. The second generation SG (CT43, 2004-2009) had strong drift. The auxiliary barometer was less resolution (0.1 hPa) and its pressure record had a lot of steps and spikes occurring frequently by housing problem. To study in seismic normal mode band, high quality pressure data is needed to remove atmospheric pressure effect to gravity from SG data because a nominal admittance factor for its effect is -3 nm/s^2/hPa. The new barometer of SG058 system has a resolution of 0.001 hPa, and the housing problem has been fixed. In this study, we investigated the unknown streaky noise in seismic normal mode band using spectrograms of the new SG and other data observed at Syowa Station. The slightly broad spectrum peaks are clearly found at 2.5, 3.5, 7.6, 8.2 13.2, 16.7 mHz from the SG data during January - May 2010. Strength of these peaks shows time variation and it is not necessarily for phase to agree with each others. These unknown peaks are not intrinsic noise of the first generation SG (TT70, 1993 - 2003) but are local or regional signal (noise) around Syowa Station. The atmospheric pressure doesn’t have this steaky feature. The sea level variation causes noise level of Syowa SG data to be high by the effect of attraction and loading [Nawa et al. 2003]. Because the noise spectral peaks less than 3 mHz are removed by

  20. Regional variation of inner core anisotropy from seismic normal mode observations.

    PubMed

    Deuss, Arwen; Irving, Jessica C E; Woodhouse, John H

    2010-05-21

    Earth's solid inner core is surrounded by a convecting liquid outer core, creating the geodynamo driving the planet's magnetic field. Seismic studies using compressional body waves suggest hemispherical variation in the anisotropic structure of the inner core, but are poorly constrained because of limited earthquake and receiver distribution. Here, using normal mode splitting function measurements from large earthquakes, based on extended cross-coupling theory, we observe both regional variations and eastern versus western hemispherical anisotropy in the inner core. The similarity of this pattern with Earth's magnetic field suggests freezing-in of crystal alignment during solidification or texturing by Maxwell stress as origins of the anisotropy. These observations limit the amount of inner core super rotation, but would be consistent with oscillation. PMID:20395476

  1. Normal mode analysis of single bunch, charge density dependent behavior in electron/positron beams

    NASA Astrophysics Data System (ADS)

    Ehrlichman, Michael

    Accelerator science in coming years will be increasingly dependent upon high single-bunch charges and/or small emittances. Under these conditions, single-particle dynamics are not a sufficient description of beam behavior and interactions between the beam particles must be taken into account. One such interaction is when collisions between the particles that compose a bunch perturb the motion of the colliding particles significantly and frequently enough to impact the beam dynamics. Multiple, small-angle, collisions blow up the emittance of the bunch and are referred to as intrabeam scattering (IBS). Here are documented the theoretical and experimental studies of IBS in storage rings undertaken as part of the CesrTA program. Under the conditions where IBS becomes dominant, other multi-particle effects can also appear. The additional effects we investigate include potential well distortion, coherent current-dependent tune shift, and direct space charge. CesrTA design and analysis is conducted in a normal mode coordinates environment which allows for natural handling of coupling. To that end, we develop a 6D normal modes decomposition of the linear beam optics. Multi-particle effects are also important for Energy Recovery Linear Accelerators (ERLs). Because the beam circulates for only a short period of time in an ERL, the beam lifetime imposed by Touschek scattering is not significant. However, the particles scattered out of the bunch can generate a radiation hazard where they collide with the beam pipe. We re-derive Piwinski's original Touschek scattering equation to check its validity when applied to ERL beams, then repurpose the formula to generate a profile of where scattered particles are generated and where they are lost. The results presented here advance our understanding of charge-dependent behavior in the sorts of high charge-density accelerators that will be implemented in coming years.

  2. Anharmonicity and necessity of phonon eigenvectors in the phonon normal mode analysis

    SciTech Connect

    Feng, Tianli; Qiu, Bo; Ruan, Xiulin

    2015-05-21

    It is well known that phonon frequencies can shift from their harmonic values when elevated to a finite temperature due to the anharmonicity of interatomic potential. Here, we show that phonon eigenvectors also have shifts, but only for compound materials in which each atom has at least two types of anharmonic interactions with other atoms. Using PbTe as the model material, we show that the shifts in some phonon modes may reach as much as 50% at 800 K. Phonon eigenvectors are used in normal mode analysis (NMA) to predict phonon relaxation times and thermal conductivity. We show, from both analytical derivations and numerical simulations, that the eigenvectors are unnecessary in frequency-domain NMA, which gives a critical revision of previous knowledge. This simplification makes the calculation in frequency-domain NMA more convenient since no separate lattice dynamics calculations are needed. On the other hand, we expect our finding of anharmonic eigenvectors may make difference in time-domain NMA and other areas, like wave-packet analysis.

  3. Constructing the frequency and wave normal distribution of whistler-mode wave power

    NASA Astrophysics Data System (ADS)

    Watt, C. E. J.; Degeling, A. W.; Rankin, R.

    2013-05-01

    We introduce a new methodology that allows the construction of wave frequency distributions due to growing incoherent whistler-mode waves in the magnetosphere. The technique combines the equations of geometric optics (i.e., raytracing) with the equation of transfer of radiation in an anisotropic lossy medium to obtain spectral energy density as a function of frequency and wavenormal angle. We describe the method in detail and then demonstrate how it could be used in an idealized magnetosphere during quiet geomagnetic conditions. For a specific set of plasma conditions, we predict that the wave power peaks off the equator at ˜15° magnetic latitude. The new calculations predict that wave power as a function of frequency can be adequately described using a Gaussian function, but as a function of wavenormal angle, it more closely resembles a skew normal distribution. The technique described in this paper is the first known estimate of the parallel and oblique incoherent wave spectrum as a result of growing whistler-mode waves and provides a means to incorporate self-consistent wave-particle interactions in a kinetic model of the magnetosphere over a large volume.

  4. Instantaneous normal mode prediction for cation and anion diffusion in ionic melts

    NASA Astrophysics Data System (ADS)

    Ribeiro, M. C. C.; Madden, P. A.

    1997-05-01

    Instantaneous normal mode (INM) analysis was undertaken for several ionic melts: NaCl at six distinct thermodynamic states, and for a particular state of liquid LiCl, LiF, KF, KI, NaI, ZnCl2, and CuCl. In this Communication, we show that, in most cases, the ratio between the diffusion constants for cations (Dca) and anions (Dan) is predicted from the average frequency of the real ("stable" <ωs>) and imaginary ("unstable" <ωu>) frequency modes of the projection of the total density of states on cations and anions, respectively. The proposed relationship, Dca/Dan=(mca-1<ωu>ca<ωs>ca-2)ṡ(man-1<ωu>an<ωs>an-2)-1, where mi is the mass of a particular species, is suggested by Keyes' INM theory for diffusion [J. Chem. Phys. 101, 5081 (1994)], with the further assumption that the parameters which are related to the topology of the multidimensional potential surface are equal for cations and anions. The above equation is shown to be valid for the simple melts NaCl, LiCl, LiF, KF, KI, and NaI, but to fail for the network forming melt ZnCl2 and for CuCl, which shows fast ionic diffusion characteristics.

  5. Notch strengthening or weakening governed by transition of shear failure to normal mode fracture

    PubMed Central

    Lei, Xianqi; Li, Congling; Shi, Xinghua; Xu, Xianghong; Wei, Yujie

    2015-01-01

    It is generally observed that the existence of geometrical discontinuity like notches in materials will lead to strength weakening, as a resultant of local stress concentration. By comparing the influence of notches to the strength of three typical materials, aluminum alloys with intermediate tensile ductility, metallic glasses with no tensile ductility, and brittle ceramics, we observed strengthening in aluminum alloys and metallic glasses: Tensile strength of the net section in circumferentially notched cylinders increases with the constraint quantified by the ratio of notch depth over notch root radius; in contrast, the ceramic exhibit notch weakening. The strengthening in the former two is due to resultant deformation transition: Shear failure occurs in intact samples while samples with deep notches break in normal mode fracture. No such deformation transition was observed in the ceramic, and stress concentration leads to its notch weakening. The experimental results are confirmed by theoretical analyses and numerical simulation. The results reported here suggest that the conventional criterion to use brittleness and/or ductility to differentiate notch strengthening or weakening is not physically sound. Notch strengthening or weakening relies on the existence of failure mode transition and materials exhibiting shear failure while subjected to tension will notch strengthen. PMID:26022892

  6. Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis.

    PubMed

    Panjkovich, Alejandro; Svergun, Dmitri I

    2016-02-17

    Structural flexibility and conformational rearrangements are often related to important functions of biological macromolecules, but the experimental characterization of such transitions with high-resolution techniques is challenging. At a lower resolution, small angle X-ray scattering (SAXS) can be used to obtain information on biomolecular shapes and transitions in solution. Here, we present SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data. The method starts from a given conformation of the protein (which does not agree with the SAXS data). The structure is partitioned into pseudo-domains either using structural classification databases or automatically from the protein dynamics as predicted by the NMA. The algorithm proceeds hierarchically employing NMA to first probe large rearrangements and progresses into smaller and more localized movements. At the large rearrangements stage the pseudo-domains stay as rigid bodies allowing one to avoid structural disruptions inherent to the earlier NMA-based algorithms. To validate the approach, we compiled a representative benchmark set of 88 conformational states known experimentally at high resolution. The performance of the algorithm is demonstrated in the simulated data on the benchmark set and also in a number of experimental examples. SREFLEX is included into the ATSAS program package freely available to the academic users, both for download and in the on-line mode. PMID:26611321

  7. Notch strengthening or weakening governed by transition of shear failure to normal mode fracture.

    PubMed

    Lei, Xianqi; Li, Congling; Shi, Xinghua; Xu, Xianghong; Wei, Yujie

    2015-01-01

    It is generally observed that the existence of geometrical discontinuity like notches in materials will lead to strength weakening, as a resultant of local stress concentration. By comparing the influence of notches to the strength of three typical materials, aluminum alloys with intermediate tensile ductility, metallic glasses with no tensile ductility, and brittle ceramics, we observed strengthening in aluminum alloys and metallic glasses: Tensile strength of the net section in circumferentially notched cylinders increases with the constraint quantified by the ratio of notch depth over notch root radius; in contrast, the ceramic exhibit notch weakening. The strengthening in the former two is due to resultant deformation transition: Shear failure occurs in intact samples while samples with deep notches break in normal mode fracture. No such deformation transition was observed in the ceramic, and stress concentration leads to its notch weakening. The experimental results are confirmed by theoretical analyses and numerical simulation. The results reported here suggest that the conventional criterion to use brittleness and/or ductility to differentiate notch strengthening or weakening is not physically sound. Notch strengthening or weakening relies on the existence of failure mode transition and materials exhibiting shear failure while subjected to tension will notch strengthen. PMID:26022892

  8. Dynamic and elastic properties of F-actin: a normal-modes analysis.

    PubMed Central

    ben-Avraham, D; Tirion, M M

    1995-01-01

    We examine the dynamic, elastic, and mechanical consequences of the proposed atomic models of F-actin, using a normal mode analysis. This initial analysis is done in vacuo and assumes that all monomers are rigid and equivalent. Our computation proceeds from the atomic level and, relying on a single fitting parameter, reproduces various experimental results, including persistence lengths, elastic moduli, and contact energies. The computations reveal modes of motion characteristic to all polymers, such as longitudinal pressure waves, torsional waves, and bending, as well as motions unique to F-actin. Motions typical to actin include a "groove-swinging" motion of the two long-pitch helices, as well as an axial slipping motion of the two strands. We prepare snapshots of thermally activated filaments and quantify the accumulation of azimuthal angular "disorder," variations in cross-over lengths, and various other fluctuations. We find that the orientation of a small number of select residues has a surprisingly large effect on the filament flexibility and elasticity characteristics. PMID:7787015

  9. Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies.

    PubMed

    De Moor, Bart A; Ghysels, An; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B

    2011-04-12

    An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated for the physisorption and chemisorption of n-octane and isobutene in H-ZSM-22 and H-FAU using periodic DFT calculations employing the Vienna Ab Initio Simulation Package. Physisorption and chemisorption entropies resulting from partial Hessian vibrational analysis (PHVA) differ at most 10 J mol(-1) K(-1) from those resulting from full Hessian vibrational analysis, even for PHVA schemes in which only a very limited number of atoms are considered free. To acquire a well-conditioned Hessian, much tighter optimization criteria than commonly used for electronic energy calculations in zeolites are required, i.e., at least an energy cutoff of 400 eV, maximum force of 0.02 eV/Å, and self-consistent field loop convergence criteria of 10(-8) eV. For loosely bonded complexes the mobile adsorbate method is applied, in which frequency contributions originating from translational or rotational motions of the adsorbate are removed from the total partition function and replaced by free translational and/or rotational contributions. The frequencies corresponding with these translational and rotational modes can be selected unambiguously based on a mobile block Hessian-PHVA calculation, allowing the prediction of physisorption entropies within an accuracy of 10-15 J mol(-1) K(-1) as compared to experimental values. The approach presented in this study is useful for studies on other extended catalytic systems. PMID:26606357

  10. Measurement of nonlinear normal modes using multi-harmonic stepped force appropriation and free decay

    NASA Astrophysics Data System (ADS)

    Ehrhardt, David A.; Allen, Matthew S.

    2016-08-01

    Nonlinear Normal Modes (NNMs) offer tremendous insight into the dynamic behavior of a nonlinear system, extending many concepts that are familiar in linear modal analysis. Hence there is interest in developing methods to experimentally and numerically determine a system's NNMs for model updating or simply to characterize its dynamic response. Previous experimental work has shown that a mono-harmonic excitation can be used to isolate a system's dynamic response in the neighborhood of a NNM along the main backbones of a system. This work shows that a multi-harmonic excitation is needed to isolate a NNM when well separated linear modes of a structure couple to produce an internal resonance. It is shown that one can tune the multiple harmonics of the input excitation using a plot of the input force versus the response velocity until the area enclosed by the force-velocity curve is minimized. Once an appropriated NNM is measured, one can increase the force level and retune the frequency to obtain a NNM at a higher amplitude or remove the excitation and measure the structure's decay down a NNM backbone. This work explores both methods using simulations and measurements of a nominally-flat clamped-clamped beam excited at a single point with a magnetic force. Numerical simulations are used to validate the method in a well defined environment and to provide comparison with the experimentally measured NNMs. The experimental results seem to produce a good estimate of two NNMs along their backbone and part of an internal resonance branch. Full-field measurements are then used to further explore the couplings between the underlying linear modes along the identified NNMs.

  11. Nonlinear acoustic experiments for landmine detection: the significance of the top-plate normal modes

    NASA Astrophysics Data System (ADS)

    Korman, Murray S.; Alberts, W. C. K., II; Sabatier, James M.

    2004-09-01

    In nonlinear acoustic detection experiments involving a buried inert VS 2.2 anti-tank landmine, airborne sound at two closely spaced primary frequencies f1 and f2 couple into the ground and interact nonlinearly with the soil-top pressure plate interface. Scattering generates soil vibration at the surface at the combination frequencies | m f1 +- n f2 | , where m and n are integers. The normal component of the particle velocity at the soil surface has been measured with a laser Doppler velocimeter (LDV) and with a geophone by Sabatier et. al. [SPIE Proceedings Vol. 4742, (695-700), 2002; Vol. 5089, (476-486), 2003] at the gravel lane test site. Spatial profiles of the particle velocity measured for both primary components and for various combination frequencies indicate that the modal structure of the mine is playing an important role. Here, an experimental modal analysis is performed on a VS 1.6 inert anti-tank mine that is resting on sand but is not buried. Five top-plate mode shapes are described. The mine is then buried in dry finely sifted natural loess soil and excited at f1 = 120 Hz and f2 = 130 Hz. Spatial profiles at the primary components and the nonlinearly generated f1 - (f2 - f1) component are characterized by a single peak. For the 2f1+f2 and 2f2 + f1 components, the doubly peaked profiles can be attributed to the familiar mode shape of a timpani drum (that is shifted lower in frequency due to soil mass loading). Other nonlinear profiles appear to be due to a mixture of modes. This material is based upon work supported by the U. S. Army RDECOM CERDEC Night Vision and Electronic Sensors Directorate under Contract DAAB15-02-C-0024.

  12. High-energy square pulses and burst-mode pulses in an all-normal dispersion double-clad mode-locked fiber laser

    NASA Astrophysics Data System (ADS)

    Qiao, Zhi; Wang, Xiaochao; Wang, Chao; Jing, Yuanyuan; Fan, Wei; Lin, Zunqi

    2016-05-01

    A double-clad Yb-doped mode-locked fiber laser that can operate in burst-mode and square-pulse states is experimentally investigated. In the burst-mode state, a burst train with 55 pulses of 500 ps duration is obtained. In the square-pulse state, which is similar to noiselike pulses, the maximum pulse energy is 820 nJ and the duration can be tuned from 15.8 to 546 ns. The square pulses have a narrow and multipeak spectrum, which is quite different from that of normal noiselike pulses. The fiber laser promises an alternative formation mechanism for burst-mode and square-pulse mode-locked fiber lasers.

  13. A New Non-linear Technique for Measurement of Splitting Functions of Normal Modes of the Earth

    NASA Astrophysics Data System (ADS)

    Pachhai, S.; Masters, G.; Tkalcic, H.

    2014-12-01

    Normal modes are the vibrating patterns of the Earth in response to the large earthquakes. Normal mode spectra are split due to Earth's rotation, ellipticity, and heterogeneity. The normal mode splitting is visualized through splitting functions, which represent the local radial average of Earth's structure seen by a mode of vibration. The analysis of the splitting of normal modes can provide unique information about the lateral variation of the Earth's elastic properties that cannot be directly imaged in body wave tomographic images. The non-linear iterative spectral fitting of the observed complex spectra and autoregressive linear inversion have been widely utilized to compute the Earth's 3-D structure. However, the non-linear inversion requires a model of the earthquake source and the retrieved 3-D structure is sensitive to the initial constraints. In contrast, the autoregressive linear inversion does not require the source model. However, this method requires many events to achieve full convergence. In addition, significant disagreement exists between different studies because of the non-uniqueness of the problem and limitations of different methods. We thus apply the neighbourhood algorithm (NA) to measure splitting functions. The NA is an efficient model space search technique and works in two steps: In the first step, the algorithm finds all the models compatible with given data while the posterior probability density of the model parameters are obtained in the second step. The NA can address the problem of non-uniqueness by taking advantage of random sampling of the full model space. The parameter trade-offs are conveniently visualized using joint marginal distributions. In addition, structure coefficients uncertainties can be extracted from the posterior probability distribution. After demonstrating the feasibility of NA with synthetic examples, we compute the splitting functions for the mode 13S2 (sensitive to the inner core) from several large

  14. Dynamical instabilities and quasi-normal modes, a spectral analysis with applications to black-hole physics

    NASA Astrophysics Data System (ADS)

    Coutant, Antonin; Michel, Florent; Parentani, Renaud

    2016-06-01

    Black hole dynamical instabilities have been mostly studied in specific models. We here study the general properties of the complex-frequency modes responsible for such instabilities, guided by the example of a charged scalar field in an electrostatic potential. We show that these modes are square integrable, have a vanishing conserved norm, and appear in mode doublets or quartets. We also study how they appear in the spectrum and how their complex frequencies subsequently evolve when varying some external parameter. When working on an infinite domain, they appear from the reservoir of quasi-normal modes obeying outgoing boundary conditions. This is illustrated by generalizing, in a non-positive definite Krein space, a solvable model (Friedrichs model) which originally describes the appearance of a resonance when coupling an isolated system to a mode continuum. In a finite spatial domain instead, they arise from the fusion of two real frequency modes with opposite norms, through a process that closely resembles avoided crossing.

  15. On the normal modes of Laplace's tidal equations for zonal wavenumber zero

    NASA Technical Reports Server (NTRS)

    Tanaka, H. L.; Kasahara, Akira

    1992-01-01

    The characteristic differences between two different rotational modes of Laplace's tidal equations for wavenumber m = 0, called the K- and the S-modes, are compared in their energy ratio and structures. It is shown that the K-mode representation captures most of the observed zonal energy with a few terms, whereas the S-mode representation requires many terms. For small vertical scale components, the K-mode series converges faster than the S-mode series. Attention is also given to the differences between the energy spectra projected upon the K- and S-modes and the merits of each set as expansion functions for the zonal atmospheric motions.

  16. Wave normal angles of whistler mode chorus rising and falling tones

    NASA Astrophysics Data System (ADS)

    Taubenschuss, Ulrich; Khotyaintsev, Yuri V.; Santolík, Ondrej; Vaivads, Andris; Cully, Christopher M.; Contel, Olivier Le; Angelopoulos, Vassilis

    2014-12-01

    We present a study of wave normal angles (θk) of whistler mode chorus emission as observed by Time History of Events and Macroscale Interactions during Substorms (THEMIS) during the year 2008. The three inner THEMIS satellites THA, THD, and THE usually orbit Earth close to the dipole magnetic equator (±20°), covering a large range of L shells from the plasmasphere out to the magnetopause. Waveform measurements of electric and magnetic fields enable a detailed polarization analysis of chorus below 4 kHz. When displayed in a frequency-θk histogram, four characteristic regions of occurrence are evident. They are separated by gaps at f/fc,e≈0.5 (f is the chorus frequency, fc,e is the local electron cyclotron frequency) and at θk˜40°. Below θk˜40°, the average value for θk is predominantly field aligned, but slightly increasing with frequency toward half of fc,e (θk up to 20°). Above half of fc,e, the average θk is again decreasing with frequency. Above θk˜40°, wave normal angles are usually close to the resonance cone angle. Furthermore, we present a detailed comparison of electric and magnetic fields of chorus rising and falling tones. Falling tones exhibit peaks in occurrence solely for θk>40° and are propagating close to the resonance cone angle. Nevertheless, when comparing rising tones to falling tones at θk>40°, the ratio of magnetic to electric field shows no significant differences. Thus, we conclude that falling tones are generated under similar conditions as rising tones, with common source regions close to the magnetic equatorial plane.

  17. Characterizing structure connectivity correlation with the default mode network in Alzheimer's patients and normal controls

    NASA Astrophysics Data System (ADS)

    Guo, Jia; Xu, Peng; Song, Chao; Yao, Li; Zhao, Xiaojie

    2012-03-01

    Magnetic resonance diffusion tensor imaging (DTI) is a kind of effective measure to do non-invasive investigation on brain fiber structure at present. Studies of fiber tracking based on DTI showed that there was structural connection of white matter fiber among the nodes of resting-state functional network, denoting that the connection of white matter was the basis of gray matter regions in functional network. Nevertheless, relationship between these structure connectivity regions and functional network has not been clearly indicated. Moreover, research of fMRI found that activation of default mode network (DMN) in Alzheimer's disease (AD) was significantly descended, especially in hippocampus and posterior cingulated cortex (PCC). The relationship between this change of DMN activity and structural connection among functional networks needs further research. In this study, fast marching tractography (FMT) algorithm was adopted to quantitative calculate fiber connectivity value between regions, and hippocampus and PCC which were two important regions in DMN related with AD were selected to compute white matter connection region between them in elderly normal control (NC) and AD patient. The fiber connectivity value was extracted to do the correlation analysis with activity intensity of DMN. Results showed that, between PCC and hippocampus of NC, there exited region with significant high connectivity value of white matter fiber whose performance has relatively strong correlation with the activity of DMN, while there was no significant white matter connection region between them for AD patient which might be related with reduced network activation in these two regions of AD.

  18. Search for solar normal modes in low-frequency seismic spectra

    NASA Astrophysics Data System (ADS)

    Caton, Ross C.

    We use seismic array processing methods to attempt to enhance very low frequency harmonic signals (0-400 microhertz, also ?Hz or uHz) recorded on broadband seismic arrays. Since the discovery of this phenomenon in the 1990s, harmonic signals at these very low frequencies have come to be known as the Earth's "hum." A number of hypotheses have been suggested for the Earth's hum, including forcing by atmospheric turbulence, ocean waves, and, most recently, the Sun. We test the solar hypothesis by searching for statistically significant harmonic lines that correlate with independently observed solar free oscillations. The solar model assumes that free oscillations of the sun modulate the solar wind, producing pure harmonic components of Earth's magnetic field that are postulated to couple to the ground by electromagnetic induction. In this thesis we search the multitaper spectrum of stacks of seismic instruments for solar normal frequencies. We use a median stack instead of the more conventional mean because a more robust estimate of center is required for these low signal-to-noise data with occasional transients. A key advantage of a stack is that data gaps are easily ignored when computing the beam. Results from a stack of 18 Transportable Array stations show multiple possible g-mode detections at the 95-99% confidence level. We are presently applying this method to data from the Homestake Mine array, and may also do so with data from a broadband borehole array currently operating at Pinon Flats, California.

  19. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-01

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  20. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-28

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  1. Time reversal imaging and cross-correlations techniques by normal mode theory

    NASA Astrophysics Data System (ADS)

    Montagner, J.; Fink, M.; Capdeville, Y.; Phung, H.; Larmat, C.

    2007-12-01

    Time-reversal methods were successfully applied in the past to acoustic waves in many fields such as medical imaging, underwater acoustics, non destructive testing and recently to seismic waves in seismology for earthquake imaging. The increasing power of computers and numerical methods (such as spectral element methods) enables one to simulate more and more accurately the propagation of seismic waves in heterogeneous media and to develop new applications, in particular time reversal in the three-dimensional Earth. Generalizing the scalar approach of Draeger and Fink (1999), the theoretical understanding of time-reversal method can be addressed for the 3D- elastic Earth by using normal mode theory. It is shown how to relate time- reversal methods on one hand, with auto-correlation of seismograms for source imaging and on the other hand, with cross-correlation between receivers for structural imaging and retrieving Green function. The loss of information will be discussed. In the case of source imaging, automatic location in time and space of earthquakes and unknown sources is obtained by time reversal technique. In the case of big earthquakes such as the Sumatra-Andaman earthquake of december 2004, we were able to reconstruct the spatio-temporal history of the rupture. We present here some new applications at the global scale of these techniques on synthetic tests and on real data.

  2. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    SciTech Connect

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-07

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  3. Multi-scaled normal mode analysis method for dynamics simulation of protein-membrane complexes: A case study of potassium channel gating motion correlations

    NASA Astrophysics Data System (ADS)

    Wu, Xiaokun; Han, Min; Ming, Dengming

    2015-10-01

    Membrane proteins play critically important roles in many cellular activities such as ions and small molecule transportation, signal recognition, and transduction. In order to fulfill their functions, these proteins must be placed in different membrane environments and a variety of protein-lipid interactions may affect the behavior of these proteins. One of the key effects of protein-lipid interactions is their ability to change the dynamics status of membrane proteins, thus adjusting their functions. Here, we present a multi-scaled normal mode analysis (mNMA) method to study the dynamics perturbation to the membrane proteins imposed by lipid bi-layer membrane fluctuations. In mNMA, channel proteins are simulated at all-atom level while the membrane is described with a coarse-grained model. mNMA calculations clearly show that channel gating motion can tightly couple with a variety of membrane deformations, including bending and twisting. We then examined bi-channel systems where two channels were separated with different distances. From mNMA calculations, we observed both positive and negative gating correlations between two neighboring channels, and the correlation has a maximum as the channel center-to-center distance is close to 2.5 times of their diameter. This distance is larger than recently found maximum attraction distance between two proteins embedded in membrane which is 1.5 times of the protein size, indicating that membrane fluctuation might impose collective motions among proteins within a larger area. The hybrid resolution feature in mNMA provides atomic dynamics information for key components in the system without costing much computer resource. We expect it to be a conventional simulation tool for ordinary laboratories to study the dynamics of very complicated biological assemblies. The source code is available upon request to the authors.

  4. A normal mode treatment of semi-diurnal body tides on an aspherical, rotating and anelastic Earth

    NASA Astrophysics Data System (ADS)

    Lau, Harriet C. P.; Yang, Hsin-Ying; Tromp, Jeroen; Mitrovica, Jerry X.; Latychev, Konstantin; Al-Attar, David

    2015-08-01

    Normal mode treatments of the Earth's body tide response were developed in the 1980s to account for the effects of Earth rotation, ellipticity, anelasticity and resonant excitation within the diurnal band. Recent space-geodetic measurements of the Earth's crustal displacement in response to luni-solar tidal forcings have revealed geographical variations that are indicative of aspherical deep mantle structure, thus providing a novel data set for constraining deep mantle elastic and density structure. In light of this, we make use of advances in seismic free oscillation literature to develop a new, generalized normal mode theory for the tidal response within the semi-diurnal and long-period tidal band. Our theory involves a perturbation method that permits an efficient calculation of the impact of aspherical structure on the tidal response. In addition, we introduce a normal mode treatment of anelasticity that is distinct from both earlier work in body tides and the approach adopted in free oscillation seismology. We present several simple numerical applications of the new theory. First, we compute the tidal response of a spherically symmetric, non-rotating, elastic and isotropic Earth model and demonstrate that our predictions match those based on standard Love number theory. Second, we compute perturbations to this response associated with mantle anelasticity and demonstrate that the usual set of seismic modes adopted for this purpose must be augmented by a family of relaxation modes to accurately capture the full effect of anelasticity on the body tide response. Finally, we explore aspherical effects including rotation and we benchmark results from several illustrative case studies of aspherical Earth structure against independent finite-volume numerical calculations of the semi-diurnal body tide response. These tests confirm the accuracy of the normal mode methodology to at least the level of numerical error in the finite-volume predictions. They also demonstrate

  5. Normal modes of oscillation of the Asinelli and Garisenda towers in Bologna (Italy)

    NASA Astrophysics Data System (ADS)

    Morelli, A.; Azzara, R. M.; Cavaliere, A.; Zaccarelli, L.

    2013-12-01

    The Asinelli and Garisenda medieval towers represent the best-know city landmark in Bologna. Asinelli is also known to physics historians for early experiments on free fall of bodies for the first measurements of g (Giovanni Battista Riccioli, ca. 1650) and proof of Earth rotation (Giovanni Battista Guglielmini, 1791). The Two Towers (as they are commonly known) are essentially tall, square cross-section hollow masonry cuboids. Taller Asinelli, built between 1109 and 1119, is 97 m high, with an overhang of 2.2 m, while more seriously leaning Garisenda has an overhang of 3.2 m with a heigth of 48 m. During the summer of 2012 -- in the aftermath of two M≈6 earthquakes occurred in the proximity of the city -- the permanent engineering monitoring system of the towers has been temporarily supplemented by 6 seismometric stations installed at different levels inside the masonry buildings, to study their dynamical response to induced vibrations. We have thus been able to observe and measure the oscillation of the two towers excited by ambient noise, mostly due to city traffic. The two towers show similar behaviour, more clear in taller Asinelli. The first three flexural normal modes of oscillation, and the first torsional mode, can easily be detected. Their frequencies are split because of the asymmetry due to leaning of the tower. This asymmetry produces slightly different frequencies of oscillation in two orthogonal directions, quite consistent with preliminary dynamical modeling. Horizontal particle-motion polarization plots clearly show the cyclic energy transfer between these two degrees of freedom of the system. Oscillations of taller Asinelli influence its close sister, such that the Asinelli spectral signature can also be easily recognized in the motion recorded at the base of Garisenda, overimposed over Garisenda own free oscillations. Horizontal component polarization analysis done simultaneously at the two ground-level stations often point to a nearby common

  6. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

  7. Normal modes of the atmosphere as estimated by principal oscillation patterns and derived from quasigeostrophic theory

    SciTech Connect

    Schnur, R.; Storch, H. von ); Schmitz, G.; Grieger, N. )

    1993-08-01

    The principal oscillation pattern (POP) analysis is a technique to empirically identify time-dependent spatial patterns in a multivariate time series of geophysical or other data. In order to investigate medium-scale and synoptic waves in the atmosphere it has been applied to tropospheric geopotential height fields of ECMWF analyses from 1984 to 1987. The data have been subjected to zonal Fourier decomposition and to time filtering so that variations with periods between 3 and 25 days were retained. Analyses have been performed separately for each zonal wavenumber 5-9 on the Northern Hemisphere in winter and on the Southern Hemisphere in summer (DJF). POPs can be seen as normal modes of a linear approximation to a more complex dynamical system. The system matrix is estimated from observations of nature. This concept is compared with conventional stability analysis where the system matrix of the linear system is derived from theoretical, in this case quasigeostrophic, reasoning. Only the mean basic flow depends on time- and space-averaged fields of observed wind and temperature from the ECMWF data. It turns out that the most significant POPs are very similar in time and spatial structure to the most unstable waves in the stability analysis. They describe the linear growth phase of baroclinic, unstable waves that propagate eastward with periods of 3-7 days. Since the POPs are purely derived from observations, the results indicate the appropriateness of the assumptions usually made in linear stability analysis of zonally symmetric flows to explain high-frequency atmospheric fluctuations. Moreover, the POP analysis reveals patterns that are not found in the linear stability analysis. These can possibly be attributed to the nonlinear decay phase of baroclinic waves. Eliassen-Palm cross sections help clarify the interpretation of the POPs in terms of the life cycle of nonlinear baroclinic waves. 24 refs., 14 figs.

  8. Normal mode analysis of macromolecular systems with the mobile block Hessian method

    SciTech Connect

    Ghysels, An; Van Speybroeck, Veronique; Van Neck, Dimitri; Waroquier, Michel; Brooks, Bernard R.

    2015-01-22

    Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N{sub a}×3N{sub a} matrix with N{sub a} the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

  9. Normal mode analysis of macromolecular systems with the mobile block Hessian method

    NASA Astrophysics Data System (ADS)

    Ghysels, An; Van Speybroeck, Veronique; Van Neck, Dimitri; Brooks, Bernard R.; Waroquier, Michel

    2015-01-01

    Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na×3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

  10. Efficient forward and adjoint calculations of normal mode spectra in laterally heterogeneous earth models using an iterative direct solution method

    NASA Astrophysics Data System (ADS)

    Al-Attar, D.; Woodhouse, J. H.

    2011-12-01

    Normal mode spectra provide a valuable data set for global seismic tomography, and, notably, are amongst the few geophysical observables that are sensitive to lateral variations in density structure within the Earth. Nonetheless, the effects of lateral density variations on mode spectra are rather subtle. In order, therefore, to reliably determine density variations with in the earth, it is necessary to make use of sufficiently accurate methods for calculating synthetic mode spectra. In particular, recent work has highlighted the need to perform 'full-coupling calculations' that take into account the interaction of large numbers of spherical earth multiplets. However, present methods for performing such full-coupling calculations require diagonalization of large coupling matrices, and so become computationally inefficient as the number of coupled modes is increased. In order to perform full-coupling calculations more efficiently, we describe a new implementation of the direct solution method for calculating synthetic spectra in laterally heterogeneous earth models. This approach is based on the solution of the inhomogeneous mode coupling equations in the frequency domain, and does not require the diagonalization of large matrices. Early implementations of the direct solution method used LU-decomposition to solve the mode coupling equations. However, as the number of coupled modes is increased, this method becomes impractically slow. To circumvent this problem, we solve the mode coupling equations iteratively using the preconditioned biconjugate gradient algorithm. We present a number of numerical tests to display the accuracy and efficiency of this method for performing large full-coupling calculations. In addition, we describe a frequency-domain formulation of the adjoint method for the calculation of Frechet kernels that show the sensitivity of normal mode observations to variations in earth structure. The calculation of such Frechet kernels involves one solution

  11. The quasi-normal modes of charged scalar fields in Kerr-Newman black hole and its geometric interpretation

    NASA Astrophysics Data System (ADS)

    Zhao, Peng; Tian, Yu; Wu, Xiaoning; Sun, Zhao-Yong

    2015-11-01

    It is well-known that there is a geometric correspondence between high-frequency quasi-normal modes (QNMs) and null geodesics (spherical photon orbits). In this paper, we generalize such correspondence to charged scalar field in Kerr-Newman space-time. In our case, the particle and black hole are all charged, so one should consider non-geodesic orbits. Using the WKB approximation, we find that the real part of quasi-normal frequency corresponds to the orbits frequency, the imaginary part of the frequency corresponds to the Lyapunov exponent of these orbits and the eigenvalue of angular equation corresponds to carter constant. From the properties of the imaginary part of quasi-normal frequency of charged massless scalar field, we can still find that the QNMs of charged massless scalar field possess the zero damping modes in extreme Kerr-Newman spacetime under certain condition which has been fixed in this paper.

  12. Default mode network connectivity in patients with idiopathic normal pressure hydrocephalus.

    PubMed

    Khoo, Hui Ming; Kishima, Haruhiko; Tani, Naoki; Oshino, Satoru; Maruo, Tomoyuki; Hosomi, Koichi; Yanagisawa, Takufumi; Kazui, Hiroaki; Watanabe, Yoshiyuki; Shimokawa, Toshio; Aso, Toshihiko; Kawaguchi, Atsushi; Yamashita, Fumio; Saitoh, Youichi; Yoshimine, Toshiki

    2016-02-01

    OBJECT Idiopathic normal pressure hydrocephalus (iNPH) is a neurological disorder characterized by gait disturbance, cognitive impairment, and incontinence. It is unclear whether the pathophysiology of iNPH is associated with alterations in the default mode network (DMN). The authors investigated alterations in the DMN of patients with iNPH and sought to determine whether a relationship exists between the resting-state functional connectivity of the DMN and a patient's clinical symptoms. METHODS Resting-state functional MRI (rs-fMRI) was performed in 16 preoperative patients with iNPH and 15 neurologically healthy control subjects of a similar age. Independent component and dual-regression analyses were used to quantify DMN connectivity. The patients' clinical symptoms were rated according to the iNPH grading scale (iNPHGS). Each of their specific clinical symptoms were rated according to the cognitive, gait, and urinary continence domains of iNPHGS, and neurocognitive status was assessed using the Mini-Mental State Examination, Frontal Assessment Battery (FAB), and Trail Making Test Part A. The strength of DMN connectivity was compared between patients and controls, and the correlation between DMN connectivity and iNPHGS was examined using both region of interest (ROI)-based analysis and voxel-based analysis. The correlation between DMN connectivity and each of the specific clinical symptoms, as well as neurocognitive status, was examined using voxel-based analysis. RESULTS Both ROI-based and voxel-based analyses revealed reduced DMN connectivity in patients with iNPH. ROI-based analysis showed increased DMN connectivity with worsening clinical symptoms of iNPH. Consistently, voxel-based analyses revealed that DMN connectivity correlated positively with the iNPHGS score, as well as the cognitive and urinary continence domain scores, and negatively with the FAB score. The significant peak in correlation in each case was localized to the precuneus. CONCLUSIONS This

  13. Antisymmetric resonant mode and negative refraction in double-ring resonators under normal-to-plane incidence.

    PubMed

    Ding, P; Liang, E J; Zhang, L; Zhou, Q; Yuan, Y X

    2009-01-01

    Compared to metallic composite metamaterials of double split-ring resonators with wires, double-ring resonators without additional wires are simple to engineer. In this paper, we have numerically studied the transmittance of double split- and closed-ring resonators at normal-to-plane incidence and identified their fundamental resonance modes. It is found that the antisymmetric and symmetric resonance modes originate from the out-of-phase and in-phase oscillations of surface charges in the neighboring legs of the double-ring resonators, respectively. The coupling of the antiparallel induced currents in the neighboring legs gives rise to magnetic resonance and consequently negative permeability of the antisymmetric mode. The negative refraction transmission of the double-ring resonators at normal-to-plane incidence is verified by dispersion curve and wedge-shaped model simulations. Our study provides a route to negative refraction metamaterial design by using the antisymmetric resonance mode of the simple double-ring structure at normal-to-plane incidence which is of particular importance for the terahertz and infrared domain. PMID:19257157

  14. The influence of phase-locking on internal resonance from a nonlinear normal mode perspective

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Neild, S. A.; Cammarano, A.; Wagg, D. J.

    2016-09-01

    When a nonlinear system is expressed in terms of the modes of the equivalent linear system, the nonlinearity often leads to modal coupling terms between the linear modes. In this paper it is shown that, for a system to exhibit an internal resonance between modes, a particular type of nonlinear coupling term is required. Such terms impose a phase condition between linear modes, and hence are denoted phase-locking terms. The effect of additional modes that are not coupled via phase-locking terms is then investigated by considering the backbone curves of the system. Using the example of a two-mode model of a taut horizontal cable, the backbone curves are derived for both the case where phase-locked coupling terms exist, and where there are no phase-locked coupling terms. Following this, an analytical method for determining stability is used to show that phase-locking terms are required for internal resonance to occur. Finally, the effect of non-phase-locked modes is investigated and it is shown that they lead to a stiffening of the system. Using the cable example, a physical interpretation of this is provided.

  15. The Coupled Spectral Element/Normal Mode Method: Application to the Testing of Several Approximations Based on Normal Mode Theory for the Computation of Seismograms in a Realistic 3D Earth.

    NASA Astrophysics Data System (ADS)

    Capdeville, Y.; Gung, Y.; Romanowicz, B.

    2002-12-01

    The spectral element method (SEM) has recently been adapted successfully for global spherical earth wave propagation applications. Its advantage is that it provides a way to compute exact seismograms in a 3D earth, without restrictions on the size or wavelength of lateral heterogeneity at any depth, and can handle diffraction and other interactions with major structural boundaries. Its disadvantage is that it is computationally heavy. In order to partly address this drawback, a coupled SEM/normal mode method was developed (Capdeville et al., 2000). This enables us to more efficiently compute bodywave seismograms to realistically short periods (10s or less). In particular, the coupled SEM/normal mode method is a powerful tool to test the validity of some analytical approximations that are currently used in global waveform tomography, and that are considerably faster computationally. Here, we focus on several approximations based on normal mode perturbation theory: the classical "path-average approximation" (PAVA) introduced by Woodhouse and Dziewonski (1984) and well suited for fundamental mode surface waves (1D sensitivity kernels); the non-linear asymptotic coupling theory (NACT), which introduces coupling between mode branches and 2D kernels in the vertical plane containing the source and the receiver (Li and Tanimoto, 1993; Li and Romanowicz, 1995); an extension of NACT which includes out of plane focusing terms computed asymptotically (e.g. Romanowicz, 1987) and introduces 3D kernels; we also consider first order perturbation theory without asymptotic approximations, such as developed for example by Dahlen et al. (2000). We present the results of comparisons of realistic seismograms for different models of heterogeneity, varying the strength and sharpness of the heterogeneity and its location in depth in the mantle. We discuss the consequences of different levels of approximations on our ability to resolve 3D heterogeneity in the earth's mantle.

  16. Joint inversion of normal-mode and finite-frequency S-wave data using an irregular tomographic grid

    NASA Astrophysics Data System (ADS)

    Zaroli, Christophe; Lambotte, Sophie; Lévêque, Jean-Jacques

    2015-12-01

    Global-scale tomographic models should aim at satisfying the full seismic spectrum. For this purpose, and to better constrain isotropic 3-D variations of shear velocities in the mantle, we tackle a joint inversion of spheroidal normal-mode structure coefficients and multiple-frequency S-wave delay times. In all previous studies for which normal modes were jointly inverted for, with body and/or surface waves, the mantle was laterally parametrized with uniform basis functions, such as spherical harmonics, equal-area blocks and evenly spaced spherical splines. In particular, spherical harmonics naturally appear when considering the Earth's free oscillations. However, progress towards higher resolution joint tomography requires a movement away from such uniform parametrization to overcome its computational inefficiency to adapt to local variations in resolution. The main goal of this study is to include normal modes into a joint inversion based upon a non-uniform parametrization that is adapted to the spatially varying smallest resolving length of the data. Thus, we perform the first joint inversion of normal-mode and body-wave data using an irregular tomographic grid, optimized according to ray density. We show how to compute the projection of 3-D sensitivity kernels for both data sets onto our parametrization made up of spherical layers spanned with irregular Delaunay triangulations. This approach, computationally efficient, allows us to map into the joint model multiscale structural informations from data including periods in the 10-51 s range for body waves and 332-2134 s for normal modes. Tomographic results are focused on the 400-2110 km depth range, where our data coverage is the most relevant. We discuss the potential of a better resolution where the grid is fine, compared to spherical harmonics up to degree 40, as the number of model parameters is similar. Our joint model seems to contain coherent structural components beyond degree 40, such as those related

  17. Stable, accurate and efficient computation of normal modes for horizontal stratified models

    NASA Astrophysics Data System (ADS)

    Wu, Bo; Chen, Xiaofei

    2016-08-01

    We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of `family of secular functions' that we herein call `adaptive mode observers' is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of `turning point', our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.

  18. Stable, accurate and efficient computation of normal modes for horizontal stratified models

    NASA Astrophysics Data System (ADS)

    Wu, Bo; Chen, Xiaofei

    2016-06-01

    We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of "family of secular functions" that we herein call "adaptive mode observers", is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of "turning point", our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.

  19. Field evolution of the magnetic normal modes in elongated permalloy nanometric rings.

    PubMed

    Gubbiotti, G; Madami, M; Tacchi, S; Carlotti, G; Pasquale, M; Singh, N; Goolaup, S; Adeyeye, A O

    2007-10-10

    The eigenmode spectrum of elongated permalloy rings with relatively wide arms is investigated by combined Brillouin light scattering and ferromagnetic resonance measurements as a function of the applied field intensity, encompassing both vortex and onion ground states. To reproduce the frequencies and the spatial profiles of the measured modes we performed micromagnetic simulations which solve the discretized Landau-Lifshitz-Gilbert equation in the time domain and calculate locally the Fourier transform. This allowed us to correlate the field dependence of different modes to their localization inside different portions of the rings. With the rings in the vortex ground state, in addition to radial, fundamental, and azimuthal modes, a localized mode, existing in the element portions where the internal field assumes its minima, has been measured and identified. This latter mode, whose frequency decreases for increasing field intensity, becomes soft near the transition from vortex to onion state and determines the change in symmetry of the magnetic ground state. After the transition, it is replaced by two edge modes, localized on the internal and external boundary of the rings, respectively. PMID:22049127

  20. Field evolution of the magnetic normal modes in elongated permalloy nanometric rings

    NASA Astrophysics Data System (ADS)

    Gubbiotti, G.; Madami, M.; Tacchi, S.; Carlotti, G.; Pasquale, M.; Singh, N.; Goolaup, S.; Adeyeye, A. O.

    2007-10-01

    The eigenmode spectrum of elongated permalloy rings with relatively wide arms is investigated by combined Brillouin light scattering and ferromagnetic resonance measurements as a function of the applied field intensity, encompassing both vortex and onion ground states. To reproduce the frequencies and the spatial profiles of the measured modes we performed micromagnetic simulations which solve the discretized Landau-Lifshitz-Gilbert equation in the time domain and calculate locally the Fourier transform. This allowed us to correlate the field dependence of different modes to their localization inside different portions of the rings. With the rings in the vortex ground state, in addition to radial, fundamental, and azimuthal modes, a localized mode, existing in the element portions where the internal field assumes its minima, has been measured and identified. This latter mode, whose frequency decreases for increasing field intensity, becomes soft near the transition from vortex to onion state and determines the change in symmetry of the magnetic ground state. After the transition, it is replaced by two edge modes, localized on the internal and external boundary of the rings, respectively.

  1. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  2. Simultaneous chiral discrimination of multiple profens by cyclodextrin-modified capillary electrophoresis in normal and reversed polarity modes.

    PubMed

    La, Sookie; Kim, Jiyung; Kim, Jung-Han; Goto, Junichi; Kim, Kyoung-Rae

    2003-08-01

    Simultaneous enantioseparations of nine profens for their accurate chiral discrimination were achieved by capillary electrophoresis (CE) in the normal polarity (NP) mode with a single cyclodextrin (CD) system and in the reversed polarity (RP) mode with a dual CD system. The single CD system in the NP mode employed heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TMbetaCD) added at 75 mM-100 mM 2-(N-morpholino)ethanesulfonic acid buffer (pH 6.0) as the optimum run buffer. The dual CD system operated in the RP mode used 30 mM TMbetaCD and 1.0% anionic carboxymethyl-beta-cyclodextrin dissolved in pH 3.0, 100 mM phosphoric acid-triethanolamine buffer containing 0.01% hexadimethrine bromide added to reverse the electroosmotic flow. Fairly good enantiomeric resolutions and the opposite enantiomer migration orders were achieved in the two modes. Relative migration times to internal standard under respective optimum conditions were characteristic of each enantiomer with good precision (< 2% relative standard deviation, RSD), thereby enabling to crosscheck the chemical identification of profens and also their accurate chiralities. The method linearity in the two modes was found to be adequate (r > or = 0.9991) for the chiral assay of the profens investigated. Simultaneous enantiomeric purity test of ibuprofen, ketoprofen and flurbiprofen in a mixture was feasible in a single analysis by the present method. PMID:12900877

  3. High-power Kerr-lens mode-locked thin-disk oscillator in the anomalous and normal dispersion regimes

    NASA Astrophysics Data System (ADS)

    Pronin, Oleg; Brons, Jonathan; Seidel, Marcus; Lücking, Fabian; Grasse, Christian; Boehm, Gerhard; Amann, Marcus C.; Pervak, Vladimir; Apolonski, Alexander; Kalashnikov, Vladimir L.; Krausz, Ferenc

    2013-03-01

    A femtosecond thin-disk Yb:YAG oscillator in both the anomalous and the normal dispersion regime is demonstrated. Both regimes are realized with practically the same resonator configuration. The power scaling potential of the anomalous and normal dispersion regimes is analyzed both theoretically and experimentally. The recipe to obtain Kerr-lens mode-locking (KLM) in the thin-disk configuration is presented here and oscillator characteristics as well as start-up difficulties are described. The oscillator stability in terms of output power, beam pointing and sensitivity to back reflections is measured and corresponds to the level of commercial systems.

  4. Calculation, normalization, and perturbation of quasinormal modes in coupled cavity-waveguide systems.

    PubMed

    Kristensen, Philip Trøst; de Lasson, Jakob Rosenkrantz; Gregersen, Niels

    2014-11-15

    We show how one can use a nonlocal boundary condition, which is compatible with standard frequency domain methods, for numerical calculation of quasinormal modes in optical cavities coupled to waveguides. In addition, we extend the definition of the quasinormal mode norm by use of the theory of divergent series to provide a framework for modeling of optical phenomena in such coupled cavity-waveguide systems. As example applications, we calculate the Purcell factor and study perturbative changes in the complex resonance frequency of a photonic crystal cavity coupled to a defect waveguide. PMID:25490468

  5. Drive Train Normal Modes Analysis for the ERDA/NASA 100-Kilowatt Wind Turbine Generator

    NASA Technical Reports Server (NTRS)

    Sullivan, T. L.; Miller, D. R.; Spera, D. A.

    1977-01-01

    Natural frequencies, as a function of power were determined using a finite element model. Operating conditions investigated were operation with a resistive electrical load and operation synchronized to an electrical utility grid. The influence of certain drive train components on frequencies and mode shapes is shown. An approximate method for obtaining drive train natural frequencies is presented.

  6. A Pictorial Visualization of Normal Mode Vibrations of the Fullerene (C[subscript 60]) Molecule in Terms of Vibrations of a Hollow Sphere

    ERIC Educational Resources Information Center

    Dunn, Janette L.

    2010-01-01

    Understanding the normal mode vibrations of a molecule is important in the analysis of vibrational spectra. However, the complicated 3D motion of large molecules can be difficult to interpret. We show how images of normal modes of the fullerene molecule C[subscript 60] can be made easier to understand by superimposing them on images of the normal…

  7. Characterization of mode-locking in an all-fiber, all normal dispersion ytterbium based fiber oscillator

    NASA Astrophysics Data System (ADS)

    Cserteg, András.; Sági, Veronika; Drozdy, András.; Varallyay, Zoltán.; Gajdátsy, Gábor

    2015-03-01

    An ytterbium based all fiber, all normal dispersion fiber oscillator with integrated SESAM can have several operation modes like mode-locked, Q-switched and noise-like. To know and to control the quality of the mode-locking is essential for the application of such laser oscillators, otherwise the whole laser setup can be damaged or the expected operation characteristics of the oscillator driven systems cannot be achieved. Usually the two-photon signal generated by the short pulses is used to indicate the mode locked operation, however such detection can be misleading in certain cases and not always able to predict the forthcoming degradation or vanishing of mode locking. The characterization method that we propose uses only the radio frequency spectrum of the oscillator output and can identify the different operation regimes of our laser setup. The optical spectra measured simultaneously with the RF signals proves the reliability of our method. With this kind of characterization stable mode locking can be initiated and maintained during the laser operation. The method combined with the ability to align the polarization states automatically in the laser cavity leads to the possibility to record a polarization map where the stability domains can be identified and classified. With such map the region where the mode locking is self starting and maintainable with minimal polarization alignment can be selected. The developed oscillator reported here with its compact setup and self alignment ability can be a reliable source with long term error free operation without the need of expensive monitoring tools.

  8. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.

    PubMed Central

    Li, Guohui; Cui, Qiang

    2002-01-01

    A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matrix involved in diagonalization. In the current work, by constructing the atomic hessian elements required in the projection operation on the fly, the memory requirement for the BNM approach has been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes, which are of interest in large-scale conformational changes of large proteins or protein-nucleic acid complexes, can be readily obtained. Comparison of the BNM results with standard normal mode analysis for a number of small proteins and nucleic acids indicates that many properties dominated by low frequency motions are well reproduced by BNM; these include atomic fluctuations, the displacement covariance matrix, vibrational entropies, and involvement coefficients for conformational transitions. Preliminary application to a fairly large system, Ca(2+)-ATPase (994 residues), is described as an example. The structural flexibility of the cytoplasmic domains (especially domain N), correlated motions among residues on domain interfaces and displacement patterns for the transmembrane helices observed in the BNM results are discussed in relation to the function of Ca(2+)-ATPase. The current implementation of the BNM approach has paved the way for developing efficient sampling algorithms with molecular dynamics or Monte Carlo for studying long-time scale dynamics of macromolecules. PMID:12414680

  9. Normal-Mode Splitting in the Coupled System of Hybridized Nuclear Magnons and Microwave Photons.

    PubMed

    Abdurakhimov, L V; Bunkov, Yu M; Konstantinov, D

    2015-06-01

    In the weak ferromagnetic MnCO_{3} system, a low-frequency collective spin excitation (magnon) is the hybridized oscillation of nuclear and electron spins coupled through the hyperfine interaction. By using a split-ring resonator, we performed transmission spectroscopy measurements of the MnCO_{3} system and observed avoided crossing between the hybridized nuclear magnon mode and the resonator mode in the NMR-frequency range. The splitting strength is quite large due to the large spin density of ^{55}Mn, and the cooperativity value C=0.2 (the magnon-photon coupling parameter) is close to the conditions of strong coupling. The results reveal a new class of spin systems, in which the coupling between nuclear spins and photons is mediated by electron spins via the hyperfine interaction. PMID:26196633

  10. QUANTUM MODE-COUPLING THEORY: Formulation and Applications to Normal and Supercooled Quantum Liquids

    NASA Astrophysics Data System (ADS)

    Rabani, Eran; Reichman, David R.

    2005-05-01

    We review our recent efforts to formulate and study a mode-coupling approach to real-time dynamic fluctuations in quantum liquids. Comparison is made between the theory and recent neutron scattering experiments performed on liquid ortho-deuterium and para-hydrogen. We discuss extensions of the theory to supercooled and glassy states where quantum fluctuations compete with thermal fluctuations. Experimental scenarios for quantum glassy liquids are briefly discussed.

  11. A Simple Reduction Process for the Normal Vibrational Modes Occurring in Linear Molecules

    ERIC Educational Resources Information Center

    McInerny, William

    2005-01-01

    The students in molecular spectroscopy courses are often required to determine the permitted normal vibrations for linear molecules that belong to particular groups. The reducible group representations generated by the use of Cartesian coordinates can be reduced by the use of a simple algebraic process applied to the group representations. The…

  12. An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

    An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858

  13. Normal-mode spectrum of finite-sized granular systems: The effects of fluid viscosity at the grain contacts

    NASA Astrophysics Data System (ADS)

    Valenza, John; Johnson, David Linton

    2012-04-01

    We investigate the effects of adsorbed films on the attenuative properties of loose granular media occupying a finite-sized rigid container that is open at the top. We measure the effective mass, M˜(ω), of loose tungsten particles prepared under two different sets of conditions: (i) We lightly coat tungsten grains with a fixed volume fraction of silicone oil (polydimethylsiloxane, PDMS), where the liquid viscosity is varied for individual realizations, and (ii) in the other set of experiments we vary the humidity. On a theoretical level, we are able to decompose the effective mass into a sum over the contributions from each of the normal modes of the granular medium. Our results indicate that increasing either the PDMS viscosity or the humidity, as the case may be, markedly increases the damping rate of each normal mode relevant to our measurements. However, there is appreciable damping even in the absence of any macroscopic film. With a notable exception in the case of the highest humidity in the humidity-controlled experiments, all the relevant modes are weakly damped in the sense of a microscopic theory based on damped contact forces between rigid particles.

  14. Flexibly controllable multi-pulse mode-locked MOPA Yb-doped fiber laser in all normal dispersion regime

    NASA Astrophysics Data System (ADS)

    Bu, Chenxi; Wang, Chinhua

    2013-09-01

    A Controllable, high energy, all normal dispersion (ANDi), passively mode-locked Yb-doped fiber laser is demonstrated with a Master Oscillator Power-Amplifier (MOPA) structure. The mode-locking is achieved by nonlinear polarization evolution (NPE). different types of laser pulse are achieved from fundamental mode-locked (FML) single pulse to twin pulse and then to harmonically mode-locked (HML) pulses (the maximum order is 7 times) by adjusting quarter-wave plates (QWPS) and a half-wave plate (HWP) in our system. Using a cascaded long-period fiber grating as the spectral filter, the center wavelength of our laser is fixed at 1034nm.The repetition frequency rate of the FML pulse is 1.53MHz with a pulse width of 817ps. The maximum average energy is 450 mW and the maximum pulse energy of FML single pulse is 294 nJ. Besides, the 517nm green laser output is also achieved by using a LiB3O5 (LBO) crystal as the frequency doubling crystal. The maximum average of the green pulse is 4.71mW.

  15. A comparison of the bounded derivative and the normal mode initialization methods using real data. [in numerical weather forecasting

    NASA Technical Reports Server (NTRS)

    Semazzi, F. H. M.; Navon, I. M.

    1985-01-01

    A bounded derivative initialization method (BDI) formerly used only in theoretical studies to balance gravitational wave influences is extended to a real world data set and the results are compared with those from a normal mode initialization (NMI). BDI proceeds by defining the characteristic scales of motion of interest and then constraining the time derivatives to match motions on a slow scale. A global barotropic model which considers orographic forcing is initialized by the scaled balance equations of the BDI scheme, which uses vorticity alone to achieve an initial balanced state. An external mode projector is employed to realize the NMI scheme, and five Machenhauer iterations reduce the total balance by four orders of magnitude. The initial states generated with both schemes are essentially equivalent, including the time evolution of a height field and divergence behavior being centered around regions of high orographic elevation.

  16. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.

    PubMed

    Yan, Xin Cindy; Tirado-Rives, Julian; Jorgensen, William L

    2016-08-25

    Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative. PMID:26901452

  17. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  18. Waveform Modeling of 3D Structure of D" Region Using A Coupled SEM/Normal Mode Approach

    NASA Astrophysics Data System (ADS)

    To, A.; Gung, Y.; Capadeville, Y.; Romanowicz, B.

    2003-12-01

    The presence of strong lateral heterogeneity in D" is now well documented and presents challenges for seismic modeling. The main challenges are the limited global sampling of D" and the theoretical limits of validity of the present modeling tools, such as standard ray theory and mode approaches. We use coupled normal mode/Spectral Element Method (SEM) to compute synthetic seismograms of Sdiff in the D" part of a tomographic model(SAW24b16, Mégnin and Romanowicz, 2000) down to corner frequency 1/12s. SEM allows to take into account strong heterogeneity in a rigorous manner. The coupled method is much faster than standard SEM, when the numerical part of the computation is restricted to the D" region. In the rest of the mantle, the wave field is computed using efficient normal mode summation. As a first step, we consider a radially symmetric model outside of the D" region, and compare Sdiff synthetics with observed waveforms for a collection of deep earthquakes, for which the effect of strong heterogeneity in the crust and upper mantle is avoided. Observed and synthetic travel time trends are very consistent and in many cases the observed residuals are significantly larger. This indicates that the tomographic model only represents the smooth features of the real structure. Observed waveform amplitudes and SEM synthetics are somewhat less consistent. We compare the predictions for 800 Sdiff phases using SEM with those obtained by more approximate methods : ray theory and NACT (Non-linear asymptotic coupling theory, a normal mode perturbation approach). We discuss systematic trends in the travel times predicted by the different methods, compared to observations. Starting with the tomographic model, and correcting for mantle structure outside of D" using approximate NACT predictions, we next invert for perturbations to the tomographic model, using the coupled SEM/mode computation for the forward part of the modeling, in several regions of D" under the Pacific, which are

  19. Mode-locked femtosecond all-normal all-PM Yb-doped fiber laser at 1060 nm

    NASA Astrophysics Data System (ADS)

    Bowen, Patrick; Singh, Harman; Runge, Antoine; Provo, Richard; Broderick, Neil G. R.

    2016-04-01

    We report an all-normal-dispersion, all-fibre, all-PM, laser operating at a central wavelength of 1060 nm. The laser is mode-locked using a nonlinear amplifying loop mirror and generates linearly polarised pulses that can be compressed to 360 fs. The laser is based on our earlier scheme operating at 1030 nm [1] and we discuss the similarities and differences between the two configurations. We also present amplification up to an output power of 1 W using a commercially built amplifier and show through numerical methods that this pulse may be recompressible to 1.65 ps.

  20. Three-dimensional volume-rendered imaging of normal and abnormal fetal fluid-filled structures using inversion mode.

    PubMed

    Hata, Toshiyuki; Mori, Nobuhiro; Tenkumo, Chiaki; Hanaoka, Uiko; Kanenishi, Kenji; Tanaka, Hirokazu

    2011-11-01

    A total of six normal and eight abnormal fetuses at 16-38 weeks of gestation were studied using transabdominal three-dimensional sonography with an inversion mode. In normal fetuses, the stomach, gallbladder and bladder could be depicted. In particular, peristalsis of the stomach was noted. In the case of holoprosencephaly, fused hemispheres were evident. In the case of hydrocephalus, the enlargement of ventricular cavities was noted. In the case of bilateral pleural effusion, the spatial relationship and size of the effusions were depicted. In the case of meconium peritonitis, the spatial relationship between the dilated intestines and ascites was depicted. In two cases of hydronephrosis, the dilated renal pelvis and calyces were clearly shown. In the case of multicystic dysplastic kidney, the number and size of cysts were clearly identified. In the case of left ovarian cyst, the anatomical relationships among the ovarian cyst, kidney, stomach and bladder could be easily understood. PMID:21790889

  1. Quasi-normal modes of a massless scalar field around the 5D Ricci-flat black string

    NASA Astrophysics Data System (ADS)

    Liu, Molin; Liu, Hongya; Gui, Yuanxing

    2008-05-01

    As one candidate of the higher dimensional black holes, the 5D Ricci-flat black string is considered in this paper. By means of a non-trivial potential Vn, the quasi-normal modes of a massless scalar field around this black string space are studied. By using the classical third-order WKB approximation, we carefully analyze the evolution of frequencies in two aspects, one is the induced cosmological constant Λ and the other is the quantum number n. The massless scalar field decays more slowly because of the existence of the fifth dimension and the induced cosmological constant. If an extra dimension has in fact existed near the black hole, the quasi-normal frequencies may have some indication of it.

  2. Cytoskeleton Influence on Normal and Tangent Fluctuation Modes in the Red Blood Cells

    NASA Astrophysics Data System (ADS)

    Rochal, S. B.; Lorman, V. L.

    2006-06-01

    We argue that the paradoxal softness of the red blood cells (RBC) in fluctuation experiments is apparent. We show that the effective surface shear modulus μs of the RBC obtained from fluctuation data and that measured in static deformation experiments have the same order of magnitude. In the RBC model developed for this purpose the spectrin network cytoskeleton with the bulk shear modulus estimated as μ≈105 165Pa contributes to both normal and tangent fluctuations of the system and confines the membrane fluctuations. The calculated ratio of the mean-square amplitudes ⟨Xn2⟩/⟨Xt2⟩ is 2 3 orders of magnitude smaller than it is in the free membrane with the same bending and shear moduli.

  3. Fourier transform infrared spectra and normal mode analysis of drug molecules: Zidovudine

    NASA Astrophysics Data System (ADS)

    Jain, Nivedita; Prabhakar, Santosh; Singh, R. A.

    2013-03-01

    The FTIR spectra of zidovudine molecule have been recorded in the range 4000-400 cm-1. The title compound is used as a drug against AIDS or HIV. The molecular structure, fundamental vibrational frequencies and intensities of vibrational bands are evaluated using density functional theory (DFT) using BLYP, B3LYP, B3PW91 and MPW1PW91 methods with 6-31+G(d,p) standard basis set. Comparison of simulated spectra with the experimental spectrum provides important informations and the ability of the computational method to describe the vibrational modes. These calculations have allowed finding most stable conformational structure of AZT. Calculated results of the title compound indicate that the drug molecule has syn orientation. The glycosidic bond in AZT and a minimum-energy structure in which the glycosy torsion angle χ and torsion angle γ values are consistent with those in the conformation of AZT in the AZT5-triphosphate bound to HIV RT is determined.

  4. Multiple-Component Crystal Fabric Measurements from Acoustically-Generated Normal Modes in Borehole

    NASA Astrophysics Data System (ADS)

    Kluskiewicz, D. J.; Waddington, E. D.; McCarthy, M.; Anandakrishnan, S.; Voigt, D.; Matsuoka, K.

    2014-12-01

    Sound wave velocities in ice are a proxy of crystal orientation fabric. Because p- and s-waves respectively travel faster and slower in the direction of an ice crystal c-axis, the velocities of these waves in a fabric are related to the clustering of ice crystal c-axes in the direction of wave propagation. Previous sonic logs at Dome C, NGRIP, WAIS, and NEEM have inferred a single component fabric description from the velocities of vertically-propagating p-waves around each ice core borehole. These records supplement thin-section measurements of crystal fabric by sampling larger numbers of crystals in a depth-continuous log. Observations of azimuthally anisotropic vertical-girdle fabrics at ice-core sites such as WAIS, NGRIP, and EDML underly a benefit for logging methods that are sensitive to such fabrics. We present a theoretical framework for using borehole flexural modes to measure azimuthal crystal-fabric anisotropy, and describe ongoing efforts to develop a sonic logging tool for this purpose. We also present data from p-wave logs and thin section measurements at the WAIS Divide, and describe how a flexural wave log could supplement the existing measurements.

  5. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  6. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.

    PubMed

    Perilla, Juan R; Hadden, Jodi A; Goh, Boon Chong; Mayne, Christopher G; Schulten, Klaus

    2016-05-19

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid-protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid-drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  7. All-atom homology model of the Escherichia coli 30S ribosomal subunit.

    PubMed

    Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y

    2002-10-01

    Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297

  8. All-atomic generation and noise-quadrature filtering of squeezed vacuum in hot Rb vapor

    NASA Astrophysics Data System (ADS)

    Horrom, Travis; Romanov, Gleb; Novikova, Irina; Mikhailov, Eugeniy E.

    2013-01-01

    With our all-atomic squeezing and filtering setup, we demonstrate control over the noise amplitudes and manipulation of the frequency-dependent squeezing angle of a squeezed vacuum quantum state by passing it through an atomic medium with electromagnetically induced transparency (EIT). We generate low sideband frequency squeezed vacuum using the polarization self-rotation effect in a hot Rb vapor cell, and direct it through a second atomic vapor subject to EIT conditions. We use the frequency-dependent absorption of the EIT window to demonstrate an example of squeeze amplitude attenuation and squeeze angle rotation of the quantum noise quadratures of the squeezed probe. These studies have implications for quantum memory and storage as well as gravitational wave interferometric detectors.

  9. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  10. Normal-mode function representation of global 3-D data sets: open-access software for the atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2015-04-01

    This article presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulations across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass and wind fields while considering the whole model depth in contrast to the majority of studies. The paper includes the theory of normal-mode function (NMF) expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the ERA Interim reanalysis data set. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim data set reveals several aspects of the large-scale circulation after it has been partitioned into the linearly balanced and IG components. The global energy distribution is dominated by the balanced energy while the IG modes contribute around 10% of the total wave energy. However, on sub-synoptic scales, IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally averaged and equatorial circulation provide a reference for the validation of climate models.

  11. Normal-mode function representation of global 3-D datasets: an open-access software for atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2014-12-01

    The paper presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulation across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass field and wind field and considering the whole model depth in contrary to majority of studies. The paper presentation includes the theory of normal-mode function expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the reanalysis dataset ERA Interim. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim dataset show some features of the large-scale circulation after it has been split into the balanced and IG components. The global energy distribution is dominated by the balanced energy with IG modes making less than 10% of the total wave energy. However, on subsynoptic scales IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally-averaged and equatorial circulation provide a reference for the validation of climate models.

  12. Ab Initio and Model-Hamiltonian Study of the Torsional Variation of the Three CH Stretching Normal Modes in Methanol

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Lees, Ronald M.; Hougen, Jon T.

    2013-06-01

    The ν_{2}, ν_{3} and ν_{9} CH stretching modes of methanol in the 3μm region exhibit a significant amount of torsion-vibration interaction, as illustrated for ν_{9} by the facts that: (i) the three hydrogen atoms each pass through a plane of symmetry of the molecule twice during the course of one full internal rotation motion, once at a minimum and once at a maximum in the three-fold potential energy curve, (ii) the H atom in the plane of symmetry is nearly motionless for the ν_{9} mode, and therefore (iii) the property of remaining motionless must be transferred from one H to another six times during one full internal rotation motion. In this talk we examine quantitatively the general phenomenon of torsion-vibration interaction in the methyl top stretching modes in two ways. First, we present plots of normal modes produced in Gaussian projected frequency calculations that are expressed either in terms of several sets of internal coordinates, or in terms of Cartesian displacement vectors for the methyl hydrogen atoms. Some of these plots display a nearly three-fold sine or cosine behavior, where the sine or cosine behavior is dictated by group-theoretical symmetry arguments. Other plots display stunning features ranging from loss of simple three-fold oscillatory pattern to cusp-like peaks or dips. Somewhat surprisingly, none of our ab initio plots for methanol exhibit a sign change after a 2π internal rotation of the methyl top. Second, we present a relatively simple model for the three CH stretching motions, characterized by three parameters associated with: (i) a vibrational A/E energy difference, (ii) a Jahn-Teller-like torsion-vibration interaction term within the vibrational E state, and (iii) a Renner-Teller-like torsion-vibration interaction term within the E state. This model gives nearly quantitative agreement with both the regular and irregular features of the ab initio plots. The good agreement suggests that various aspects of the physics of the

  13. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  14. Mars global atmospheric oscillations - Annually synchronized, transient normal-mode oscillations and the triggering of global dust storms

    NASA Technical Reports Server (NTRS)

    Tillman, James E.

    1988-01-01

    Transient events of an unusual character have been discovered in the daily pressure variations of the Mars atmosphere's pressure at the planetary surface which last only a few Martian days, appear to repeat on an annual basis, cover a large part of the given day's hemisphere, occur in pairs separated by 20-days in some cases, and coincide with the annual pressure minimum. They also consist of spectral components nearly identical in frequency with diurnal and semidiurnal harmonics. It is presently suggested that these events are Kelvin, normal-mode, transient, global oscillations. An almost-diurnal and an almost-semidiurnal high-frequency global oscillation distinct from solar-driven tides may be common on Mars.

  15. On the computation of long period seismograms in a 3-D earth using normal mode based approximations

    NASA Astrophysics Data System (ADS)

    Romanowicz, Barbara A.; Panning, Mark P.; Gung, Yuancheng; Capdeville, Yann

    2008-11-01

    Tomographic inversions for large-scale structure of the earth's mantle involve a forward modelling step of wave propagation through 3-D heterogeneity. Until now, most investigators have worked in the framework of the simplest theoretical assumptions, namely the infinite frequency `ray theory' in the case of body wave traveltime inversions, or the `path-average' approximation (PAVA) to normal mode perturbation theory, in the case of surface waves and long-period waveforms. As interest is shifting to mapping shorter wavelength structures, the need for a more accurate theoretical account of the interaction of seismic waves with mantle heterogeneity, coupled with improvements in path coverage, has been realized. Here we discuss different levels of approximations used in the context of normal mode perturbation theory, when modelling time domain seismic waveforms. We compare the performance of asymptotic approximations, which collapse the effects of 3-D structure onto the great circle vertical plane: the 1-D PAVA and a 2-D approximation called non-linear asymptotic coupling theory (NACT), which both are zeroth order asymptotic approximations. We then discuss how off-vertical plane effects can be introduced using higher order asymptotics. These computationally efficient approximations are compared to the linear Born formalism (BORN), which computes scattering integrals over the entire surface of the sphere. We point out some limitations of this linear formalism in the case of spatially extended anomalies, and show how that can be remedied through the introduction of a non-linear term (NBORN). All these approximations are referenced to a precise 3-D numerical computation afforded by the spectral element method. We discuss simple geometries, and explore a range of sizes of anomalies compared to the wavelength of the seismic waves considered, thus illustrating the range of validity and limitations of the various approximations considered.

  16. Elastic parabolic equation and normal mode solutions for seismo-acoustic propagation in underwater environments with ice covers.

    PubMed

    Collis, Jon M; Frank, Scott D; Metzler, Adam M; Preston, Kimberly S

    2016-05-01

    Sound propagation predictions for ice-covered ocean acoustic environments do not match observational data: received levels in nature are less than expected, suggesting that the effects of the ice are substantial. Effects due to elasticity in overlying ice can be significant enough that low-shear approximations, such as effective complex density treatments, may not be appropriate. Building on recent elastic seafloor modeling developments, a range-dependent parabolic equation solution that treats the ice as an elastic medium is presented. The solution is benchmarked against a derived elastic normal mode solution for range-independent underwater acoustic propagation. Results from both solutions accurately predict plate flexural modes that propagate in the ice layer, as well as Scholte interface waves that propagate at the boundary between the water and the seafloor. The parabolic equation solution is used to model a scenario with range-dependent ice thickness and a water sound speed profile similar to those observed during the 2009 Ice Exercise (ICEX) in the Beaufort Sea. PMID:27250161

  17. Normal Mode Analysis of Ambient-Noise Induced Free Oscillations of a Slender Medieval Masonry Tower in Bologna (Italy)

    NASA Astrophysics Data System (ADS)

    Morelli, A.; Azzara, R. M.; Cavaliere, A.; Zaccarelli, L.

    2014-12-01

    Analysis of the oscillations of buildings — either excited by earthquakes or by ambient noise — has become an effective tool to evaluate the response of such structures to strong ground motion, and hence to assess their seismic vulnerability. Response to small-amplitude ground motion may also provide crucial information on the elastic and anelastic properties of a structure — essential in the case of historical buildings — and constrain numerical full dynamic structural analyses. We report about an analysis carried out for a tall medieval monumental building in the urban center of the Norther Italian city of Bologna. Seismic monitoring, carried on for six months using field seismic instrumentation, has revealed the response to ambient noise, and has allowed to reconstruct, with high detail, the free oscillation modes of the tower. At 97 meters, the XII-century tower of the Asinelli is the tallest masonry building in Europe, and the most slender. We measured the fundamental, and several higher-order, flexural normal modes of oscillation, as well as the fundamental torsional mode. Asymmetry due to non-coincidence of centers of mass and of stiffness produces slightly different modal frequencies of oscillation in two orthogonal directions, consistently with dynamical modeling. Horizontal particle-motion polarization plots show the cyclic energy transfer between two degrees of freedom of the system. The Asinelli spectral signature can also be easily recognized in the motion recorded at the base of nearby Garisenda. We verify that there is correlation of spectral amplitudes with time of the day — in agreement with expected time-variance of anthropic disturbance —- but also with wind velocity and, intriguingly, with temperature variations inside the buidings. We are using these data to adjust the numerical dynamical models of the buildings, to examine time variations of behavior, and to identify the origin of anthropogenic sources of vibration in view of their

  18. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  19. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  20. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

  1. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

  2. All-atom molecular dynamics simulation studies of fully hydrated gel phase DPPG and DPPE bilayers

    NASA Astrophysics Data System (ADS)

    Pimthon, Jutarat; Willumeit, Regine; Lendlein, Andreas; Hofmann, Dieter

    2009-03-01

    Here in silico lipid membranes are described providing a structural background of the organization of the lipid components of membranes and aiding further biological or biophysical studies. An all-atom molecular dynamics simulations has been performed to investigate structural and dynamical properties of two fully hydrated gel-phase bilayers of 1,2-dipalmitoyl- sn-glycero-3-phosphoglycerol (DPPG) and 1,2-dipalmitoyl- sn-glycero-3-phospho-ethanolamine (DPPE) bilayers at 303 K. The respective starting configuration of lipids in the simulation bilayer unit cells were taken on the basis of scattering data. In both simulations, we found overall reasonably good agreement with the available experimental data (area per lipid, phosphorus-phosphorus distance). The distribution of the water/counterions at the membrane interface, interactions/orientations of lipid headgroups, and hydrocarbon chain organization were extensively studied in terms of pair distribution functions between main structural components of the system. Intra/intermolecular hydrogen bond formation was discussed in detail. The water orientation at the lipid membrane interface was explored thoroughly in terms of dipole moment as a function of the water molecule positions along the membrane, where we found that the counterions changed the orientation of the water at the interface. Special attention has been devoted to the distribution of the sodium counterions around the DPPG headgroup. We found preferential binding of Na + ions to the phosphate oxygen species.

  3. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    NASA Astrophysics Data System (ADS)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  4. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    PubMed

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids. PMID:21361557

  5. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

    PubMed Central

    Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D.

    2012-01-01

    Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein. PMID:22685386

  6. All-atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

    PubMed Central

    Miao, Yinglong; Johnson, John E.; Ortoleva, Peter J.

    2010-01-01

    An all-atom multiscale computational modeling approach, Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly-varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is ~0.25 nm/ns (npn) during early stage of the simulation and propagation of the structural transition across the capsid is roughly 0.6npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed. PMID:20695471

  7. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  8. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  9. Local elasticity of strained DNA studied by all-atom simulations

    NASA Astrophysics Data System (ADS)

    Mazur, Alexey K.

    2011-08-01

    Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

  10. Effects of brain amyloid deposition and reduced glucose metabolism on the default mode of brain function in normal aging.

    PubMed

    Kikuchi, Mitsuru; Hirosawa, Tetsu; Yokokura, Masamichi; Yagi, Shunsuke; Mori, Norio; Yoshikawa, Etsuji; Yoshihara, Yujiro; Sugihara, Genichi; Takebayashi, Kiyokazu; Iwata, Yasuhide; Suzuki, Katsuaki; Nakamura, Kazuhiko; Ueki, Takatoshi; Minabe, Yoshio; Ouchi, Yasuomi

    2011-08-01

    Brain β-amyloid (Aβ) deposition during normal aging is highlighted as an initial pathogenetic event in the development of Alzheimer's disease. Many recent brain imaging studies have focused on areas deactivated during cognitive tasks [the default mode network (DMN), i.e., medial frontal gyrus/anterior cingulate cortex and precuneus/posterior cingulate cortex], where the strength of functional coordination was more or less affected by cerebral Aβ deposits. In the present positron emission tomography study, to investigate whether regional glucose metabolic alterations and Aβ deposits seen in nondemented elderly human subjects (n = 22) are of pathophysiological importance in changes of brain hemodynamic coordination in DMN during normal aging, we measured cerebral glucose metabolism with [(18)F]FDG, Aβ deposits with [(11)C]PIB, and regional cerebral blood flow during control and working memory tasks by H(2)(15)O on the same day. Data were analyzed using both region of interest and statistical parametric mapping. Our results indicated that the amount of Aβ deposits was negatively correlated with hemodynamic similarity between medial frontal and medial posterior regions, and the lower similarity was associated with poorer working memory performance. In contrast, brain glucose metabolism was not related to this medial hemodynamic similarity. These findings suggest that traceable Aβ deposition, but not glucose hypometabolism, in the brain plays an important role in occurrence of neuronal discoordination in DMN along with poor working memory in healthy elderly people. PMID:21813680

  11. High-latitude filtering in a global grid-point model using model normal modes. [Fourier filters for synoptic weather forecasting

    NASA Technical Reports Server (NTRS)

    Takacs, L. L.; Kalnay, E.; Navon, I. M.

    1985-01-01

    A normal modes expansion technique is applied to perform high latitude filtering in the GLAS fourth order global shallow water model with orography. The maximum permissible time step in the solution code is controlled by the frequency of the fastest propagating mode, which can be a gravity wave. Numerical methods are defined for filtering the data to identify the number of gravity modes to be included in the computations in order to obtain the appropriate zonal wavenumbers. The performances of the model with and without the filter, and with a time tendency and a prognostic field filter are tested with simulations of the Northern Hemisphere winter. The normal modes expansion technique is shown to leave the Rossby modes intact and permit 3-5 day predictions, a range not possible with the other high-latitude filters.

  12. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  13. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V

    2015-09-01

    Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936

  14. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    NASA Astrophysics Data System (ADS)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan

    2015-04-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  15. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    PubMed

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  16. CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450

  17. Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations.

    PubMed

    Yuan, Shuguang; Wu, Rongliang; Latek, Dorota; Trzaskowski, Bartosz; Filipek, Slawomir

    2013-01-01

    Sphingosine 1-phosphate (S1P) is a lysophospholipid mediator which activates G protein-coupled sphingosine 1-phosphate receptors and thus evokes a variety of cell and tissue responses including lymphocyte trafficking, endothelial development, integrity, and maturation. We performed five all-atom 700 ns molecular dynamics simulations of the sphingosine 1-phosphate receptor 1 (S1P₁) based on recently released crystal structure of that receptor with an antagonist. We found that the initial movements of amino acid residues occurred in the area of highly conserved W269⁶·⁴⁸ in TM6 which is close to the ligand binding location. Those residues located in the central part of the receptor and adjacent to kinks of TM helices comprise of a transmission switch. Side chains movements of those residues were coupled to the movements of water molecules inside the receptor which helped in the gradual opening of intracellular part of the receptor. The most stable parts of the protein were helices TM1 and TM2, while the largest movement was observed for TM7, possibly due to the short intracellular part starting with a helix kink at P⁷·⁵⁰, which might be the first helix to move at the intracellular side. We show for the first time the detailed view of the concerted action of the transmission switch and Trp (W⁶·⁴⁸) rotamer toggle switch leading to redirection of water molecules flow in the central part of the receptor. That event is a prerequisite for subsequent changes in intracellular part of the receptor involving water influx and opening of the receptor structure. PMID:24098103

  18. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  19. All-atom force field for the prediction of vapor-liquid equilibria and interfacial properties of HFA134a.

    PubMed

    Peguin, Robson P S; Kamath, Ganesh; Potoff, Jeffrey J; da Rocha, Sandro R P

    2009-01-01

    A new all-atom force field capable of accurately predicting the bulk and interfacial properties of 1,1,1,2-tetrafluoroethane (HFA134a) is reported. Parameterization of several force fields with different initial charge configurations from ab initio calculations was performed using the histogram reweighting method and Monte Carlo simulations in the grand canonical ensemble. The 12-6 Lennard-Jones well depth and diameter for the different HFA134a models were determined by fitting the simulation results to pure-component vapor-equilibrium data. Initial screening of the force fields was achieved by comparing the calculated and experimental bulk properties. The surface tension of pure HFA134a served as an additional screening property to help discriminate an optimum model. The proposed model reproduces the experimental saturated liquid and vapor densities, and the vapor pressure for HFA134a within average errors of 0.7%, 4.4%, and 3.1%, respectively. Critical density, temperature, vapor pressure, normal boiling point, and heat of vaporization at 298 K are also in good agreement with experimental data with errors of 0.2%, 0.1%, 6.2%, 0%, 2.2%, respectively. The calculated surface tension is found to be within the experimental range of 7.7-8.1 mN.m(-1). The dipole moment of the different models was found to significantly affect the prediction of the vapor pressure and surface tension. The ability of the HFA134a models in predicting the interfacial tension against water is also discussed. The results presented here are relevant in the development of technologies where the more environmentally friendly HFA134a is utilized as a substitute to the ozone depleting chlorofluorocarbon propellants. PMID:19086791

  20. cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

    PubMed Central

    Oliwa, Tomasz; Shen, Yang

    2015-01-01

    Motivation: It remains both a fundamental and practical challenge to understand and anticipate motions and conformational changes of proteins during their associations. Conventional normal mode analysis (NMA) based on anisotropic network model (ANM) addresses the challenge by generating normal modes reflecting intrinsic flexibility of proteins, which follows a conformational selection model for protein–protein interactions. But earlier studies have also found cases where conformational selection alone could not adequately explain conformational changes and other models have been proposed. Moreover, there is a pressing demand of constructing a much reduced but still relevant subset of protein conformational space to improve computational efficiency and accuracy in protein docking, especially for the difficult cases with significant conformational changes. Method and results: With both conformational selection and induced fit models considered, we extend ANM to include concurrent but differentiated intra- and inter-molecular interactions and develop an encounter complex-based NMA (cNMA) framework. Theoretical analysis and empirical results over a large data set of significant conformational changes indicate that cNMA is capable of generating conformational vectors considerably better at approximating conformational changes with contributions from both intrinsic flexibility and inter-molecular interactions than conventional NMA only considering intrinsic flexibility does. The empirical results also indicate that a straightforward application of conventional NMA to an encounter complex often does not improve upon NMA for an individual protein under study and intra- and inter-molecular interactions need to be differentiated properly. Moreover, in addition to induced motions of a protein under study, the induced motions of its binding partner and the coupling between the two sets of protein motions present in a near-native encounter complex lead to the improved

  1. Estimation of earthquake source parameters from GRACE observations of changes in Earth's gravitational potential field using normal modes

    NASA Astrophysics Data System (ADS)

    Sterenborg, G.; Simons, F. J.; Welch, E.; Morrow, E.; Mitrovica, J. X.

    2013-12-01

    Since its launch in 2002, the Gravity Recovery and Climate Experiment (GRACE) has yielded tremendous insights into the spatio-temporal changes of mass redistribution in the Earth system. Such changes occur on widely varying spatial and temporal scales and take place both on Earth's surface, e.g., atmospheric mass fluctuations and the exchange of water, snow and ice, as well as in its interior, e.g., glacial isostatic adjustment and earthquakes. Each of these processes causes changes in the Earth's gravitational potential field which GRACE observes. One example is the Antarctic and Greenland ice mass changes inferred from GRACE observations of the changing geopotential as well as the associated time rate of change of its degree 2 and 4 zonal harmonics observed by satellite laser ranging. Deforming the Earth's surface and interior both co- and post-seismically, with some of the deformation permanent, earthquakes can affect the geopotential at a spatial scale up to thousands of kilometers and at temporal scales from seconds to months. Traditional measurements of earthquakes, e.g., by seismometers, GPS and inSAR, observe the co- and post-seismic surface displacements and are invaluable in understanding earthquake triggering mechanisms, slip distributions, rupture dynamics and slow post-seismic changes. Space-based observations of geopotential changes can add a whole new dimension to this as such observations are also sensitive to changes in the Earth's interior, over a larger area affected by the earthquake, over longer timescales, beyond that of Earth's longest period normal mode, and because they have global sensitivity including over sparsely instrumented oceanic domains. We use a joint seismic and gravitational normal-mode formalism to quantify changes in the gravitational potential due to different types of earthquakes, comparing them to predictions from dislocation models. We discuss the inverse problem of estimating the source parameters of large earthquakes

  2. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  3. Observation of multipulse bunches in a graphene oxide passively mode-locked ytterbium-doped fiber laser with all-normal dispersion

    NASA Astrophysics Data System (ADS)

    Huang, Shisheng; Wang, Yonggang; Peiguang, Yan; Zhang, Gelin; Zhao, Junqing; Li, Huiquan; Lin, Rongyong; Cao, Guangzhong; Duan, Ji'an

    2014-09-01

    We give a systematic experimental study of multipulse bunches in a graphene oxide saturable absorber (GOSA) passively mode-locked all-normal dispersion ytterbium-doped fiber laser (YDFL). Some special phenomena such as harmonic multipulse bunches, harmonic mode-locking, and chaotic multipulse states are also obtained. Our experiment reveals that the inserted 2.5-nm narrow bandwidth filter plays an important role in the formation of multipulse in all-normal dispersion fiber lasers. Because of the effective gain bandwidth depends on both the 2.5-nm narrow bandwidth filter and the artificial fiber birefringence filter, the multipulse operation states are sensitive to the polarization. It is the first demonstration of multipulse evolution in a GOSA passively mode-locked all-normal dispersion YDFL.

  4. Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics

    PubMed Central

    2014-01-01

    The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs. PMID:24673391

  5. Efficient method for the computation of wave propagation in the atmosphere: horizontal rays and vertical normal modes

    NASA Astrophysics Data System (ADS)

    Lahaye, Noe; Llewellyn Smith, Stefan

    2015-11-01

    The development of efficient methods for computing the propagation of waves throughout the atmosphere is a longstanding issue. The widely-used WKBJ approximation is inaccurate when the typical scale of the fluid properties is of the order of the wave scale, or in particular regions such as turning points or critical levels. Homogeneity in the horizontal allows one to reduce the problem to an ODE (generally in the vertical) and solve this numerically with no further approximation. However, this may not be a valid approximation in applications; for example tsunami-generated acoustic-gravity waves have a large length scale and propagate over long distances up to the ionosphere. We propose a resolution method for 3D wave propagation that combines normal-modes and ray tracing, relying on scale separation between vertical and horizontal directions. This method has been widely used in the oceanic acoustic context and in waveguide theory, yet few applications in the atmospheric context seem to have been reported. First, we present some results in a simple framework (quiescent fluid, rigid boundary conditions), then show how the method may be adapted in the atmospheric context (including compressibility) to the propagation of waves emitted by a moving source and/or in a moving fluid.

  6. From Dark to Bright: First-Order Perturbation Theory with Analytical Mode Normalization for Plasmonic Nanoantenna Arrays Applied to Refractive Index Sensing

    NASA Astrophysics Data System (ADS)

    Weiss, T.; Mesch, M.; Schäferling, M.; Giessen, H.; Langbein, W.; Muljarov, E. A.

    2016-06-01

    We present a first-order perturbation theory to calculate the frequency shift and linewidth change of photonic resonances in one- and two-dimensional periodic structures under modifications of the surrounding refractive index. Our method is based on the resonant state expansion, for which we extend the analytical mode normalization to periodic structures. We apply this theory to calculate the sensitivity of bright dipolar and much darker quadrupolar plasmonic modes by determining the maximum shift and optimal sensing volume.

  7. From Dark to Bright: First-Order Perturbation Theory with Analytical Mode Normalization for Plasmonic Nanoantenna Arrays Applied to Refractive Index Sensing.

    PubMed

    Weiss, T; Mesch, M; Schäferling, M; Giessen, H; Langbein, W; Muljarov, E A

    2016-06-10

    We present a first-order perturbation theory to calculate the frequency shift and linewidth change of photonic resonances in one- and two-dimensional periodic structures under modifications of the surrounding refractive index. Our method is based on the resonant state expansion, for which we extend the analytical mode normalization to periodic structures. We apply this theory to calculate the sensitivity of bright dipolar and much darker quadrupolar plasmonic modes by determining the maximum shift and optimal sensing volume. PMID:27341256

  8. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  9. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

    PubMed Central

    2016-01-01

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran–cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1–12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide–monosaccharide and protein–glycan linkages are derived

  10. Instantaneous normal mode theory of diffusion and the potential energy landscape: Application to supercooled liquid CS2

    NASA Astrophysics Data System (ADS)

    Li, Wu-Xiong; Keyes, T.

    1999-09-01

    The pure translation (TR) imaginary-frequency (or unstable) instantaneous normal modes (INM), which we have proposed as representative of barrier crossing and diffusion, are obtained for seven densities and eight temperatures of supercooled and near-melting liquid CS2 via computer simulation. The self-diffusion constant D, with a range of over two decades, has been determined previously for these 56 states [Li and Keyes, J. Chem. Phys. 111, 328 (1999)], allowing a comprehensive test of the relation of INM to diffusion. INM theory is reviewed and extended. At each density Arrhenius T-dependence is found for the fraction fu of unstable modes, for the product <ω>ufu of the fraction times the averaged unstable frequency, and for D. The T-dependence of D is captured very accurately by fu at higher densities and by <ω>ufu at lower densities. Since the T-dependence of <ω>u is weak at high density, the formula D∝<ω>ufu provides a good representation at all densities; it is derived for the case of low-friction barrier crossing. Density-dependent activation energies determined by Arrhenius fits to <ω>ufu are in excellent agreement with those found from D. Thus, activation energies may be obtained with INM, requiring far less computational effort than an accurate simulation of D in supercooled liquids. Im-ω densities of states, <ρuTR(ω,T)>, are fit to the function a(T)ω exp[-(a2(T)ω/√T )a3(T)]. The strong T-dependence of D, absent in Lennard-Jones (LJ) liquids, arises from the multiplicative factor a(T); its activation energy is determined by the inflection-point energy on barriers to diffusion. Values of the exponent a3(T) somewhat greater than 2.0 suggest that liquid CS2 is nonfragile in the extended Angell-Kivelson scheme for the available states. A striking contrast is revealed between CS2 and LJ; a3→2 at low-T in CS2 and at high-T in LJ. The INM interpretation is that barrier height fluctuations in CS2 are negligible at low-T but grow with increasing T

  11. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.

    PubMed

    Li, Guohui; Cui, Qiang

    2004-02-01

    The structural flexibilities of two molecular machines, myosin and Ca(2+)-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The normal mode analysis with physical intermolecular interactions was made possible by an improved implementation of the block normal mode (BNM) approach. The BNM results clearly illustrated that the large-scale conformational transitions implicated in the functional cycles of the two motor systems can be largely captured with a small number of low-frequency normal modes. Therefore, the results support the idea that structural flexibility is an essential part of the construction principle of molecular motors through evolution. Such a feature is expected to be more prevalent in motor proteins than in simpler systems (e.g., signal transduction proteins) because in the former, large-scale conformational transitions often have to occur before the chemical events (e.g., ATP hydrolysis in myosin and ATP binding/phosphorylation in Ca(2+)-ATPase). This highlights the importance of Brownian motions associated with the protein domains that are involved in the functional transitions; in this sense, Brownian molecular machines is an appropriate description of molecular motors, although the normal mode results do not address the origin of the ratchet effect. The results also suggest that it might be more appropriate to describe functional transitions in some molecular motors as intrinsic elastic motions modulating local structural changes in the active site, which in turn gets stabilized by the subsequent chemical events, in contrast with the conventional idea of local changes somehow getting amplified into larger-scale motions. In the case of myosin, for example, we favor the idea that Brownian motions associated with the flexible converter propagates to the Switch I/II region, where the salt-bridge formation gets stabilized by ATP hydrolysis, in contrast with the textbook notion that

  12. Ultra-broadband dissipative soliton and noise-like pulse generation from a normal dispersion mode-locked Tm-doped all-fiber laser.

    PubMed

    Sobon, Grzegorz; Sotor, Jaroslaw; Martynkien, Tadeusz; Abramski, Krzysztof M

    2016-03-21

    We report generation of ultra-broadband dissipative solitons and noise-like pulses from a simple, fully fiberized mode-locked Tm-doped fiber laser. The oscillator operates in the normal net dispersion regime and is mode-locked via nonlinear polarization evolution. Depending on the cavity dispersion, the laser was capable of generating 60 nm or 100 nm broad dissipative solitons. These are the broadest spectra generated from a normal dispersion mode-locked Tm-doped fiber laser so far. The same oscillator might also operate in the noise-like pulse regime with extremely broad emission spectra (over 300 nm), which also significantly outperforms the previous reports. PMID:27136809

  13. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon; Kwak, Wooseop

    2014-12-01

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.

  14. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging. PMID:23181323

  15. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations.

    PubMed

    Cota, Junio; Oliveira, Leandro C; Damásio, André R L; Citadini, Ana P; Hoffmam, Zaira B; Alvarez, Thabata M; Codima, Carla A; Leite, Vitor B P; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T; Ruller, Roberto; Squina, Fabio M

    2013-08-01

    Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. PMID:23459129

  16. High frequency normal mode statistics in a shallow water waveguide: the effect of random linear internal waves.

    PubMed

    Raghukumar, Kaustubha; Colosi, John A

    2014-07-01

    Using transport theory and Monte Carlo numerical simulation, the statistical properties of mode propagation at a frequency of 1 kHz are studied in a shallow water environment with random sound-speed perturbations from linear internal waves. The environment is typical of summer conditions in the mid-Atlantic bight during the Shallow Water 2006 experiment. Observables of interest include the second and fourth moments of the mode amplitudes, which are relevant to full-field mean intensity and scintillation index. It is found that mode phase randomization has a strong adiabatic component while at the same time mode coupling rates are significant. As a consequence, a computationally efficient transport theory is presented, which models cross-mode correlation adiabatically, but accounts for mode coupling using the mode energy equations of Creamer [(1996). J. Acoust. Soc. Am. 99, 2825-2838]. The theory also has closed-form expressions for the internal wave scattering matrix and a correction for an edge effect. The hybrid transport theory is shown to accurately reproduce many statistical quantities from the Monte Carlo simulations. PMID:24993196

  17. Effect of damping on excitability of high-order normal modes. [for a large space telescope spacecraft

    NASA Technical Reports Server (NTRS)

    Merchant, D. H.; Gates, R. M.; Straayer, J. W.

    1975-01-01

    The effect of localized structural damping on the excitability of higher-order large space telescope spacecraft modes is investigated. A preprocessor computer program is developed to incorporate Voigt structural joint damping models in a finite-element dynamic model. A postprocessor computer program is developed to select critical modes for low-frequency attitude control problems and for higher-frequency fine-stabilization problems. The selection is accomplished by ranking the flexible modes based on coefficients for rate gyro, position gyro, and optical sensor, and on image-plane motions due to sinusoidal or random PSD force and torque inputs.

  18. Dynamic analysis of space frames: The method of reverberation-ray matrix and the orthogonality of normal modes

    NASA Astrophysics Data System (ADS)

    Guo, Y. Q.; Chen, W. Q.; Pao, Y.-H.

    2008-11-01

    The formulation of reverberation-ray matrix analysis has been proposed to study wave propagation in planar frames. It is applied here to modal analysis of complex three-dimensional framed structures, optionally with lumped masses and/or elastic supports. Furthermore, by means of Betti's reciprocity theorem, orthogonal conditions are established for different natural modes, and hence transient response analysis based on mode superposition is developed. Both the reverberation-ray matrix analysis for free vibration and the mode superposition method for transient response are illustrated by numerical examples.

  19. Steady-state entanglement and normal-mode splitting in an atom-assisted optomechanical system with intensity-dependent coupling

    SciTech Connect

    Barzanjeh, Sh.; Naderi, M. H.; Soltanolkotabi, M.

    2011-12-15

    In this paper, we study theoretically bipartite and tripartite continuous variable entanglement as well as normal-mode splitting in a single-atom cavity optomechanical system with intensity-dependent coupling. The system under consideration is formed by a Fabry-Perot cavity with a thin vibrating end mirror and a two-level atom in the Gaussian standing wave of the cavity mode. We first derive the general form of the Hamiltonian describing the tripartite intensity-dependent atom-field-mirror coupling due to the presence of the cavity mode structure. We then restrict our treatment to the first vibrational sideband of the mechanical resonator and derive a tripartite atom-field-mirror Hamiltonian. We show that when the optical cavity is intensely driven, one can generate bipartite entanglement between any pair in the tripartite system and that, due to entanglement sharing, atom-mirror entanglement is efficiently generated at the expense of optical-mechanical and optical-atom entanglement. We also find that in such a system, when the Lamb-Dicke parameter is large enough, one can simultaneously observe the normal mode splitting into three modes.

  20. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  1. High-frequency normal-mode statistics in shallow water: the combined effect of random surface and internal waves.

    PubMed

    Raghukumar, Kaustubha; Colosi, John A

    2015-05-01

    In an earlier article, the statistical properties of mode propagation were studied at a frequency of 1 kHz in a shallow water environment with random sound-speed perturbations from linear internal waves, using a hybrid transport theory and Monte Carlo numerical simulations. Here, the analysis is extended to include the effects of random linear surface waves, in isolation and in combination with internal waves. Mode coupling rates for both surface and internal waves are found to be significant, but strongly dependent on mode number. Mode phase randomization by surface waves is found to be dominated by coupling effects, and therefore a full transport theory treatment of the range evolution of the cross mode coherence matrix is needed. The second-moment of mode amplitudes is calculated using transport theory, thereby providing the mean intensity while the fourth-moment is calculated using Monte Carlo simulations, which provides the scintillation index. The transport theory results for second-moment statistics are shown to closely reproduce Monte Carlo simulations. Both surface waves and internal waves strongly influence the acoustic field fluctuations. PMID:25994721

  2. Three key regimes of single pulse generation per round trip of all-normal-dispersion fiber lasers mode-locked with nonlinear polarization rotation.

    PubMed

    Smirnov, Sergey; Kobtsev, Sergey; Kukarin, Sergey; Ivanenko, Aleksey

    2012-11-19

    We show experimentally and numerically new transient lasing regime between stable single-pulse generation and noise-like generation. We characterize qualitatively all three regimes of single pulse generation per round-trip of all-normal-dispersion fiber lasers mode-locked due to effect of nonlinear polarization evolution. We study spectral and temporal features of pulses produced in all three regimes as well as compressibility of such pulses. Simple criteria are proposed to identify lasing regime in experiment. PMID:23187603

  3. High order harmonic mode-locking in an all-normal-dispersion Yb-doped fiber laser with a graphene oxide saturable absorber

    NASA Astrophysics Data System (ADS)

    Huang, S. S.; Wang, Y. G.; Yan, P. G.; Zhang, G. L.; Zhao, J. Q.; Li, H. Q.; Lin, R. Y.

    2014-01-01

    A high order passive harmonic mode-locking (HML) Yb-doped all-normal-dispersion fiber laser based on a graphene oxide saturable absorber has been experimentally demonstrated. For two different pump powers and different polarization states of the laser cavity, lower order and higher order HML have been achieved. The highest 30th-order harmonic (31.86 MHz) was achieved with subnanosecond pulse duration; this is transitional from a bunched multipulse state.

  4. High energy pulses generation with giant spectrum bandwidth and submegahertz repetition rate from a passively mode-locked Yb-doped fiber laser in all normal dispersion cavity

    NASA Astrophysics Data System (ADS)

    Lin, J.-H.; Wang, D.; Lin, K.-H.

    2011-01-01

    Robust passively mode-locked pulse generation with low pulse repetition rate and giant spectrum bandwidth in an all-fiber, all-normal-dispersion ytterbium-doped fiber laser has been experimentally demonstrated using nonlinear polarization evolution technique. The highest pulse energy over 20 nJ with spectrum bandwidth over 50 nm can be experimentally obtained at 175 mW pump power. The mode-locked pulses reveal broadened 3-dB pulsewidth about several nanosecond and widened pedestal in time trace that is resulted from enormous dispersion in laser cavity and gain dynamics. At certain mode-locking state, a spectrum gap around 1056 nm are observed between the three and four energy levels of Yb-doped fiber laser. By properly rotating the polarization controller, the gap can be eliminated due to four-wave mixing to produce more flattened spectrum output.

  5. Analysis of AB Initio Normal-Mode Displacement Vectors Along the Internal Rotation Path for the Three C-H Stretching Vibrations in Methanol

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Lees, Ronald M.; Hougen, Jon T.

    2012-06-01

    Stemming from the observation of inverted A/E splittings for the ν2 and ν9 asymmetric CH-stretching modes in methanol, there has been much theoretical interest in attempting to explain the nature of the inversion. We have recently examined the ab initio normal-mode vibrational displacement vectors along the internal rotation path for the three C-H stretching vibrations in methanol, both in the symmetrized and non-symmetrized PAM coordinates. Graphical representations of the Cartesian atomic normal mode displacement vectors di(γ) determined by the Gaussian suite of programs for the three CH stretching motions, ν2(A1), ν3(A1) and ν9(A2), along the steepest-descent internal rotation path γ in methanol (CH_3OH) will be presented and discussed, where A1 and A2 are notations in permutation-inversion group G6. These modes are interesting because the symmetry environment of each C-H bond changes significantly during the internal rotation, i.e., each of the methyl bonds takes turns passing (twice for a complete torsional revolution) through the plane of symmetry of the COH frame of the molecule. We present some simple theoretical models which can be used to help understand these displacement vectors. Although this is work in progress, some explanation is already possible for the rather irregular (avoided-crossing-like) behavior of these displacement vectors.

  6. Infrared spectrum and normal-mode assignment in methyl-ammonium lead halide perovskite CH3NH3PbI3

    NASA Astrophysics Data System (ADS)

    Perez Osorio, Miguel Angel; Filip, Marina; Docherty, Callum; Herz, Laura; Johnston, Michael; Giustino, Feliciano

    2015-03-01

    Solar cells based on MAPbI3 (MA=CH3NH3) have attracted enormous attention during the past two years owing to their high energy-conversion efficiency, reaching up to 19.3 % in record devices. A detailed understanding of the structure/property relations of this compound may help us explain its extraordinary performance. Here, we investigate the vibrational modes and infrared (IR) absorption spectrum of MAPbI3 by combining first-principles calculations and experiment. Our calculations indicate that the normal modes at high frequency, 400-3100 cm-1, correspond to internal vibrations of the MA cations, whereas those at low frequency, up to 180 cm-1, can be assigned either to vibrations of the PbI nework or to the libration and spinning of the cations. Using a factor group analysis we establish the symmetry of the normal modes and predict which mode will be IR or Raman active. In order to confirm these assignments we explicitly calculate the IR spectrum of the MAPbI3. The calculated spectrum is in good agreement with experiment, therefore we now have a complete characterization of the vibrational properties of MAPbI3. This work will serve as a solid reference for future structural and characterization studies of hybrid organic-inorganic perovskites.

  7. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)2

    NASA Astrophysics Data System (ADS)

    Téllez Soto, C. A.; Costa, A. C.; Versiane, O.; Lemma, T.; Machado, N. C. F.; Mondragón, M. A.; Martin, A. A.

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained.

  8. Surface enhanced Raman scattering, electronic spectrum, natural bond orbital, and Mulliken charge distribution in the normal modes of diethyldithiocarbamate copper (II) complex, [Cu(DDTC)2].

    PubMed

    Téllez Soto, C A; Costa, A C; Ramos, J M; Vieira, L S; Rost, N C V; Versiane, O; Rangel, J L; Mondragón, M A; Raniero, L; Martin, A A

    2013-12-01

    Surface-enhanced Raman scattering (SERS) was used to study the interactions of the normal modes of the diethyldithiocarbamate copper (II) complex, [Cu(DDTC)2] on nano-structured mixture silver-gold surfaces and on silver surfaces. The electronic spectrum of this complex was measured and the charge transfer bands were assigned through the TD-PBE1PBE procedure. Natural bond orbital (NBO) were also carried out to study the Cu(II) hybridation leading to the square planar geometry of the framework of the [Cu(DDTC)2] complex, and to study which are the donor NBO and the acceptor NBO in meaningful charge transfer through the Second Order Perturbation Theory Analysis of the Fox Matrix in NBO basis. To see the electronic dispersion, the Mulliken electronic charges (MAC) were calculated for each normal mode and correlated with the SERS effect. Full assignment of the SERS spectra was also supported by carefully analysis of the distorted geometries generated by the normal modes. PMID:23978740

  9. Surface enhanced Raman scattering, natural bond orbitals and Mulliken atomic charge distribution in the normal modes of diethyldithiocarbamate cadmium (II) complex, [Cd(DDTC)₂].

    PubMed

    Soto, C A Téllez; Costa, A C; Versiane, O; Lemma, T; Machado, N C F; Mondragón, M A; Martin, A A

    2015-07-01

    Theoretical and experimental bands have been assigned to the Fourier Transform Infrared (FT-IR) and FT-Raman spectra of the bis(diethyldithiocarbamate)Cd(II) complex, abbreviated as ([Cd(DDTC)2]). The calculations and spectral interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra, and band deconvolution analysis to assist in the assignment of observed fundamentals. This study validated the unusual pseudo tetrahedral molecular structure formed around the Cd(II) cation. Surface-enhanced Raman scattering (SERS) was used to determine the interactions of the normal-modes of the diethyldithiocarbamate cadmium (II) complex on nano-structured silver surfaces. Natural bond orbital (NBO) analysis was also carried out to study the Cd(II) hybridization causing the pseudo tetrahedral geometry of the framework of the [Cd(DDTC)2] complex, and to confirm the charge transfer mechanisms through second order perturbation theory analysis of the Fox Matrix. In order to find out the electronic dispersion of the Mulliken atomic charges (MAC) in the normal modes, we calculated the MAC for each normal mode and correlated these values with the SERS effect. Experimental UV-Vis spectra were obtained and charge transfer bands were assigned. Good agreement between the calculated and experimental values for the vibrational and UV-Vis spectra was obtained. PMID:25813176

  10. Computation of synthetic seismograms in a 3 dimensional Earth and inversion of eigenfrequency and Q quality factor datasets of normal modes

    NASA Astrophysics Data System (ADS)

    Roch, Julien; Clevede, Eric; Roult, Genevieve

    2010-05-01

    The 26 December 2004 Sumatra-Andaman event is the third biggest earthquake that has never been recorded but the first recorded with high quality broad-band seismometers. Such an earthquake offered a good opportunity for studying the normal modes of the Earth and particularly the gravest ones (frequency lower than 1 mHz) which provide important information on deep Earth. The splitting of some modes has been carefully analyzed. The eigenfrequencies and the Q quality factors of particular singlets have been retrieved with an unprecedented precision. In some cases, the eigenfrequencies of some singlets exhibit a clear shift when compared to the theoretical eigenfrequencies. Some core modes such as the 3S2 mode present an anomalous splitting, that is to say, a splitting width much larger than the expected one. Such anomalous splitting is presently admitted to be due to the existence of lateral heterogeneities in the inner core. We need an accurate model of the whole Earth and a method to compute synthetic seismograms in order to compare synthetic and observed data and to explain the behavior of such modes. Synthetic seismograms are computed by normal modes summation using a perturbative method developed up to second order in amplitude and up to third order in frequency (HOPT method). The last step consists in inverting both eigenfrequency and Q quality factor datasets in order to better constrain the deep Earth structure and especially the inner core. In order to find models of acceptable data fit in a multidimensional parameter space, we use the neighborhood algorithm method which is a derivative-free search method. It is particularly well adapted in our case (non linear problem) and is easy to tune with only 2 parameters. Our purpose is to find an ensemble of models that fit the data rather than a unique model.

  11. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    PubMed

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. PMID:24403006

  12. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    SciTech Connect

    Fry-Petit, A. M. E-mail: afry@fullerton.edu; Sheckelton, J. P.; McQueen, T. M. E-mail: afry@fullerton.edu; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn{sub 2}Mo{sub 3}O{sub 8}, this approach allows direct assignment of the constrained rotational mode of Mo{sub 3}O{sub 13} clusters and internal modes of MoO{sub 6} polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems.

  13. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique.

    PubMed

    Fry-Petit, A M; Rebola, A F; Mourigal, M; Valentine, M; Drichko, N; Sheckelton, J P; Fennie, C J; McQueen, T M

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn2Mo3O8, this approach allows direct assignment of the constrained rotational mode of Mo3O13 clusters and internal modes of MoO6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems. PMID:26429001

  14. Wilsonville SRC-I pilot plant: I. Fractionation area corrosion studies; II. Hot vs. normal separation mode of operation

    SciTech Connect

    Lee, J.M.

    1981-04-01

    Extensive corrosion studies in solvent recovery columns have been done with different coals (mainly Kentucky number 9 Lafayette, Dotiki and Fies). Sodium carbonate (0.1 to 1.1% of coal) was added as neutralizer to control corrosion rate. Chloride balance runs were made for isolation of corrosive streams with high chlorine content. A caustic wash program of inlet streams has been developed for selective treatment of corrosive streams as an alternative means for possible replacement of sodium carbonate addition. High chlorine content coals such as Kentucky number 9 Lafayette and Dotiki (0.2 to 0.3%) were very corrosive, compared to low chlorine content coal, Kentucky number 9 Fies (< 0.1%). Sodium carbonate addition (0.6 to 0.7% of coal) reduced corrosion rate from 500 MPY to an insignificant level of less than 5 MPY. Caustic wash of solvents could reduce corrosion rate by 50%, removing most corrosive compounds present in the 440 to 480/sup 0/F boiling fraction. Extensive studies for the hot separator mode of operation have been done as a means of saving substantial energy by elimination of dissolver slurry cooling (0.3 MM Btu/hr) and reheating for solvent recovery (1 MM Btu/h). Impacts of the hot separator mode on plant operability, product quality and Kerr-McGee CSD Unit recovery have been studied. The hot separator mode of operation was carried out by controlling the V103 temperature to 740/sup 0/F. It was observed that preasphaltene contents increased in the SRC products such as V110 L/F SRC and CSD feed; CSD unit recovery was not affected significantly; solvent quality was not affected significantly.

  15. Consistent porphyrin force field. 1. Normal-mode analysis for nickel porphine and nickel tetraphenylporphine from resonance Raman and infrared spectra and isotope shifts

    SciTech Connect

    Li, Xiaoyuan; Czernuszewicz, R.S.; Su, Y.O.; Spiro, T.G. ); Kincaid, J.R. )

    1990-01-11

    Resonance Raman spectra with variable-wavelength excitation are reported for Ni{sup II} porphine (NiP) and for the pyrrole-d{sub 8}, meso-d{sub 4}, and (pyrrole + meso)-d{sub 12} isotopomers, as well as for Ni{sup II} meso-tetraphenylporphine (NiTPP) and its pyrrole-{sup 15}N{sub 4}, pyrrole-d{sub 8}, {sup 13}C{sub 4}-meso, and phenyl-d{sub 20} isotopomers. All the Raman-active in-plane modes have been identified and are assigned to local coordinates which take into account the phasing of adjacent bond stretches within the pyrrole rings and at the methine bridges. The IR spectra of NiP and its isotopomers are also assigned. For most of the local coordinates good frequency agreement is seen for the different symmetry blocks, showing that longer range phasings have minor effects. These in-plane mode assignments are supported by normal-coordinate calculations with a physically reasonable valence force field, which is nearly the same for NiP and NiTPP. The principal force constants are in good accord with bond length relationships selected on the basis of scaled ab initio calculations. The phenyl substituents of NiTPP lower the frequencies of the asymmetric methine bridge stretching modes {nu}{sub 10}(B{sub 1g}) and {nu}{sub 19}(A{sub 2g}) by {approximately}60 cm{sup {minus}1}; this shift is attributable partly to the loss of coupling with the C{sub m}H bending modes in NiP and partly to an electronic effect of the phenyl group. There are also near-resonant interactions in NiTPP between porphyrin and phenyl modes near 740 and 200 cm{sup {minus}1} resulting in strongly displaced modes. Otherwise the phenyl groups have little influence on the porphyrin skeletal mode frequencies. Several phenyl modes are subject to moderate RR enhancement, probably via intensity borrowing from nearby porphyrin modes.

  16. Study of different HILIC, mixed-mode, and other aqueous normal-phase approaches for the liquid chromatography/mass spectrometry-based determination of challenging polar pesticides.

    PubMed

    Vass, Andrea; Robles-Molina, José; Pérez-Ortega, Patricia; Gilbert-López, Bienvenida; Dernovics, Mihaly; Molina-Díaz, Antonio; García-Reyes, Juan F

    2016-07-01

    The aim of the study was to evaluate the performance of different chromatographic approaches for the liquid chromatography/mass spectrometry (LC-MS(/MS)) determination of 24 highly polar pesticides. The studied compounds, which are in most cases unsuitable for conventional LC-MS(/MS) multiresidue methods were tested with nine different chromatographic conditions, including two different hydrophilic interaction liquid chromatography (HILIC) columns, two zwitterionic-type mixed-mode columns, three normal-phase columns operated in HILIC-mode (bare silica and two silica-based chemically bonded columns (cyano and amino)), and two standard reversed-phase C18 columns. Different sets of chromatographic parameters in positive (for 17 analytes) and negative ionization modes (for nine analytes) were examined. In order to compare the different approaches, a semi-quantitative classification was proposed, calculated as the percentage of an empirical performance value, which consisted of three main features: (i) capacity factor (k) to characterize analyte separation from the void, (ii) relative response factor, and (iii) peak shape based on analytes' peak width. While no single method was able to provide appropriate detection of all the 24 studied species in a single run, the best suited approach for the compounds ionized in positive mode was based on a UHPLC HILIC column with 1.8 μm particle size, providing appropriate results for 22 out of the 24 species tested. In contrast, the detection of glyphosate and aminomethylphosphonic acid could only be achieved with a zwitterionic-type mixed-mode column, which proved to be suitable only for the pesticides detected in negative ion mode. Finally, the selected approach (UHPLC HILIC) was found to be useful for the determination of multiple pesticides in oranges using HILIC-ESI-MS/MS, with limits of quantitation in the low microgram per kilogram in most cases. Graphical Abstract HILIC improves separation of multiclass polar pesticides

  17. Reduction of timing jitter and intensity noise in normal-dispersion passively mode-locked fiber lasers by narrow band-pass filtering.

    PubMed

    Qin, Peng; Song, Youjian; Kim, Hyoji; Shin, Junho; Kwon, Dohyeon; Hu, Minglie; Wang, Chingyue; Kim, Jungwon

    2014-11-17

    Fiber lasers mode-locked with normal cavity dispersion have recently attracted great attention due to large output pulse energy and femtosecond pulse duration. Here we accurately characterized the timing jitter of normal-dispersion fiber lasers using a balanced cross-correlation method. The timing jitter characterization experiments show that the timing jitter of normal-dispersion mode-locked fiber lasers can be significantly reduced by using narrow band-pass filtering (e.g., 7-nm bandwidth filtering in this work). We further identify that the timing jitter of the fiber laser is confined in a limited range, which is almost independent of cavity dispersion map due to the amplifier-similariton formation by insertion of the narrow bandpass filter. The lowest observed timing jitter reaches 0.57 fs (rms) integrated from 10 kHz to 10 MHz Fourier frequency. The rms relative intensity noise (RIN) is also reduced from 0.37% to 0.02% (integrated from 1 kHz to 5 MHz Fourier frequency) by the insertion of narrow band-pass filter. PMID:25402069

  18. Full-dimensional quantum dynamics study of vinylidene-acetylene isomerization: a scheme using the normal mode Hamiltonian.

    PubMed

    Ren, Yinghui; Li, Bin; Bian, Wensheng

    2011-02-14

    Full-dimensional quantum dynamics calculations of vinylidene-acetylene isomerization are performed and the state-specific resonance decay lifetimes of vinylidene(-d(2)) are computed. The theoretical scheme is a combination of several methods: normal coordinates are chosen to describe the nuclear motion of vinylidene, with both the parity and permutation symmetry exploited; phase space optimization in combination with physical considerations is used to generate an efficient discrete variable representation; the reaction coordinate is defined by us according to the three most relevant normal coordinates, along which a kind of optimal complex absorbing potential is imposed; the preconditioned inexact spectral transform method combined with an efficient preconditioner is employed to extract the energies and lifetimes of vinylidene. The overall computation is efficient. The computed energy levels generally agree with experiment well, and several state-specific lifetimes are reported for the first time. PMID:21186383

  19. Whistler mode waves observed by MGF search coil magnetometer -Polarization and wave normal features of upstream waves near the bow-shock

    NASA Astrophysics Data System (ADS)

    Hayashi, K.; Matsui, H.; Kawano, H.; Yamamoto, T.; Kokubun, S.

    1994-12-01

    Whistler mode waves observed in the upstream region very close to the bow-shock is focused from the initial survey for magnetic fed data in a frequency range between 1Hz and 50Hz observed by the search coil magnetometer on board the Geotail satellite. Based on the three component wave form data polarization and wave-normal characteristics of foreshock waves is first shown as dynamic spectra for the whole Fourier components of the 50 Hz band width. Intense whistler mode waves generated in the foot region of the bow-shock are found strongly controlled in the observed polarization dependent on the angle between directions of the wave propagation and the solar wind flow but not very dependent on frequency. Our simple scheme to derive the ware characteristics which is effective to survey large amount of data continuously growing is also introduced.

  20. Application of normal mode theory to seismic source and structure problems: Seismic investigations of upper mantle lateral heterogeneity. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Okal, E. A.

    1978-01-01

    The theory of the normal modes of the earth is investigated and used to build synthetic seismograms in order to solve source and structural problems. A study is made of the physical properties of spheroidal modes leading to a rational classification. Two problems addressed are the observability of deep isotropic seismic sources and the investigation of the physical properties of the earth in the neighborhood of the Core-Mantle boundary, using SH waves diffracted at the core's surface. Data sets of seismic body and surface waves are used in a search for possible deep lateral heterogeneities in the mantle. In both cases, it is found that seismic data do not require structural differences between oceans and continents to extend deeper than 250 km. In general, differences between oceans and continents are found to be on the same order of magnitude as the intrinsic lateral heterogeneity in the oceanic plate brought about by the aging of the oceanic lithosphere.

  1. Ab initio calculation of transition state normal mode properties and rate constants for the H(T)+CH4(CD4) abstraction and exchange reactions

    NASA Astrophysics Data System (ADS)

    Schatz, George C.; Walch, Stephen P.; Wagner, Albert F.

    1980-11-01

    We present ab initio (GVB-POL-CI) calculations for enough of the region about the abstraction and exchange saddle points for H(T)+CH4(CD4) to perform a full normal mode analysis of the transition states. The resulting normal mode frequencies are compared to four other published surfaces: an ab initio UHF-SCF calculation by Carsky and Zahradnik, a semiempirical surface by Raff, and two semiempirical surfaces by Kurylo, Hollinden, and Timmons. Significant quantitative and qualitative differences exist between the POL-CI results and those of the other surfaces. Transition state theory rate constants and vibrationally adiabatic reaction threshold energies were computed for all surfaces and compared to available experimental values. For abstraction, the POL-CI rates are in good agreement with experimental rates and in better agreement than are the rates of any of the other surfaces. For exchange, uncertainties in the experimental values and in the importance of vibrationally nonadiabatic effects cloud the comparison of theory to experiment. Tentative conclusions are that the POL-CI barrier is too low by several kcal. Unless vibrationaly nonadiabatic effects are severe, the POL-CI surface is still in better agreement with experiment than are the other surfaces. The rates for a simple 3-atom transition state theory model (where CH3 is treated as an atom) are compared to the rates for the full 6-atom model. The kinetic energy coupling of reaction coordinate modes to methyl group modes is identified as being of primary importance in determining the accuracy of the 3-atom model for this system. Substantial coupling in abstraction, but not exchange, causes the model to fail for abstraction but succeed for exchange.

  2. Normal mode analysis of a rotating group of lashed turbine blades by substructures. [calculations for blades at rest and at operating speed

    NASA Technical Reports Server (NTRS)

    Filstrup, A. W.

    1973-01-01

    A group of 5 lashed identical stream turbine blades is studied through the use of single level substructuring using NASTRAN level 15.1. An altered version, similar to DMAP Program Number 3 of the NASTRAN Newsletter, of Rigid Format 13.0 was used. Steady-state displacements and stresses due to centrifugal loads are obtained both without and with consideration of differential stiffness. The normal mode calculations were performed for blades at rest and at operating speed. Substructuring lowered the computation costs of the analysis by a factor of four.

  3. Note: amplification characteristics of all-normal-dispersion mode-locked Yb-doped fiber laser: influence of input pulse shape.

    PubMed

    Mukhopadhyay, Pranab K; Gupta, Pradeep K; Bindra, Kushvinder S; Oak, Shrikant M

    2013-07-01

    The amplification properties of the pulses at and after the nonlinear polarization rejection (NPR) port of an all-normal-dispersion Yb-doped mode-locked fiber laser are studied. The experimental results show that the spectra of the output pulses after the NPR port are considerably resistant to distortions on amplification and can be compressed in the femtosecond regime without any significant side-lobes and hence can serve as an excellent seed source for further power amplification. The experimental results are substantiated by numerical analysis of the amplifier setup. PMID:23902124

  4. Enhanced Power Within the Default Mode Network in Normal Subjects with Elevated Scores on an Egocentric Scale

    PubMed Central

    Collins, Mark W.G; Persinger, Michael A

    2014-01-01

    Integrated global power from the primary structures that composed the Default Mode Network (DMN) and from a random collection of other structures were measured by sLORETA (standardized low-resolution electromagnetic tomography) for young university volunteers who had completed an inventory that contained a subscale by which egocentricity has been inferred. Subjects who exhibited higher scores for egocentricity displayed significantly more power within the DMN structures relative to comparison areas. This was not observed for individuals whose egocentricity scores were lowest where the power differences between the DMN and comparison structures were not significant statistically. DMN power was greater in the right hemisphere than the left for men but greater in the left hemisphere than the right for women. The results are consistent with our operating metaphor that elevation of power or activity within the DMN is associated with greater affiliation with the self and its cognitive contents. PMID:25419254

  5. Normal-Mode Excitation by Sumatran Earthquake and Short-Timescale THERMO-MECHANICS AND RHEOLOGY OF THE EARTH'S LITHOSPHERE

    NASA Astrophysics Data System (ADS)

    Regenauer-Lieb, K.; Yuen, D. A.

    2005-05-01

    Solutions of the free-oscillation amplitudes,excited by the recent Sumatran wallop, by Okal and Stein ( 2005 ) have revealed a linearly growing trend in the semi-log plot between amplitude and period from 300 seconds to around an hour. This tantalizing plot (http://www.earth.northwestern.edu/people/seth/research/sumatra.html ) is very much reminiscent of the Rayleigh-Jeans portion of the Planck function in radiation physics, which was called the ultra-violet catastrophe. This distinct signature at long periods shows that some other physics must intervene to neutralize this singular tendency at a longer timescale. Thus in earthquake thermo-mechanics the size of an earthquake or moment is analogous to temperature in statistical physics. In this vein we have studied the thermal-mechanical shear interaction within the framework of a two-dimensional time-dependent model wherein a realistic visco-elastic-plastic rheology is implemented, and the governing equations include the momentum equation without inertia, the rheological and energy equations. We have retained all mechanical heating terms and heating terms involving volumetric expansion in the energy eq uation. In our simulations wherein we have modeled a bending situation, we encou nter two basically different bifurcation phenomena at the brittle-ductile transition-zone in the lithosphere, which can be attributed to two different families of eigenmodes of the system. One in which the shear zone nucleates on thermal perturbations in the ductile field, and the second which is fully associated with elasto-plastic (brittle, pressure-dependent) displacements. A quartz slab has all two modes operating simultaneously at three different depth levels. The bottom of the crust is controlled by the elasto-visco-plastic mode while the top is controlled by the elasto-plastic mode. The exchange of the two modes appears to communicate on a sub-horizontal layer in a flip-flop fashion, which may yield a fractal-like signature in time

  6. Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

    PubMed

    Genheden, Samuel; Cabedo Martinez, Ana I; Criddle, Michael P; Essex, Jonathan W

    2014-03-01

    We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment. PMID:24488307

  7. Simple all-PM-fiber laser system seeded by an all-normal-dispersion oscillator mode-locked with a nonlinear optical loop mirror

    NASA Astrophysics Data System (ADS)

    Szczepanek, Jan; Kardaś, Tomasz; Nejbauer, Michał; Radzewicz, Czesław; Stepanenko, Yuriy

    2016-03-01

    In this paper we report an all-PM-fiber laser amplifier system seeded by an all-normal-dispersion oscillator mode-locked with a Nonlinear Optical Loop Mirror (NOLM). The presented all-normal-dispersion cavity works in a dissipative soliton regime and delivers highly-chirped, high energy pulses above 2.5 nJ with full width at half maximum below 200 fs. The ultrafast oscillator followed by the all-PM-fiber amplifying stage delivered pulses with the energy of 42.5 nJ and time duration below 190 fs. The electrical field of optical pulses from the system was reconstructed using the SPIDER technique. The influence of nonlinear processes on the pulse temporal envelope was investigated.

  8. Quasi normal modes and P-V criticallity for scalar perturbations in a class of dRGT massive gravity around black holes

    NASA Astrophysics Data System (ADS)

    Prasia, P.; Kuriakose, V. C.

    2016-07-01

    We investigate black holes in a class of dRGT massive gravity for their quasi normal modes (QNMs) for neutral and charged ones using Improved Asymptotic Iteration Method and their thermodynamic behavior. The QNMs are studied for different values of the massive parameter m_g for both neutral and charged dRGT black holes under a massless scalar perturbation. As m_g increases, the magnitude of the quasi normal frequencies are found to be increasing. The results are also compared with the Schwarzchild de Sitter case. P-V criticallity of the aforesaid black hoels under massles scalar perturbation in the de Sitter space are also studied in this paper. It is found that the thermodynamic behavior of a neutral black hole shows no physically feasible phase transition while a charged black hole shows a definite phase transition.

  9. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  10. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

    PubMed Central

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID

  11. Normal Mode Analysis of the Spectral Density of the Fenna–Matthews–Olson Light-Harvesting Protein: How the Protein Dissipates the Excess Energy of Excitons

    PubMed Central

    2012-01-01

    We report a method for the structure-based calculation of the spectral density of the pigment–protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna–Matthews–Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment–protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons’ excess energy. PMID:23163520

  12. Normal mode sensitivity to Earth's D″ layer and topography on the core-mantle boundary: what we can and cannot see

    NASA Astrophysics Data System (ADS)

    Koelemeijer, P. J.; Deuss, A.; Trampert, J.

    2012-07-01

    The core-mantle boundary (CMB) is Earth's most profound internal boundary separating the liquid iron outer core and the solid silicate mantle. The detailed structure near the CMB has a major influence on mantle convection and the evolution of the core. Seismic observations, such as topography on the CMB, thin ultra-low velocity zones (ULVZs), seismic anisotropy and the anticorrelation between shear wave and bulk sound velocity heterogeneities have mainly been made using body waves and are still poorly constrained. We investigate the sensitivity of Earth's free oscillations to these features and specifically show how large individual anomalies must be for them to be observable. In addition, we discuss the possible trade-offs between these different lowermost mantle structures. Although modes have strong sensitivity to all the structures inserted, the results illustrate the limits of what normal modes can resolve. Our tests show that: (i) Even small scale features, such as ULVZs, with a thickness larger than 19 km can be observed as long as their distribution contains a long wavelength component. (ii) The peak-to-peak amplitude of CMB topography has a larger influence than its pattern and has to be smaller than 5 km to fit the data. (iii) The effect of scaling between shear wave velocity and density anomalies is less constrained, but a laterally varying pattern is implied by a simple test, suggesting the presence of chemical variations. (iv) A strong trade-off exists between anisotropy in compressional wave velocity and incidence angle whereas shear wave anisotropy is less observable. These findings provide valuable information for future normal mode studies on structures in Earth's lowermost mantle and their trade-offs.

  13. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    SciTech Connect

    Comandi, G.L.; Chiofalo, M.L.; Toncelli, R.; Bramanti, D.; Polacco, E.; Nobili, A.M.

    2006-03-15

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration {eta} between two test bodies-of different compositions, falling in the gravitational field of a source mass--if the measurement is made to the level of {eta}{approx_equal}10{sup -13} or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the 'Galileo Galilei on the ground' (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation-in particular, its normal modes (Part I) and rejection of common mode effects (Part II)-can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.

  14. Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes

    NASA Astrophysics Data System (ADS)

    Comandi, G. L.; Chiofalo, M. L.; Toncelli, R.; Bramanti, D.; Polacco, E.; Nobili, A. M.

    2006-03-01

    Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration η between two test bodies—of different compositions, falling in the gravitational field of a source mass—if the measurement is made to the level of η ≃10-13 or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the "Galileo Galilei on the ground" (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation—in particular, its normal modes (Part I) and rejection of common mode effects (Part II)—can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.

  15. Cardiac Time Intervals by Tissue Doppler Imaging M-Mode: Normal Values and Association with Established Echocardiographic and Invasive Measures of Systolic and Diastolic Function

    PubMed Central

    Mogelvang, Rasmus; de Knegt, Martina Chantal; Olsen, Flemming Javier; Galatius, Søren; Jensen, Jan Skov

    2016-01-01

    Purpose To define normal values of the cardiac time intervals obtained by tissue Doppler imaging (TDI) M-mode through the mitral valve (MV). Furthermore, to evaluate the association of the myocardial performance index (MPI) obtained by TDI M-mode (MPITDI) and the conventional method of obtaining MPI (MPIConv), with established echocardiographic and invasive measures of systolic and diastolic function. Methods In a large community based population study (n = 974), where all are free of any cardiovascular disease and cardiovascular risk factors, cardiac time intervals, including isovolumic relaxation time (IVRT), isovolumic contraction time (IVCT), and ejection time (ET) were obtained by TDI M-mode through the MV. IVCT/ET, IVRT/ET and the MPI ((IVRT+IVCT)/ET) were calculated. We also included a validation population (n = 44) of patients who underwent left heart catheterization and had the MPITDI and MPIConv measured. Results IVRT, IVRT/ET and MPI all increased significantly with increasing age in both genders (p<0.001 for all). IVCT, ET, IVRT/ET, and MPI differed significantly between males and females, displaying that women, in general exhibit better cardiac function. MPITDI was significantly associated with invasive (dP/dt max) and echocardiographic measures of systolic (LVEF, global longitudinal strain and global strainrate s) and diastolic function (e’, global strainrate e)(p<0.05 for all), whereas MPIConv was significantly associated with LVEF, e’ and global strainrate e (p<0.05 for all). Conclusion Normal values of cardiac time intervals differed between genders and deteriorated with increasing age. The MPITDI (but not MPIConv) is associated with most invasive and established echocardiographic measures of systolic and diastolic function. PMID:27093636

  16. An anisotropic shear velocity model of the Earth's mantle using normal modes, body waves, surface waves and long-period waveforms

    NASA Astrophysics Data System (ADS)

    Moulik, P.; Ekström, G.

    2014-12-01

    We use normal-mode splitting functions in addition to surface wave phase anomalies, body wave traveltimes and long-period waveforms to construct a 3-D model of anisotropic shear wave velocity in the Earth's mantle. Our modelling approach inverts for mantle velocity and anisotropy as well as transition-zone discontinuity topographies, and incorporates new crustal corrections for the splitting functions that are consistent with the non-linear corrections we employ for the waveforms. Our preferred anisotropic model, S362ANI+M, is an update to the earlier model S362ANI, which did not include normal-mode splitting functions in its derivation. The new model has stronger isotropic velocity anomalies in the transition zone and slightly smaller anomalies in the lowermost mantle, as compared with S362ANI. The differences in the mid- to lowermost mantle are primarily restricted to features in the Southern Hemisphere. We compare the isotropic part of S362ANI+M with other recent global tomographic models and show that the level of agreement is higher now than in the earlier generation of models, especially in the transition zone and the lower mantle. The anisotropic part of S362ANI+M is restricted to the upper 300 km in the mantle and is similar to S362ANI. When radial anisotropy is allowed throughout the mantle, large-scale anisotropic patterns are observed in the lowermost mantle with vSV > vSH beneath Africa and South Pacific and vSH > vSV beneath several circum-Pacific regions. The transition zone exhibits localized anisotropic anomalies of ˜3 per cent vSH > vSV beneath North America and the Northwest Pacific and ˜2 per cent vSV > vSH beneath South America. However, small improvements in fits to the data on adding anisotropy at depth leave the question open on whether large-scale radial anisotropy is required in the transition zone and in the lower mantle. We demonstrate the potential of mode-splitting data in reducing the trade-offs between isotropic velocity and

  17. Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

    PubMed

    Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

    2016-04-14

    Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties. PMID:27007011

  18. All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

    PubMed Central

    Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto

    2016-01-01

    In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663

  19. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    PubMed

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  20. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  1. Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

    PubMed Central

    Ulmschneider, Jakob P.; Smith, Jeremy C.; Ulmschneider, Martin B.; Ulrich, Anne S.; Strandberg, Erik

    2012-01-01

    The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state 2H-, 15N-, and 19F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ∼95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR. PMID:22947863

  2. Inelastic X-Ray Scattering (IXS) of a Transition Metal Complex (FeCl4−)– Vibrational Spectroscopy for All Normal Modes

    PubMed Central

    Wang, Hongxin; Dong, Weibing; Olmstead, Marilyn M.; Fettinger, James C.; Nix, Jay; Uchiyama, Hiroshi; Tsutsui, Satoshi; Baron, Alfred Q. R.; Dowty, Eric; Cramer, Stephen P.

    2015-01-01

    The tetraethylammonium salt of the transition metal complex (FeCl4−) has been examined using inelastic x-ray scattering (IXS) with 1.5 meV resolution (12 cm−1) at 21.747 keV. This sample serves as a feasibility test for more complex transition metal complexes. The IXS spectra were compared with previously recorded infrared, Raman, and NRVS spectra, revealing the same normal modes but with less strict selection rules. Calculations with a previously derived Urey Bradley force field were used to simulate the expected Q and orientation dependence of the IXS intensities. The relative merits of IXS, as compared to other photon based vibrational spectroscopies such as NRVS, Raman, and IR are discussed. PMID:23668798

  3. Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

    PubMed

    Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma

    2008-06-01

    Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes. PMID:18186477

  4. Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations

    PubMed Central

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand

    2015-01-01

    Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330

  5. On the physical interpretation of ab initio normal-mode coordinates for the three C-H stretching vibrations of methanol along the internal-rotation path

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Hougen, Jon T.; Lees, R. M.

    2013-11-01

    Graphical representations are presented for variation along the steepest-descent internal-rotation path in methanol of the normal mode frequencies and their associated eigenvectors in several sets of internal coordinates and in Cartesian atomic displacement vectors di(γ), as determined for the three CH stretching vibrations (ν3, ν2, and ν9) by projected-frequency calculations from the Gaussian suite of programs. The methyl-group CH stretching modes are interesting because the symmetry environment of each C-H bond changes significantly during the internal rotation, i.e., each of the methyl bonds takes turns passing (twice for a complete torsional revolution) through the plane of symmetry of the COH frame of the molecule. No accumulation of geometric phase is observed in any of these plots, and all quantities return to their original values after the internal rotation angle γ increases by 2π. A simple two-vibrational-state, three-parameter model, closely based on earlier models from the literature, can be used to understand nearly quantitatively much of the γ-variation observed in the Gaussian plots, including a number of cusp-like features. In particular, when the three parameters in the model are determined from a fit to the Gaussian projected frequencies for ν2 and ν9 at the top and bottom of the internal rotation path, it is found that the Renner-Teller-like torsion-vibration interaction term is slightly larger in magnitude than the Jahn-Teller-like term, which is consistent with no accumulation of geometric phase in the various plots. Finally, a highly simplified computation is presented to illustrate the changes that will be necessary in order to move from the usual diabatic torsion-vibration treatments in the literature to adiabatic treatments, in which the normal-mode Cartesian displacement vectors given at each point along the internal rotation path by the Gaussian projected frequency calculation are used directly in the torsion-vibration energy

  6. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  7. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

    NASA Astrophysics Data System (ADS)

    Wang, Guan M.; Sandberg, William C.

    2007-04-01

    In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated

  8. All-normal dispersion passively mode-locked Yb-doped fiber laser using MoS2-PVA saturable absorber

    NASA Astrophysics Data System (ADS)

    Sathiyan, S.; Velmurugan, V.; Senthilnathan, K.; Babu, P. Ramesh; Sivabalan, S.

    2016-05-01

    We demonstrate the generation of a dissipative soliton in an all-normal dispersion ytterbium (Yb)-doped fiber laser using few-layer molybdenum disulfide (MoS2) as a saturable absorber. The saturable absorber is prepared by mixing few-layer MoS2 solution with polyvinyl alcohol (PVA) to form a free-standing composite film. The modulation depth and saturation intensity of the MoS2-PVA film are 11% and 5.86 MW cm-2, respectively. By incorporating the MoS2 saturable absorber in the fiber laser cavity, the mode-locked pulses are generated with a pulse width of 1.55 ns and a 3 dB spectral bandwidth of 0.9 nm centered at 1037.5 nm. The fundamental repetition rate and the average power are measured as 15.43 MHz and 1.5 mW, respectively. These results reveal the feasibility of deploying liquid-phase exfoliated few-layer MoS2 nanosheets for dissipative soliton generation in the near-IR region.

  9. Vibrational normal modes calculation in the crystalline state of methylated monosaccharides: Anomers of the methyl-D-glucopyranoside and methyl-D-xylopyranoside molecules.

    PubMed

    Taleb-Mokhtari, Ilham Naoual; Lazreg, Abbassia; Sekkal-Rahal, Majda; Bestaoui, Noreya

    2016-01-15

    A structural investigation of the organic molecules is being carried out using vibrational spectroscopy. In this study, normal co-ordinate calculations of anomers of the methyl-D-glucopyranoside and methyl-β-D-xylopyranoside in the crystalline state have been performed using the modified Urey-Bradley-Shimanouchi force field (mUBSFF) combined with an intermolecular potential energy function. The latter includes Van der Waals interactions, electrostatic terms, and explicit hydrogen bond functions. The vibrational spectra of the compounds recorded in the crystalline state, in the 4000-500 cm(-1) spectral region for the IR spectra, and in the 4000-20 cm(-1) spectral range for the Raman spectra are presented. After their careful examination, several differences in the intensities and frequency shifts have been observed. The theoretical spectra have been obtained after a tedious refinement of the force constants. Thus, on the basis of the obtained potential distribution, each observed band in IR and in Raman has been assigned to a vibrational mode. The obtained results are indeed in agreement with those observed experimentally and thus confirm the previous assignments made for the methyl-α and β-D-glucopyranoside, as well as for the methyl-β-D-xylopyranoside. PMID:26342821

  10. Vibrational normal modes calculation in the crystalline state of methylated monosaccharides: Anomers of the methyl-D-glucopyranoside and methyl-D-xylopyranoside molecules

    NASA Astrophysics Data System (ADS)

    Taleb-Mokhtari, Ilham Naoual; Lazreg, Abbassia; Sekkal-Rahal, Majda; Bestaoui, Noreya

    2016-01-01

    A structural investigation of the organic molecules is being carried out using vibrational spectroscopy. In this study, normal co-ordinate calculations of anomers of the methyl-D-glucopyranoside and methyl-β-D-xylopyranoside in the crystalline state have been performed using the modified Urey-Bradley-Shimanouchi force field (mUBSFF) combined with an intermolecular potential energy function. The latter includes Van der Waals interactions, electrostatic terms, and explicit hydrogen bond functions. The vibrational spectra of the compounds recorded in the crystalline state, in the 4000-500 cm- 1 spectral region for the IR spectra, and in the 4000-20 cm- 1 spectral range for the Raman spectra are presented. After their careful examination, several differences in the intensities and frequency shifts have been observed. The theoretical spectra have been obtained after a tedious refinement of the force constants. Thus, on the basis of the obtained potential distribution, each observed band in IR and in Raman has been assigned to a vibrational mode. The obtained results are indeed in agreement with those observed experimentally and thus confirm the previous assignments made for the methyl-α and β-D-glucopyranoside, as well as for the methyl-β-D-xylopyranoside.

  11. Mode-locking pulse generation with MoS2-PVA saturable absorber in both anomalous and ultra-long normal dispersion regimes.

    PubMed

    Ahmed, M H M; Latiff, A A; Arof, H; Harun, S W

    2016-05-20

    We experimentally demonstrate a stable and simple mode locked erbium doped fiber laser (EDFL) utilizing passive few-layer molybdenum disulfide (MoS2) as a saturable absorber. The MoS2 is obtained by liquid phase exfoliation before it is embedded in a polymer composite film and then inserted in the laser cavity. A stable soliton pulse train started at a low threshold pump power of 20 mW in the anomalous dispersion regime after fine-tuning the rotation of the polarization controller. The central wavelength, 3 dB bandwidth, pulse width, and repetition rate of the soliton pulses are 1574.6 nm, 9.5 nm, 790 fs, and 29.5 MHz, respectively. By inserting a 850 m long dispersion shifted fiber (DSF) in the cavity, a dissipative soliton with square pulse train is obtained in the normal dispersion regime where the operating wavelength is centered at 1567.44 nm with a 3 dB bandwidth of 19.68 nm. The dissipative soliton pulse has a pulse width of 90 ns at a low repetition rate of 231.5 kHz due to the long DSF used. These results are a contribution to the pool of knowledge in nonlinear optical properties of two-dimensional nanomaterials especially for ultrafast photonic applications. PMID:27411156

  12. Computational modeling of the Fc αRI receptor binding in the Fc α domain of the human antibody IgA: Normal Modes Analysis (NMA) study

    NASA Astrophysics Data System (ADS)

    Jayasinghe, Manori; Posgai, Monica; Tonddast-Navaei, Sam; Ibrahim, George; Stan, George; Herr, Andrew; George Stan Group Collaboration; Herr's Group Team

    2014-03-01

    Fc αRI receptor binding in the Fc α domain of the antibody IgA triggers immune effector responses such as phagocytosis and antibody-dependent cell-mediated cytotoxicity in eukaryotic cells. Fc α is a dimer of heavy chains of the IgA antibody and each Fc α heavy chain which consisted of two immunoglobulin constant domains, CH2 and CH3, can bind one Fc αRI molecule at the CH2-CH3 interface forming a 2:1 stoichiometry. Experimental evidences confirmed that Fc αRI binding to the Fc α CH2-CH3 junction altered the kinetics of HAA lectin binding at the distant IgA1 hinge. Our focus in this research was to understand the conformational changes and the network of residues which co-ordinate the receptor binding dynamics of the Fc α dimer complex. Structure-based elastic network modeling was used to compute normal modes of distinct Fc α configurations. Asymmetric and un-liganded Fc α configurations were obtained from the high resolution crystal structure of Fc α-Fc αRI 2:1 symmetric complex of PDB ID 1OW0. Our findings confirmed that Fc αRI binding, either in asymmetric or symmetric complex with Fc α, propagated long-range conformational changes across the Fc domains, potentially also impacting the distant IgA1 hinge.

  13. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer. PMID:26930454

  14. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  15. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

    SciTech Connect

    Bell, Jeffrey A.; Ho, Kenneth L.; Farid, Ramy

    2012-08-01

    All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications. All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R{sub free} values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.

  16. Normal-mode frequency band view of the Off-the-West-Coast of Northern Sumatra Earthquake of April 11, 2012

    NASA Astrophysics Data System (ADS)

    Igarashi, M.; Tanimoto, T.

    2012-12-01

    Many studies with body-wave and long-period surface wave analyses on the Off-the-West-coast of Northern Sumatra Earthquake of April 11, 2012, have already pointed out complexities of this event (e.g., Meng et al., 2012). A sequence of events with fairly wide spatial and temporal extent are clearly needed to explain many facets of seismic data. In this study, we attempt to summarize a few distinct features from the normal-mode frequency band (0.3-2.0 mHz) which are obviously much simpler by their long wavelength and long periods. We analyzed long-period seismic data from STS1 and KS54000 sensors for the first 12 hours of the main event using the time-domain waveform fitting technique (Tanimoto, et al., 2012). Adoption of this short time series is partly to avoid uncertain Q parameters on amplitudes but also to avoid the effects from two earthquakes in Oregon (Mw6.0) and Mexico (Mw6.7) that occurred about 23rd hour on the same day. These events are much smaller but their effects cannot be ignored in seismic stations in North America. Two major events reported by the Global CMT project, the Mw8.6 main shock and the Mw8.2 aftershock that occurred two hours later, are clearly not sufficient to explain the amplitude data at about 1 mHz (0.6-1.5 mHz). Synthetic seismograms for the two events under-predicts data by about 30 percent. Amplitudes also show two-theta azimuthal variation that indicates a necessity of at least one hidden event (if not rupture propagation). This necessity has already been pointed out by various groups (e.g., Duputel et al., 2012, Shao et al., 2012). Duputel et al. (2012), for example, reports that the Mw8.6 main event by GCMT should be split up by two large events, the Mw8.5 main event and Mw8.3 event that occurred 70 seconds later. Our analysis shows that their three-source solution, including the Mw8.2 event two hours later, satisfies overall amplitude data in the normal-mode frequency band. However, their solution still shows two

  17. QuickView video preview software of colon capsule endoscopy: reliability in presenting colorectal polyps as compared to normal mode reading.

    PubMed

    Farnbacher, Michael J; Krause, Horst H; Hagel, Alexander F; Raithel, Martin; Neurath, Markus F; Schneider, Thomas

    2014-03-01

    OBJECTIVE. Colon capsule endoscopy (CCE) proved to be highly sensitive in detection of colorectal polyps (CP). Major limitation is the time-consuming video reading. The aim of this prospective, double-center study was to assess the theoretical time-saving potential and its possible impact on the reliability of "QuickView" (QV), in the presentation of CP as compared to normal mode (NM). METHODS. During NM reading of 65 CCE videos (mean patient´s age 56 years), all frames showing CPs were collected and compared to the number of frames presented by QV at increasing QV settings (10, 20, ... 80%). Reliability of QV in presenting polyps <6 mm and ≥6 mm (significant polyp), and identifying patients for subsequent therapeutic colonoscopy, capsule egestion rate, cleansing level, and estimated time-saving potential were assessed. RESULTS. At a 30% QV setting, the QV video presented 89% of the significant polyps and 86% of any polyps with ≥1 frame (per-polyp analysis) identified in NM before. At a 10% QV setting, 98% of the 52 patients with significant polyps could be identified (per-patient analysis) by QV video analysis. Capsule excretion rate was 74% and colon cleanliness was adequate in 85%. QV´s presentation rate correlates to the QV setting, the polyp size, and the number of frames per finding. CONCLUSIONS. Depending on its setting, the reliability of QV in presenting CP as compared to NM reading is notable. However, if no significant polyp is presented by QV, NM reading must be performed afterwards. The reduction of frames to be analyzed in QV might speed up identification of candidates for therapeutic colonoscopy. PMID:24325660

  18. Complexity of spontaneous BOLD activity in default mode network is correlated with cognitive function in normal male elderly: a multiscale entropy analysis.

    PubMed

    Yang, Albert C; Huang, Chu-Chung; Yeh, Heng-Liang; Liu, Mu-En; Hong, Chen-Jee; Tu, Pei-Chi; Chen, Jin-Fan; Huang, Norden E; Peng, Chung-Kang; Lin, Ching-Po; Tsai, Shih-Jen

    2013-02-01

    The nonlinear properties of spontaneous fluctuations in blood oxygen level-dependent (BOLD) signals remain unexplored. We test the hypothesis that complexity of BOLD activity is reduced with aging and is correlated with cognitive performance in the elderly. A total of 99 normal older and 56 younger male subjects were included. Cognitive function was assessed using Cognitive Abilities Screening Instrument and Wechsler Digit Span Task. We employed a complexity measure, multiscale entropy (MSE) analysis, and investigated appropriate parameters for MSE calculation from relatively short BOLD signals. We then compared the complexity of BOLD signals between the younger and older groups, and examined the correlation between cognitive test scores and complexity of BOLD signals in various brain regions. Compared with the younger group, older subjects had the most significant reductions in MSE of BOLD signals in posterior cingulate gyrus and hippocampal cortex. For older subjects, MSE of BOLD signals from default mode network areas, including hippocampal cortex, cingulate cortex, superior and middle frontal gyrus, and middle temporal gyrus, were found to be positively correlated with major cognitive functions, such as attention, orientation, short-term memory, mental manipulation, and language. MSE from subcortical regions, such as amygdala and putamen, were found to be positively correlated with abstract thinking and list-generating fluency, respectively. Our findings confirmed the hypothesis that complexity of BOLD activity was correlated with aging and cognitive performance based on MSE analysis, and may provide insights on how dynamics of spontaneous brain activity relates to aging and cognitive function in specific brain regions. PMID:22683008

  19. Convergence of normal mode variational calculations of methane spectra: Theoretical linelist in the icosad range computed from potential energy and dipole moment surfaces

    NASA Astrophysics Data System (ADS)

    Rey, Michaël; Nikitin, Andrei V.; Tyuterev, Vladimir G.

    2015-10-01

    Accurate basis set convergence of first-principles predictions of rotationally resolved spectra at high energy range is a common challenging issue for variational methods. In this paper, a detailed convergence study for the methane spectra is presented both for vibrational and rotational degrees of freedom as well as for intensities. For this purpose, we use our previously reported nine-dimensional potential energy and dipole moment surfaces of the methane molecule [Nikitin et al. Chem Phys Lett 2011;501:179-86; 2013;565:5-11]. Vibration-rotation calculations were carried out using variational normal mode approach with a full account of the Td symmetry. The aim was to obtain accurate theoretical methane line lists for the wavenumber range beyond currently available spectra analyses. The focus of this paper is the complicated icosad range (6280-7900 cm-1) containing 20 bands and 134 sub-bands where over 90% of experimental lines still remain unassigned. We provide variational line lists converged to a "spectroscopic precision" for icosad transitions for T=80 K and T=296 K. The first one contains 70 300 lines and the second one 286 170 lines with the intensity cut-off 10-29cm-1 /(moleculecm-2) with Jmax=18. An average error in line positions of theoretical predictions up to J=15 is estimated as 0.2-0.5 cm-1 from the comparisons with currently analyzed bands. Ab initio line strength calculations give the integrated intensity 4.37 ×10-20cm-1 /(moleculecm-2) at T=80 K for the sum of all icosad bands. This is to be compared to the integrated intensity 4.36 ×10-20cm-1 /(moleculecm-2) of the experimental icosad line list recorded in Grenoble University [Campargue et al., J Mol Spectrosc 2013;291:16-22] using very sensitive laser techniques. The shapes of absorption bands are also in a good qualitative agreement with experimental spectra.

  20. NASTRAN component-mode synthesis

    NASA Technical Reports Server (NTRS)

    Guyan, R. J.

    1976-01-01

    Procedure for dynamic substructuring analysis technique is generally as follows: calculation of component modes; selection of component normal modes, calculation of component generalized matrices, assembly of system matrices, and computation of normal modes; and retrieval of component response.

  1. Observations of the azimuthal dependence of normal mode coupling below 4 mHz at the South Pole and its nearby stations: Insights into the anisotropy beneath the Transantarctic Mountains

    NASA Astrophysics Data System (ADS)

    Hu, Xiao Gang

    2016-08-01

    Normal mode coupling pair 0S26-0T26 and 0S27-0T27 are significantly present at the South Pole station QSPA after the 2011/03/11 Mw9.1 Tohoku earthquake. In an attempt to determine the mechanisms responsible for the coupling pairs, I first investigate mode observations at 43 stations distributed along the polar great-circle path for the earthquake and observations at 32 Antarctic stations. I rule out the effect of Earth's rotation as well as the effect of global large-scale lateral heterogeneity, but argue instead for the effect of small-scale local azimuthal anisotropy in a depth extent about 300 km. The presence of quasi-Love waveform in 2-5 mHz at QSPA and its nearby stations confirms the predication. Secondly, I analyze normal mode observations at the South Pole location after 28 large earthquakes from 1998 to 2015. The result indicates that the presence of the mode coupling is azimuthal dependent, which is related to event azimuths in -46° to -18°. I also make a comparison between the shear-wave splitting measurements of previous studies and the mode coupling observations of this study, suggesting that their difference can be explained by a case that the anisotropy responsible for the mode coupling is not just below the South Pole location but located below region close to the Transantarctic Mountains (TAM). Furthermore, more signals of local azimuthal anisotropy in normal-mode observations at QSPA and SBA, such as coupling of 0S12-0T11 and vertical polarization anomaly for 0T10, confirms the existence of deep anisotropy close to TAM, which may be caused by asthenospheric mantle flow and edge convection around cratonic keel of TAM.

  2. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

    PubMed

    Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy

    2012-08-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions. PMID:22868759

  3. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-10-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527

  4. Generation of high fidelity 62-fs, 7-nJ pulses at 1035 nm from a net normal-dispersion Yb-fiber laser with anomalous dispersion higher-order-mode fiber.

    PubMed

    Zhu, L; Verhoef, A J; Jespersen, K G; Kalashnikov, V L; Grüner-Nielsen, L; Lorenc, D; Baltuška, A; Fernández, A

    2013-07-15

    Fiber oscillators operating in the normal dispersion regime allow generating high energy output pulses. The best stability of such oscillators is observed when the intracavity dispersion is close to zero. Intracavity dispersion compensation in such oscillators can be achieved using a higher-order mode fiber, which substantially reduces the higher order dispersion compared to all-normal dispersion oscillators or oscillators using intracavity gratings for dispersion compensation. Using this approach, we are able to obtain relatively high energy pulses, with high fidelity. Our modeling based on an analytic approach for oscillators operating in the normal dispersion regime predicts that at intermediate pulse energies an almost flat chirp can be obtained at the oscillator output enabling good pulse compression with a grating compressor close to Fourier limited duration. Here, we present a mode-locked ytterbium-doped fiber oscillator with a higher-order mode fiber operating in the net normal-dispersion regime, delivering 7.2 nJ pulses that can be dechirped down to 62 fs using a simple grating compressor. PMID:23938476

  5. High-quality lowest-frequency normal mode strain observations at the Black Forest Observatory (SW-Germany) and comparison with horizontal broad-band seismometer data and synthetics

    NASA Astrophysics Data System (ADS)

    Zürn, W.; Ferreira, A. M. G.; Widmer-Schnidrig, R.; Lentas, K.; Rivera, L.; Clévédé, E.

    2015-12-01

    We present spectra concentrating on the lowest-frequency normal modes of the Earth obtained from records of the invar-wire strainmeters and STS-1 broad-band seismometers located in the Black Forest Observatory, Germany after the disastrous earthquakes off the NW coast of Sumatra in 2004 and off the coast near Tohoku, Japan in 2011. We compare the spectra to ones obtained from synthetic seismograms computed using a mode summation technique for an anelastic, elliptical, rotating, spherically symmetric Earth model. The synthetics include strain-strain-coupling effects by using coupling coefficients obtained from comparisons between Earth tide signals recorded by the strainmeters and synthetic tidal records. We show that for the low-frequency toroidal and spheroidal modes up to 1 mHz, the strainmeters produce better signal-to-noise ratios than the broad-band horizontal seismometers. Overall, the comparison with the synthetics is satisfactory but not as good as for vertical accelerations. In particular, we demonstrate the high quality of the strainmeter data by showing the Coriolis splitting of toroidal modes for the first time in individual records, the first clear observation of the singlet _2S_1^0 and the detection of the fundamental radial mode 0S0 with good signal-to-noise ratio and with a strain amplitude of 10-11. We also identify the latter mode in a record of the Isabella strainmeter after the great Chilean quake in 1960, the detection of which was missed by the original studies.

  6. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  7. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  8. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  9. Analysis of solvation structure and thermodynamics of methane in water by reference interaction site model theory using an all-atom model

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2000-12-01

    An all-atom molecular model and optimized site-site pair potential parameters are employed for methane solute. By use of the reference interaction site model theory, the methane hydration structure is analyzed at the atomic level and its hydration free energies, energies, enthalpies, and entropies for four different thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3 are calculated. Our calculated thermodynamic properties are in rather good agreement with experiments.

  10. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

    PubMed

    Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T

    2016-01-01

    Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. PMID:27232456

  11. Peptides (P1, P2 and its mutations) binding with a graphene sheet: an all-atom to all-residue hierarchical coarse-grained approach

    NASA Astrophysics Data System (ADS)

    Kuang, Zhifeng; Farmer, Barry; Pandey, Ras

    2013-03-01

    Binding of peptide P2 (EPLQLKM) [1] and its mutations (P2G, P2Q) to a graphene sheet are studied by a coarse-grained computer simulation. Our hierarchical coarse-grained approach involves all-atom MD simulation to assess the binding interaction of each residue with the graphene sheet. Data from all-atom simulations are then used as input to phenomenological interaction in a coarse-grained MC simulation [2]. Binding of each peptide and its residue in corresponding sequence (P2, P2G, P2Q) are evaluated by analyzing the adsorption of each residue, its mobility, and structural profiles. Although it is difficult to identify overall morphological differences in adsorbed peptides by visual inspections, quantitative analysis of the conformational changes of adsorbed peptides shows variations in size among P2E and its mutations. Results on binding of peptide P1 (HSSYWYAFNNKT) may also be presented if data become available. This work is supported by the Air Force Research Laboratory.

  12. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2001-08-01

    Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).

  13. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-01

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups. PMID:26593668

  14. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-01

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  15. Poly(Ethylene Glycol) in Drug Delivery, Why Does it Work, and Can We do Better? All Atom Molecular Dynamics Simulation Provides Some Answers

    NASA Astrophysics Data System (ADS)

    Bunker, Alex

    We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl2. We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.

  16. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems. PMID:25612718

  17. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-01

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  18. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  19. FTIR spectra and normal-mode analysis of a tetranuclear Manganese adamantane-like complex in two electrochemically prepared oxidation states: Relevance to the oxygen-evolving complex of Photosystem II

    SciTech Connect

    Visser, Hendrik; Dube, Christopher E.; Armstrong, William H.; Sauer, Kenneth; Yachandra, Vittal K.

    2002-03-19

    The IR spectra and normal-mode analysis of the adamantane-like compound [Mn4O6(bpea)4]n+ in two oxidation states, MnIV4 and MnIIIMnIV3, that are relevant to the oxygen-evolving complex of photosystem II are presented. Mn-O vibrational modes are identified with isotopic exchange, 16O->18O, of the mono-(mu)-oxo bridging atoms in the complex. IR spectra of the MnIIIMnIV3 species are obtained by electrochemical reduction of the MnIV4 species using a spectroelectrochemical cell, based on attenuated total reflection [Visser et al. Anal Chem 2001, 73, 4374-4378]. A novel method of subtraction is used to reduce background contributions from solvent and ligand modes, and the difference and double-difference spectra are used in identifying Mn-O bridging modes that are sensitive to oxidation state change. Two strong IR bands are observed for the MnIV4 species at 745 and 707 cm-1 and a weaker band at 510 cm-1. Upon reduction, the MnIIIMnIV3 species exhibits two strong IR bands at 745 and 680 cm-1, and several weaker bands are observed in the 510 - 425 cm-1 range. A normal mode analysis is performed to assign all the relevant bridging modes in the oxidized MnIV4 and reduced MnIIIMnIV3 species. The calculated force constants for the MnIV4 species are = 3.15 mdynAngstrom, = 0.55 mdyn/Angstrom, and = 0.20 mdyn/Angstrom. The force constants for the MnIIIMnIV3 species are = 3.10 mdyn/Angstrom, = 2.45 mdyn/Angstrom, = 0.40, and = 0.15 mdyn/Angstrom. This study provides insights for the identification of Mn-O modes in the IR spectra of the photosynthetic oxygen-evolving complex during its catalytic cycle.

  20. Normal faults, normal friction?

    NASA Astrophysics Data System (ADS)

    Collettini, Cristiano; Sibson, Richard H.

    2001-10-01

    Debate continues as to whether normal faults may be seismically active at very low dips (δ < 30°) in the upper continental crust. An updated compilation of dip estimates (n = 25) has been prepared from focal mechanisms of shallow, intracontinental, normal-slip earthquakes (M > 5.5; slip vector raking 90° ± 30° in the fault plane) where the rupture plane is unambiguously discriminated. The dip distribution for these moderate-to-large normal fault ruptures extends from 65° > δ > 30°, corresponding to a range, 25° < θr < 60°, for the reactivation angle between the fault and inferred vertical σ1. In a comparable data set previously obtained for reverse fault ruptures (n = 33), the active dip distribution is 10° < δ = θr < 60°. For vertical and horizontal σ1 trajectories within extensional and compressional tectonic regimes, respectively, dip-slip reactivation is thus restricted to faults oriented at θr ≤ 60° to inferred σ1. Apparent lockup at θr ≈ 60° in each dip distribution and a dominant 30° ± 5° peak in the reverse fault dip distribution, are both consistent with a friction coefficient μs ≈ 0.6, toward the bottom of Byerlee's experimental range, though localized fluid overpressuring may be needed for reactivation of less favorably oriented faults.

  1. Non-extremal Reissner-Nordström black hole: do asymptotic quasi-normal modes carry information about the quantum properties of the black hole?

    NASA Astrophysics Data System (ADS)

    Skákala, Jozef

    2012-01-01

    We analyze the largely accepted formulas for the asymptotic quasi-normal frequencies of the non-extremal Reissner-Nordström black hole, (for the electromagnetic-gravitational/scalar perturbations). We focus on the question of whether the gap in the spacing in the imaginary part of the QNM frequencies has a well defined limit as n goes to infinity and if so, what is the value of the limit. The existence and the value of this limit has a crucial importance from the point of view of the currently popular Maggiore's conjecture, which represents a way of connecting the asymptotic behavior of the quasi-normal frequencies to the black hole thermodynamics. With the help of previous results and insights we will prove that the gap in the imaginary part of the frequencies does not converge to any limit, unless one puts specific constraints on the ratio of the two surface gravities related to the two spacetime horizons. Specifically the constraints are that the ratio of the surface gravities must be rational and such that it is given by two relatively prime integers n ± whose product is an even number. If the constraints are fulfilled the limit of the sequence is still not guaranteed to exist, but if it exists its value is given as the lowest common multiplier of the two surface gravities. At the end of the paper we discuss the possible implications of our results.

  2. Micromagnetic simulations of spin-wave normal modes and the spin-transfer-torque driven magnetization dynamics of a ferromagnetic cross

    SciTech Connect

    Pramanik, Tanmoy Roy, Urmimala; Register, Leonard F.; Banerjee, Sanjay K.; Tsoi, Maxim

    2014-05-07

    We studied spin-transfer-torque (STT) switching of a cross-shaped magnetic tunnel junction in a recent report [Roy et al., J. Appl. Phys. 113, 223904 (2013)]. In that structure, the free layer is designed to have four stable energy states using the shape anisotropy of a cross. STT switching showed different regions with increasing current density. Here, we employ the micromagnetic spectral mapping technique in an attempt to understand how the asymmetry of cross dimensions and spin polarization direction of the injected current affect the magnetization dynamics. We compute spatially averaged frequency-domain spectrum of the time-domain magnetization dynamics in the presence of the current-induced STT term. At low currents, the asymmetry of polarization direction and that of the arms are observed to cause a splitting of the excited frequency modes. Higher harmonics are also observed, presumably due to spin-wave wells caused by the regions of spatially non-uniform effective magnetic field. The results could be used towards designing a multi-bit-per-cell STT-based random access memory with an improved storage density.

  3. Dark current studies on a normal-conducting high-brightness very-high-frequency electron gun operating in continuous wave mode

    NASA Astrophysics Data System (ADS)

    Huang, R.; Filippetto, D.; Papadopoulos, C. F.; Qian, H.; Sannibale, F.; Zolotorev, M.

    2015-01-01

    We report on measurements and analysis of a field-emitted electron current in the very-high-frequency (VHF) gun, a room temperature rf gun operating at high field and continuous wave (CW) mode at the Lawrence Berkeley National Laboratory (LBNL). The VHF gun is the core of the Advanced Photo-injector Experiment (APEX) at LBNL, geared toward the development of an injector for driving the next generation of high average power x-ray free electron lasers. High accelerating fields at the cathode are necessary for the high-brightness performance of an electron gun. When coupled with CW operation, such fields can generate a significant amount of field-emitted electrons that can be transported downstream the accelerator forming the so-called "dark current." Elevated levels of a dark current can cause radiation damage, increase the heat load in the downstream cryogenic systems, and ultimately limit the overall performance and reliability of the facility. We performed systematic measurements that allowed us to characterize the field emission from the VHF gun, determine the location of the main emitters, and define an effective strategy to reduce and control the level of dark current at APEX. Furthermore, the energy spectra of isolated sources have been measured. A simple model for energy data analysis was developed that allows one to extract information on the emitter from a single energy distribution measurement.

  4. CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

    PubMed Central

    Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.

    2010-01-01

    The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467

  5. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

    PubMed

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  6. Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

    PubMed Central

    Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; MacKerell, Alexander D.

    2011-01-01

    Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick (WC) base pair opening which is not consistent with experiment while analysis of MD simulations show the 2′-hydroxyl moiety to almost exclusively sample the O3′ orientation. Quantum mechanical studies of RNA related model compounds indicate the energy minimum associated with the O3′ orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2′-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3′ orientations of the 2′-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and non-canonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′-hydroxyl moiety and support a model whereby the 2′-hydroxyl can enhance the probability of conformational transitions in RNA. PMID:21469161

  7. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  8. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system. PMID:27117093

  9. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    PubMed Central

    Nguyen, Trang Truc; Viet, Man Hoang

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329

  10. The Ensemble Folding Kinetics of the FBP28 WW Domain Revealed by an All-atom Monte Carlo Simulation in a Knowledge-based Potential

    PubMed Central

    Xu, Jiabin; Huang, Lei; Shakhnovich, Eugene I.

    2011-01-01

    In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo (REMC) simulations starting from random coils find native-like (C α RMSD of 2.68Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β –hairpins, the folding mechanism of each individual β– hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. PMID:21365688

  11. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    PubMed

    Gould, Tim; Bučko, Tomáš

    2016-08-01

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases. PMID:27304856

  12. Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates.

    PubMed

    Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P

    2010-10-12

    Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation. PMID:26616783

  13. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    NASA Astrophysics Data System (ADS)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  14. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    NASA Astrophysics Data System (ADS)

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  15. Substorm recurrence during steady and variable solar wind driving: Evidence for a normal mode in the unloading dynamics of the magnetosphere

    NASA Technical Reports Server (NTRS)

    Klimas, A. J.; Baker, D. N.; Vassiliadis, D.; Roberts, D. A.

    1994-01-01

    recurrence rate observed by Farrugia et al. can be interpreted as both being due to the existence of a normal unloading recurrence period in the dynamics of the magnetosphere.

  16. A new approach and some criteria to deal with the theory of the normal modes of vibrations in the elpasolite stoichiometric type systems short range intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Acevedo, Roberto; Soto-Bubert, Andrés; Bosch, Paul; Strek, W.

    2007-10-01

    There are a number of stoichiometric elpasolite type systems, for which a considerable amount of experimental data has being accumulated over the last three decades. For these purposes, data from linear and non linear optics is available, though we must emphasize, that the experimental evidence is rather scarce or incomplete, and as a consequence, it is not obvious to claim that many relevant problems in the solid state spectroscopy for these systems have been adequately solved. We have been working on systems such as Cs 2NaLnCl 6 for Ln = Pr, Eu, Tb, Dy, Ho, Er, and Tm, aiming to advance our understanding in those electronic and vibrational factors, upon which the one photon electronic transitions depend upon. We have chosen in this article, to report a novel strategy to rationalize the normal coordinate analysis so as to get a closer and more realistic approach to deal with those contributions which determine, what we regard as a natural potential energy distribution (NPED). It is essential to agree on the conditions upon which, we develop our convergence tests based on a physical view, so as to discern between selections of experimental assignments from a more comprehensive viewpoint. As a starting point, we review the magnificent contribution put forward by Lentz, who may claim priority in this area of the vibrational spectroscopy for the cryolite and elpasolite compounds and subsequently by other authors, whom have introduced some correction terms in the description of the vibrational force field. It is indeed a major task to produce a better description for this interacting potential, based on a maximum of 10 vibrational frequencies. In this work, our description is based upon a total of 72 internal coordinates and an initial number of 98 internal force constants. We show that the potential energy matrix F may be symmetrized by reducing the number of these latter to 81 internal force constants. For each of the elpasolite type systems, we have considered a

  17. Spectral fitting inversion of low-frequency normal modes with self-coupling and cross-coupling of toroidal and spheroidal multiplets: Numerical experiments to estimate the isotropic and anisotropic velocity structures

    NASA Astrophysics Data System (ADS)

    Oda, Hitoshi

    2016-03-01

    The aspherical structure of the Earth is described in terms of lateral heterogeneity and anisotropy of the P- and S-wave velocities, density heterogeneity, ellipticity and rotation of the Earth, and undulation of the discontinuity interfaces of the seismic wave velocities. Its structure significantly influences the normal mode spectra of the Earth's free oscillation in the form of cross-coupling between toroidal and spheroidal multiplets and self-coupling between the singlets forming them. Thus, the aspherical structure must be conversely estimated from the free oscillation spectra influenced by the cross-coupling and self-coupling. In the present study, we improve a spectral fitting inversion algorithm which was developed in a previous study to retrieve the global structures of the isotropic and anisotropic velocities of the P and S waves from the free oscillation spectra. The main improvement is that the geographical distribution of the intensity of the S-wave azimuthal anisotropy is represented by a non-linear combination of structure coefficients for the anisotropic velocity structure, whereas in the previous study it was expanded into a generalized spherical harmonic series. Consequently, the improved inversion algorithm reduces the number of unknown parameters that must be determined compared to the previous inversion algorithm, and employs a one-step inversion method by which the structure coefficients for the isotropic and anisotropic velocities are directly estimated from the fee oscillation spectra. The applicability of the improved inversion is examined by several numerical experiments using synthetic spectral data, which are produced by supposing a variety of isotropic and anisotropic velocity structures, earthquake source parameters and station-event pairs. Furthermore, the robustness of the inversion algorithm is investigated with respect to the back-ground noise contaminating the spectral data as well as truncating the series expansions by finite

  18. Spectral fitting inversion of low-frequency normal modes with self-coupling and cross-coupling of toroidal and spheroidal multiplets: numerical experiments to estimate the isotropic and anisotropic velocity structures

    NASA Astrophysics Data System (ADS)

    Oda, Hitoshi

    2016-06-01

    The aspherical structure of the Earth is described in terms of lateral heterogeneity and anisotropy of the P- and S-wave velocities, density heterogeneity, ellipticity and rotation of the Earth and undulation of the discontinuity interfaces of the seismic wave velocities. Its structure significantly influences the normal mode spectra of the Earth's free oscillation in the form of cross-coupling between toroidal and spheroidal multiplets and self-coupling between the singlets forming them. Thus, the aspherical structure must be conversely estimated from the free oscillation spectra influenced by the cross-coupling and self-coupling. In the present study, we improve a spectral fitting inversion algorithm which was developed in a previous study to retrieve the global structures of the isotropic and anisotropic velocities of the P and S waves from the free oscillation spectra. The main improvement is that the geographical distribution of the intensity of the S-wave azimuthal anisotropy is represented by a nonlinear combination of structure coefficients for the anisotropic velocity structure, whereas in the previous study it was expanded into a generalized spherical harmonic series. Consequently, the improved inversion algorithm reduces the number of unknown parameters that must be determined compared to the previous inversion algorithm and employs a one-step inversion method by which the structure coefficients for the isotropic and anisotropic velocities are directly estimated from the fee oscillation spectra. The applicability of the improved inversion is examined by several numerical experiments using synthetic spectral data, which are produced by supposing a variety of isotropic and anisotropic velocity structures, earthquake source parameters and station-event pairs. Furthermore, the robustness of the inversion algorithm is investigated with respect to the back-ground noise contaminating the spectral data as well as truncating the series expansions by finite terms

  19. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  20. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  1. Using outcrop observations, 3D discrete feature network (DFN) fluid-flow simulations, and subsurface data to constrain the impact of normal faults and opening mode fractures on fluid flow in an active asphalt mine

    NASA Astrophysics Data System (ADS)

    Wilson, C. E.; Aydin, A.; Durlofsky, L.; Karimi-Fard, M.; Brownlow, D. T.

    2008-12-01

    An active quarry near Uvalde, TX which mines asphaltic limestone from the Anacacho Formation offers an ideal setting to study fluid-flow in fractured and faulted carbonate rocks. Semi-3D exposures of normal faults and fractures in addition to visual evidence of asphalt concentrations in the quarry help constrain relationships between geologic structures and the flow and transport of hydrocarbons. Furthermore, a subsurface dataset which includes thin sections and measured asphalt concentration from the surrounding region provides a basis to estimate asphalt concentrations and constrain the depositional architecture of both the previously mined portions of the quarry and the un-mined surrounding rock volume. We characterized a series of normal faults and opening mode fractures at the quarry and documented a correlation between the intensity and distribution of these structures with increased concentrations of asphalt. The three-dimensional depositional architecture of the Anacacho Formation was characterized using the subsurface thin sections. Then outcrop exposures of faults, fractured beds, and stratigraphic contacts were mapped and their three-dimensional positions were recorded with differential gps devices. These two datasets were assimilated and a quarry-scale, geologically realistic, three-dimensional Discrete Feature Network (DFN) which represents the geometries and material properties of the matrix, normal faults, and fractures within the quarry was constructed. We then performed two-point flux, control-volume finite- difference fluid-flow simulations with the DFN to investigate the 3D flow and transport of fluids. The results were compared and contrasted with available asphalt concentration estimates from the mine and the aforementioned data from the surrounding drill cores.

  2. Multidimentional Normal Mode Calculations for the OH Vibrational Spectra of (H_2O)_3^+, (H_2O)_3^+Ar, H^+(H_2O)_3, and H^+(H_2O)_3Ar

    NASA Astrophysics Data System (ADS)

    Li, Ying-Cheng; Chuang, Hsiao-Han; Tan, Jake Acedera; Takahashi, Kaito; Kuo, Jer-Lai

    2014-06-01

    Recent experimental observations of (H_2O)_3^+, (H_2O)_3^+Ar, H^+(H_2O)_3, and H^+(H_2O)_3Ar clusters in the region 1400-3800 wn show that the OH stretching vibration has distinct characteristics. Multidimensional normal mode calculations were carried out for OH stretching vibrations in the 1200-4000 wn photon energy range. The potential energy and dipole surfaces were evaluated by using first-principles methods. By comparing the calculated frequencies and intensities of OH stretching vibration with experimental spectra, we found that the assignment of OH strecthing of H_3O^+ moiety and free OH strectching vibration have resonable agreement with experimental data. Jeffrey M. Headrick, Eric G. Diken, Richard S. Walters, Nathan I. Hammer, Richard A. Christie, Jun Cui, Evgeniy M. Myshakin, Michael A. Duncan, Mark A. Johnson, Kenneth D. Jordan, Science, 2005, 17, 1765. Kenta Mizuse, Jer-Lai Kuo and Asuka Fujii, Chem. Sci., 2011, 2, 868 Kenta Mizuse and Asuka Fujii, J. Phys. Chem. A, 2013, 117, 929.

  3. Multivariate normality

    NASA Technical Reports Server (NTRS)

    Crutcher, H. L.; Falls, L. W.

    1976-01-01

    Sets of experimentally determined or routinely observed data provide information about the past, present and, hopefully, future sets of similarly produced data. An infinite set of statistical models exists which may be used to describe the data sets. The normal distribution is one model. If it serves at all, it serves well. If a data set, or a transformation of the set, representative of a larger population can be described by the normal distribution, then valid statistical inferences can be drawn. There are several tests which may be applied to a data set to determine whether the univariate normal model adequately describes the set. The chi-square test based on Pearson's work in the late nineteenth and early twentieth centuries is often used. Like all tests, it has some weaknesses which are discussed in elementary texts. Extension of the chi-square test to the multivariate normal model is provided. Tables and graphs permit easier application of the test in the higher dimensions. Several examples, using recorded data, illustrate the procedures. Tests of maximum absolute differences, mean sum of squares of residuals, runs and changes of sign are included in these tests. Dimensions one through five with selected sample sizes 11 to 101 are used to illustrate the statistical tests developed.

  4. The detection rate of inspiral and quasi-normal modes of Population III binary black holes which can confirm or refute the general relativity in the strong gravity region

    NASA Astrophysics Data System (ADS)

    Kinugawa, Tomoya; Miyamoto, Akinobu; Kanda, Nobuyuki; Nakamura, Takashi

    2016-02-01

    Using our population synthesis code, we found that the typical chirp mass defined by (m1m2)3/5/(m1 + m2)1/5 of Population III (Pop III) binary black holes (BH-BHs) is ˜30 M⊙ with the total mass of ˜60 M⊙ so that the inspiral chirp signal as well as quasi-normal mode (QNM) of the merging black hole (BH) are interesting targets of KAGRA. The detection rate of the coalescing Pop III BH-BHs is ˜180 events yr- 1 (SFRp/(10-2.5 M⊙ yr-1 Mpc-3))([fb/(1 + fb)]/0.33)Errsys in our standard model, where SFRp, fb and Errsys are the peak value of the Pop III star formation rate, the binary fraction and the systematic error with Errsys = 1 for our standard model, respectively. To evaluate the robustness of chirp mass distribution and the range of Errsys, we examine the dependence of the results on the unknown parameters and the distribution functions in the population synthesis code. We found that the chirp mass has a peak at ˜30 M⊙ in most of parameters and distribution functions as well as Errsys ranges from 0.046 to 4. Therefore, the detection rate of the coalescing Pop III BH-BHs ranges about 8.3-720 events yr- 1(SFRp/(10- 2.5 M⊙ yr- 1 Mpc- 3))([fb/(1 + fb)]/0.33). The minimum rate corresponds to the worst model which we think unlikely so that unless (SFRp/(10- 2.5 M⊙ yr- 1 Mpc- 3))([fb/(1 + fb)]/0.33) ≪ 0.1, we expect the Pop III BH-BHs merger rate of at least one event per year by KAGRA. Nakano, Tanaka & Nakamura show that if signal-to-noise ratio (S/N) of QNM is larger than 35, we can confirm or refute the general relativity (GR) more than 5σ level. In our standard model, the detection rate of Pop III BH-BHs whose S/N is larger than 35 is 3.2 events yr- 1 (SFRp/(10- 2.5 M⊙ yr- 1 Mpc- 3))([fb/(1 + fb)]/0.33)Errsys. Thus, there is a good chance to check whether GR is correct or not in the strong gravity region.

  5. Normalizing Rejection.

    PubMed

    Conn, Vicki S; Zerwic, Julie; Jefferson, Urmeka; Anderson, Cindy M; Killion, Cheryl M; Smith, Carol E; Cohen, Marlene Z; Fahrenwald, Nancy L; Herrick, Linda; Topp, Robert; Benefield, Lazelle E; Loya, Julio

    2016-02-01

    Getting turned down for grant funding or having a manuscript rejected is an uncomfortable but not unusual occurrence during the course of a nurse researcher's professional life. Rejection can evoke an emotional response akin to the grieving process that can slow or even undermine productivity. Only by "normalizing" rejection, that is, by accepting it as an integral part of the scientific process, can researchers more quickly overcome negative emotions and instead use rejection to refine and advance their scientific programs. This article provides practical advice for coming to emotional terms with rejection and delineates methods for working constructively to address reviewer comments. PMID:26041785

  6. Normal development.

    PubMed

    Girard, Nadine; Koob, Meriam; Brunel, Herv

    2016-01-01

    Numerous events are involved in brain development, some of which are detected by neuroimaging. Major changes in brain morphology are depicted by brain imaging during the fetal period while changes in brain composition can be demonstrated in both pre- and postnatal periods. Although ultrasonography and computed tomography can show changes in brain morphology, these techniques are insensitive to myelination that is one of the most important events occurring during brain maturation. Magnetic resonance imaging (MRI) is therefore the method of choice to evaluate brain maturation. MRI also gives insight into the microstructure of brain tissue through diffusion-weighted imaging and diffusion tensor imaging. Metabolic changes are also part of brain maturation and are assessed by proton magnetic resonance spectroscopy. Understanding and knowledge of the different steps in brain development are required to be able to detect morphologic and structural changes on neuroimaging. Consequently alterations in normal development can be depicted. PMID:27430460

  7. All-atom Simulation of Amyloid Aggregates

    NASA Astrophysics Data System (ADS)

    Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

    Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

  8. Nonlinear mode coupling in whispering-gallery-mode resonators

    NASA Astrophysics Data System (ADS)

    D'Aguanno, Giuseppe; Menyuk, Curtis R.

    2016-04-01

    We present a first-principles derivation of the coupled nonlinear Schrödinger equations that govern the interaction between two families of modes with different transverse profiles in a generic whispering-gallery-mode resonator. We find regions of modulational instability and the existence of trains of bright solitons in both the normal and the anomalous dispersion regime.

  9. Theory of psychological adaptive modes.

    PubMed

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. PMID:27063089

  10. Generalised Hermite-Gaussian beams and mode transformations

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Chen, Yujie; Zhang, Yanfeng; Chen, Hui; Yu, Siyuan

    2016-05-01

    Generalised Hermite-Gaussian modes (gHG modes), an extended notion of Hermite-Gaussian modes (HG modes), are formed by the summation of normal HG modes with a characteristic function α, which can be used to unite conventional HG modes and Laguerre-Gaussian modes (LG modes). An infinite number of normalised orthogonal modes can thus be obtained by modulation of the function α. The gHG mode notion provides a useful tool in analysis of the deformation and transformation phenomena occurring in propagation of HG and LG modes with astigmatic perturbation.

  11. TUTOR User's Memo Using AUTHOR MODE.

    ERIC Educational Resources Information Center

    Avner, R. A.

    While a PLATO station is normally used to present lessons (STUDENT MODE), a station can also be used by a teacher to produce or alter lessons or to control lesson presentation (AUTHOR MODE). This memo describes the manner in which student records and lesson material are stored in the computer memory, prescribes the method of entry to AUTHOR MODE,…

  12. Numerical evaluation of uniform beam modes.

    SciTech Connect

    Tang, Y.; Reactor Analysis and Engineering

    2003-12-01

    The equation for calculating the normal modes of a uniform beam under transverse free vibration involves the hyperbolic sine and cosine functions. These functions are exponential growing without bound. Tables for the natural frequencies and the corresponding normal modes are available for the numerical evaluation up to the 16th mode. For modes higher than the 16th, the accuracy of the numerical evaluation will be lost due to the round-off errors in the floating-point math imposed by the digital computers. Also, it is found that the functions of beam modes commonly presented in the structural dynamics books are not suitable for numerical evaluation. In this paper, these functions are rearranged and expressed in a different form. With these new equations, one can calculate the normal modes accurately up to at least the 100th mode. Mike's Arbitrary Precision Math, an arbitrary precision math library, is used in the paper to verify the accuracy.

  13. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  14. All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

    PubMed

    Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

    2013-10-31

    A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row). PMID:24079472

  15. Automatic determination of important mode-mode correlations in many-mode vibrational wave functions

    NASA Astrophysics Data System (ADS)

    König, Carolin; Christiansen, Ove

    2015-04-01

    We introduce new automatic procedures for parameterizing vibrational coupled cluster (VCC) and vibrational configuration interaction wave functions. Importance measures for individual mode combinations in the wave function are derived based on upper bounds to Hamiltonian matrix elements and/or the size of perturbative corrections derived in the framework of VCC. With a threshold, this enables an automatic, system-adapted way of choosing which mode-mode correlations are explicitly parameterized in the many-mode wave function. The effect of different importance measures and thresholds is investigated for zero-point energies and infrared spectra for formaldehyde and furan. Furthermore, the direct link between important mode-mode correlations and coordinates is illustrated employing water clusters as examples: Using optimized coordinates, a larger number of mode combinations can be neglected in the correlated many-mode vibrational wave function than with normal coordinates for the same accuracy. Moreover, the fraction of important mode-mode correlations compared to the total number of correlations decreases with system size. This underlines the potential gain in efficiency when using optimized coordinates in combination with a flexible scheme for choosing the mode-mode correlations included in the parameterization of the correlated many-mode vibrational wave function. All in all, it is found that the introduced schemes for parameterizing correlated many-mode vibrational wave functions lead to at least as systematic and accurate calculations as those using more standard and straightforward excitation level definitions. This new way of defining approximate calculations offers potential for future calculations on larger systems.

  16. The double-mode Cepheids

    NASA Astrophysics Data System (ADS)

    Balona, L. A.

    1985-06-01

    Recent observational and theoretical results on double-mode Cepheids are reviewed. The likelihood that recently proposed candidate Cepheids are indeed Cepheids is evaluated. Periods, period ratios, and semi-amplitudes of the light and radial velocity variations of double-mode Cepheids are given. The physical and pulsational properties of double-mode Cepheids are discussed, reviewing evidence that these stars are Population I objects of high mass and that they all have the same mean effective temperature. The discovery of strong H-alpha emission occurring at seemingly random phases is addressed. Attempts to resolve the mass discrepancy problem of double-mode Cepheids, which results from observations showing that these Cepheids are indistinguishable from normal Cepheids of similar period, are reviewed along with attempts to find the cause of double-mode pulsation.

  17. The mode switching of PSR B2020+28

    NASA Astrophysics Data System (ADS)

    Wen, Z. G.; Wang, N.; Yan, W. M.; Yuan, J. P.; Liu, Z. Y.; Chen, M. Z.; Chen, J. L.

    2016-08-01

    This paper reports on polarimetric radiation properties based on the switching modes of normal PSR B2020+28 by analyzing the data acquired from the Nanshan 25-m radio telescope at 1556 MHz. With nearly 8 hours quasi-continuous observation, the data presented some striking and updated phenomena. The change of relative intensity between the leading and trailing components is the predominant feature of mode switching. The intensity ratio between the leading and trailing components are measured for the individual profiles averaged over 30 seconds. It is found that there is an excess of high ratios over the normal distribution, which indicates that two modes exist in the pulsar. The distribution of abnormal mode has a narrower width indicating that the abnormal mode is more stable than the normal mode. A total of 76 mode switching events are detected in our data. It spends 89 % in the normal mode and 11 % in the abnormal mode. The intrinsic distributions of mode timescales are constrained with power-law distributions. The significant difference in the index of the duration distribution between normal and abnormal modes possibly indicates that the timescale for the abnormal mode to get stable is shorter than that for the normal mode. The frequent switching between both modes may indicate that the oscillations between different magnetospheric states are rapid.

  18. Intrinsic Localized Modes in Proteins

    PubMed Central

    Nicolaï, Adrien; Delarue, Patrice; Senet, Patrick

    2015-01-01

    Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states). PMID:26658321

  19. Intrinsic Localized Modes in Proteins.

    PubMed

    Nicolaï, Adrien; Delarue, Patrice; Senet, Patrick

    2015-01-01

    Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states). PMID:26658321

  20. Normal Pressure Hydrocephalus

    MedlinePlus

    ... Enhancing Diversity Find People About NINDS NINDS Normal Pressure Hydrocephalus Information Page Synonym(s): Hydrocephalus - Normal Pressure Table ... Español Additional resources from MedlinePlus What is Normal Pressure Hydrocephalus? Normal pressure hydrocephalus (NPH) is an abnormal ...

  1. The excitation of normal modes by a curved line source

    NASA Astrophysics Data System (ADS)

    Mochizuki, E.

    1987-12-01

    The polynomial moments, up to total degree two, of the stress glut are calculated for a curved line source. The significance of the moments, whose total degree is one, is emphasized and the implication for inversion is discussed.

  2. Is My Penis Normal?

    MedlinePlus

    ... I Help a Friend Who Cuts? Is My Penis Normal? KidsHealth > For Teens > Is My Penis Normal? Print A A A Text Size en ... any guy who's ever worried about whether his penis is a normal size. There's a fairly wide ...

  3. Fluid involvement in normal faulting

    NASA Astrophysics Data System (ADS)

    Sibson, Richard H.

    2000-04-01

    Evidence of fluid interaction with normal faults comes from their varied role as flow barriers or conduits in hydrocarbon basins and as hosting structures for hydrothermal mineralisation, and from fault-rock assemblages in exhumed footwalls of steep active normal faults and metamorphic core complexes. These last suggest involvement of predominantly aqueous fluids over a broad depth range, with implications for fault shear resistance and the mechanics of normal fault reactivation. A general downwards progression in fault rock assemblages (high-level breccia-gouge (often clay-rich) → cataclasites → phyllonites → mylonite → mylonitic gneiss with the onset of greenschist phyllonites occurring near the base of the seismogenic crust) is inferred for normal fault zones developed in quartzo-feldspathic continental crust. Fluid inclusion studies in hydrothermal veining from some footwall assemblages suggest a transition from hydrostatic to suprahydrostatic fluid pressures over the depth range 3-5 km, with some evidence for near-lithostatic to hydrostatic pressure cycling towards the base of the seismogenic zone in the phyllonitic assemblages. Development of fault-fracture meshes through mixed-mode brittle failure in rock-masses with strong competence layering is promoted by low effective stress in the absence of thoroughgoing cohesionless faults that are favourably oriented for reactivation. Meshes may develop around normal faults in the near-surface under hydrostatic fluid pressures to depths determined by rock tensile strength, and at greater depths in overpressured portions of normal fault zones and at stress heterogeneities, especially dilational jogs. Overpressures localised within developing normal fault zones also determine the extent to which they may reutilise existing discontinuities (for example, low-angle thrust faults). Brittle failure mode plots demonstrate that reactivation of existing low-angle faults under vertical σ1 trajectories is only likely if

  4. Do normal hips dislocate?

    PubMed

    Alshameeri, Zeiad; Rehm, Andreas

    2014-11-01

    There have been a small number of case reports describing late normal-hip dislocations in children who were later diagnosed with developmental dysplasia of the hip. Here, we contest the assumption that normal hips can dislocate. We argue that (as in our case) the ultrasound scans in all published case reports on late dislocated normal hips did not show results that were entirely normal and therefore, so far, there has been no convincing evidence of a dislocation of a normal hip. We also want to highlight the importance of meticulous ultrasound and clinical assessments of high-risk children by an experienced orthopaedic surgeon. PMID:25144883

  5. Bicervical Normal Uterus with Normal Vagina

    PubMed Central

    Okeke, CE; Anele, TI; Onyejelam, CC

    2014-01-01

    This is a report of the form of uterine anomaly involving a dual cervical canal in a side-by-side disposition with normal uterine cavity and normal vagina. It portrays a form of congenital uterine anomaly not explicable by the existing classical theory of mullerian anomalies. However, there has been a proposed reclassification of mullerian anomalies, which includes this type of anomaly under Type IIIc. The patient was a 31-year-old woman being managed for “secondary infertility.” To report a case of uterine anomaly that is not explicable by the existing classical theory of mullerian anomalies. To the best of our knowledge, only few cases of bicervical normal uterus with normal vagina exist in the literature; one of the cases had an anterior-posterior disposition. This form of uterine abnormality is not explicable by the existing classical theory of mullerian anomalies and suggests that a complex interplay of events beyond the classical postulate gives rise to the female genital tract. PMID:25364608

  6. Cubic-normal distribution

    NASA Astrophysics Data System (ADS)

    Peng, Gan Chew; Hin, Pooi Ah; Ho, C. K.

    2015-12-01

    The power-normal distribution given in Yeo and Johnson in year 2000 is a unimodal distribution with wide ranges of skewness and kurtosis. A shortcoming of the power-normal distribution is that the negative and positve parts of the underlying random variable have to be specified by two different expressions of the standard normal random variable. In this paper, we construct a new distribution, called the cubic-normal distribution, via a single polynomial expression in cubic root function. Apart from having the properties which are similar to those of the power-normal distribution, this cubic-normal distribution can be developed into a multivariate version which is more attractive from the theoretical and computational points of view.

  7. Perspectives on Normalization.

    ERIC Educational Resources Information Center

    Thurman, S. Kenneth; Fiorelli, Joseph S.

    1979-01-01

    The paper discusses the principle of normalization for developmentally disabled persons from five viewpoints: empirical approaches, social integration, specialization and congregation, cultural norms, and prevention. (Author/CL)

  8. Suspensions with reduced violin string modes

    NASA Astrophysics Data System (ADS)

    Lee, B. H.; Ju, L.; Blair, D. G.

    2006-03-01

    We discuss the possibility of significantly reducing the number and Q-factor of violin string modes in the mirror suspension. Simulations of a bar-flexure suspension and an orthogonal ribbon have shown a reduction in the number of violin string modes when compared to a normal ribbon suspension. By calculating the expected suspension thermal noise, we find that the orthogonal ribbon provides a promising suspension alternative. A lower number of violin modes oscillating in the direction of the laser and a reduction in violin mode peak values of at least 23dB can be achieved with a slight increase in thermal noise above 40Hz.

  9. Berreman mode and epsilon near zero mode.

    PubMed

    Vassant, Simon; Hugonin, Jean-Paul; Marquier, Francois; Greffet, Jean-Jacques

    2012-10-01

    In this paper, we discuss the existence of an electromagnetic mode propagating in a thin dielectric film deposited on a metallic film at the particular frequency such that the dielectric permittivity vanishes. We discuss the remarkable properties of this mode in terms of extreme subwavelength mode confinment and its potential applications. We also discuss the link between this mode, the IR absorption peak on a thin dielectric film known as Berreman effect and the surface phonon polariton mode at the air/dielectric interface. Finally, we establish a connection with the polarization shift occuring in quantum wells. PMID:23188363

  10. Mixed-mode fracture of ceramics

    SciTech Connect

    Petrovic, J.J.

    1985-01-01

    The mixed-mode fracture behavior of ceramic materials is of importance for monolithic ceramics in order to predict the onset of fracture under generalized loading conditions and for ceramic composites to describe crack deflection toughening mechanisms. Experimental data on surface flaw mixed-mode fracture in various ceramics indicate that the flaw-plane normal stress at fracture decreases with increasing in-flaw-plane shear stress, although present data exhibit a fairly wide range in details of this sigma - tau relationship. Fracture from large cracks suggests that Mode II has a greater effect on Mode I fracture than Mode III. A comparison of surface flaw and large crack mixed-mode I-II fracture responses indicated that surface flaw behavior is influenced by shear resistance effects.

  11. Breathing Mode in Complex Plasmas

    NASA Astrophysics Data System (ADS)

    Fujioka, K.; Henning, C.; Ludwig, P.; Bonitz, M.; Melzer, A.; Vitkalov, S.

    2007-11-01

    The breathing mode is a fundamental normal mode present in Coulomb systems, and may have utility in identifying particle charge and the Debye length of certain systems. The question remains whether this mode can be extended to strongly coupled Yukawa balls [1]. These systems are characterized by particles confined within a parabolic potential well and interacting through a shielded Coulomb potential [2,3]. The breathing modes for a variety of systems in 1, 2, and 3 dimensions are computed by solving the eigenvalue problem given by the dynamical (Hesse) matrix. These results are compared to theoretical investigations that assume a strict definition for a breathing mode within the system, and an analysis is made of the most fitting model to utilize in the study of particular systems of complex plasmas [1,4]. References [1] T.E. Sheridan, Phys. of Plasmas. 13, 022106 (2006)[2] C. Henning et al., Phys. Rev. E 74, 056403 (2006)[3] M. Bonitz et al., Phys. Rev. Lett. 96, 075001 (2006)[4] C. Henning et al., submitted for publication

  12. Normal Functioning Family

    MedlinePlus

    ... Spread the Word Shop AAP Find a Pediatrician Family Life Medical Home Family Dynamics Adoption & Foster Care ... Español Text Size Email Print Share Normal Functioning Family Page Content Article Body Is there any way ...

  13. Normal pressure hydrocephalus

    MedlinePlus

    ... gait) is not normal. You may also have memory problems. Tests that may be done include: Lumbar puncture (spinal tap) with careful testing of walking before and after the spinal tap Head CT scan or MRI of the head

  14. Normality in Analytical Psychology

    PubMed Central

    Myers, Steve

    2013-01-01

    Although C.G. Jung’s interest in normality wavered throughout his career, it was one of the areas he identified in later life as worthy of further research. He began his career using a definition of normality which would have been the target of Foucault’s criticism, had Foucault chosen to review Jung’s work. However, Jung then evolved his thinking to a standpoint that was more aligned to Foucault’s own. Thereafter, the post Jungian concept of normality has remained relatively undeveloped by comparison with psychoanalysis and mainstream psychology. Jung’s disjecta membra on the subject suggest that, in contemporary analytical psychology, too much focus is placed on the process of individuation to the neglect of applications that consider collective processes. Also, there is potential for useful research and development into the nature of conflict between individuals and societies, and how normal people typically develop in relation to the spectrum between individuation and collectivity. PMID:25379262

  15. Normal Variants in Echocardiography.

    PubMed

    Sanchez, Daniel R; Bryg, Robert J

    2016-11-01

    Echocardiography is a powerful and convenient tool used routinely in the cardiac evaluation of many patients. Improved resolution and visualization of cardiac anatomy has led to the discovery of many normal variant structures that have no known pathologic consequence. Importantly, these findings may masquerade as pathology prompting unnecessary further evaluation at the expense of anxiety, cost, or potential harm. This review provides an updated and comprehensive collection of normal anatomic variants on both transthoracic and transesophageal imaging. PMID:27612473

  16. Spun Almost Normal Form

    NASA Astrophysics Data System (ADS)

    Paullin, Katherine L.

    Many of a 3-manifold's properties are determined by the surfaces they contain, and this knowledge leads to the foundation of decision algorithms for 3- manifolds. Popular work influencing the work of 3-manifold algorithms has it's roots in normal surface theory. In a triangulated 3-manifold, Haken and Kneser showed that we could put any incompressible surface into normal form. Expanding on those techniques, Rubinstein and Stocking later showed we could put any strongly irreducible surface into almost normal form. Walsh has more recently shown that in an ideal triangulation of a hyperbolic manifold many surfaces can be spun normalized. One unsolved problem in 3-manifold algorithms is studying the complexity of Lens Space Recognition. Spun almost normalization appears to be a part of solving this larger problem. In this dissertation, I will first discuss a nontraditional technique using graphs of equivalence classes of compressing disks that allows us to take a combinatorial approach to generalize the result of Walsh's to nonhyperbolic manifolds. Using that method, I'll also explore the conditions needed to show that a surface can be spun almost normalized.

  17. List mode multichannel analyzer

    DOEpatents

    Archer, Daniel E.; Luke, S. John; Mauger, G. Joseph; Riot, Vincent J.; Knapp, David A.

    2007-08-07

    A digital list mode multichannel analyzer (MCA) built around a programmable FPGA device for onboard data analysis and on-the-fly modification of system detection/operating parameters, and capable of collecting and processing data in very small time bins (<1 millisecond) when used in histogramming mode, or in list mode as a list mode MCA.

  18. Quantifying surface normal estimation

    NASA Astrophysics Data System (ADS)

    Reid, Robert B.; Oxley, Mark E.; Eismann, Michael T.; Goda, Matthew E.

    2006-05-01

    An inverse algorithm for surface normal estimation from thermal polarimetric imagery was developed and used to quantify the requirements on a priori information. Building on existing knowledge that calculates the degree of linear polarization (DOLP) and the angle of polarization (AOP) for a given surface normal in a forward model (from an object's characteristics to calculation of the DOLP and AOP), this research quantifies the impact of a priori information with the development of an inverse algorithm to estimate surface normals from thermal polarimetric emissions in long-wave infrared (LWIR). The inverse algorithm assumes a polarized infrared focal plane array capturing LWIR intensity images which are then converted to Stokes vectors. Next, the DOLP and AOP are calculated from the Stokes vectors. Last, the viewing angles, θ v, to the surface normals are estimated assuming perfect material information about the imaged scene. A sensitivity analysis is presented to quantitatively describe the a priori information's impact on the amount of error in the estimation of surface normals, and a bound is determined given perfect information about an object. Simulations explored the impact of surface roughness (σ) and the real component (n) of a dielectric's complex index of refraction across a range of viewing angles (θ v) for a given wavelength of observation.

  19. Orifice Blocks Heat Pipe in Reverse Mode

    NASA Technical Reports Server (NTRS)

    Alario, J. P.

    1982-01-01

    High forward-mode conductance is combined with rapid reverse-mode shutoff in a heat pipe originally developed to cool spacecraft payloads. A narrow orifice within the pipe "chokes off" the evaporator if heat sink becomes warmer than source. During normal operation, with source warmer than sink, orifice has little effect. Design is simpler and more compact than other thermal-diode heat pipes and requires no special materials, forgings, or unusual construction techniques.

  20. Implementing torsional-mode Doppler ladar.

    PubMed

    Fluckiger, David U

    2002-08-20

    Laguerre-Gaussian laser modes carry orbital angular momentum as a consequence of their helical-phase front screw dislocation. This torsional beam structure interacts with rotating targets, changing the orbital angular momentum (azimuthal Doppler) of the scattered beam because angular momentum is a conserved quantity. I show how to measure this change independently from the usual longitudinal momentum (normal Doppler shift) and derive the apropos coherent mixing efficiencies for monostatic, truncated Laguerre and Gaussian-mode ladar antenna patterns. PMID:12206220

  1. Normals to a Parabola

    ERIC Educational Resources Information Center

    Srinivasan, V. K.

    2013-01-01

    Given a parabola in the standard form y[superscript 2] = 4ax, corresponding to three points on the parabola, such that the normals at these three points P, Q, R concur at a point M = (h, k), the equation of the circumscribing circle through the three points P, Q, and R provides a tremendous opportunity to illustrate "The Art of Algebraic…

  2. Document Length Normalization.

    ERIC Educational Resources Information Center

    Singhal, Amit; And Others

    1996-01-01

    Describes a study that investigated document retrieval relevance based on document length in an experimental text collection. Topics include term weighting and document ranking, retrieval strategies such as the vector-space cosine match, and a modified technique called the pivoted cosine normalization. (LRW)

  3. Normal Birth: Two Stories

    PubMed Central

    Scaer, Roberta M.

    2002-01-01

    The author shares two stories: one of a normal birth that took place in a hospital with a nurse-midwife in attendance and another of a home birth unexpectedly shared by many colleagues. Both are told with the goal to inform, inspire, and educate. PMID:17273292

  4. Normal Psychosexual Development

    ERIC Educational Resources Information Center

    Rutter, Michael

    1971-01-01

    Normal sexual development is reviewed with respect to physical maturation, sexual interests, sex drive", psychosexual competence and maturity, gender role, object choice, children's concepts of sexual differences, sex role preference and standards, and psychosexual stages. Biologic, psychoanalytic and psychosocial theories are briefly considered.…

  5. Polarization Dependent Whispering Gallery Modes in Microspheres

    NASA Technical Reports Server (NTRS)

    Adamovsky, Grigory (Inventor); Wrbanek, Susan Y. (Inventor)

    2016-01-01

    A tunable resonant system is provided and includes a microsphere that receives an incident portion of a light beam generated via a light source, the light beam having a fundamental mode, a waveguide medium that transmits the light beam from the light source to the microsphere, and a polarizer disposed in a path of the waveguide between the light source and the microsphere. The incident portion of the light beam creates a fundamental resonance inside the microsphere. A change in a normalized frequency of the wavelength creates a secondary mode in the waveguide and the secondary mode creates a secondary resonance inside the microsphere.

  6. 'Snowflake' H Mode in a Tokamak Plasma

    SciTech Connect

    Piras, F.; Coda, S.; Duval, B. P.; Labit, B.; Marki, J.; Moret, J.-M.; Pitzschke, A.; Sauter, O.; Medvedev, S. Yu.

    2010-10-08

    An edge-localized mode (ELM) H-mode regime, supported by electron cyclotron heating, has been successfully established in a 'snowflake' (second-order null) divertor configuration for the first time in the TCV tokamak. This regime exhibits 2 to 3 times lower ELM frequency and 20%-30% increased normalized ELM energy ({Delta}W{sub ELM}/W{sub p}) compared to an identically shaped, conventional single-null diverted H mode. Enhanced stability of mid- to high-toroidal-mode-number ideal modes is consistent with the different snowflake ELM phenomenology. The capability of the snowflake to redistribute the edge power on the additional strike points has been confirmed experimentally.

  7. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  8. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  9. Microstructural effects on fracture toughness of polycrystalline ceramics in combined mode I and mode II loading

    NASA Technical Reports Server (NTRS)

    Singh, D.; Shetty, D. K.

    1988-01-01

    Fracture toughness of polycrystalline alumina and ceria partially-stabilized tetragonal zirconia (CeO2-TZP) ceramics were assessed in combined mode I and mode II loading using precracked disk specimens in diametral compression. Stress states ranging from pure mode I, combined mode I and mode II, and pure mode II were obtained by aligning the center crack at specific angles relative to the loading diameter. The resulting mixed-mode fracture toughness envelope showed significant deviation to higher fracture toughness in mode II relative to the predictions of the linear elastic fracture mechanics theory. Critical comparison with corresponding results on soda-lime glass and fracture surface observations showed that crack surface resistance arising from grain interlocking and abrasion was the main source of the increased fracture toughness in mode II loading of the polycrystalline ceramics. The normalized fracture toughness for pure mode II loading, (KII/KIc), increased with increasing grain size for the CeO2-TZP ceramics. Quantitative fractography confirmed an increased percentage of transgranular fracture of the grains in mode II loading.

  10. Spectrum of resistive MHD modes in cylindrical plasmas

    SciTech Connect

    Ryu, C.M.; Grimm, R.C.

    1983-07-01

    A numerical study of the normal modes of a compressible resistive MHD fluid in cylindrical geometry is presented. Resistivity resolves the shear Alfven and slow magnetosonic continua of ideal MHD into discrete spectra and gives rise to heavily damped modes whose frequencies lie on specific lines in the complex plane. Fast magnetosonic waves are less affected but are also damped. Overstable modes arise from the shear Alfven spectrum. The stabilizing effect of favorable average curvature is shown. Eigenfunctions illustrating the nature of typical normal modes are displayed.

  11. Normal-reflection image

    SciTech Connect

    Huang, L.; Fehler, Michael C.

    2003-01-01

    Common-angle wave-equation migration using the double-square-root is generally less accurate than the common-shot migration because the wavefield continuation equation for thc former involves additional approximations compared to that for the latter. We present a common-angle wave-equation migration that has the same accuracy as common-shot wave-equation migration. An image obtained from common-angle migration is a four- to five-dimensional output volume for 3D cases. We propose a normal-reflection imaging condition for common-angle migration to produce a 3D output volume for 3D migration. The image is closely related to the normal-reflection coefficients at interfaces. This imaging condition will allow amplitude-preserving migration to generate an image with clear physical meaning.

  12. Normal and Malignant Megakaryopoiesis

    PubMed Central

    Wen, Qiang; Goldenson, Benjamin; Crispino, John D.

    2016-01-01

    Megakaryopoiesis is the process by which bone marrow progenitor cells develop into mature megakaryocytes (MKs), which in turn produce platelets required for normal hemostasis. Over the past decade, the molecular mechanisms that contribute to MK development and differentiation have begun to be elucidated. In this review, we provide an overview of megakaryopoiesis and summarize the latest developments in this field. Specially, we focus on polyploidization, a unique form of the cell cycle that allows MKs to increase their DNA content, and the genes that regulate this process. In addition, since megakaryocytes play an important role in the pathogenesis of acute megakaryocytic leukemia (AMKL) and a subset of myeloproliferative neoplasms (MPNs), including essential thrombocythemia (ET) and primary myelofibrosis (PMF), we discuss the biology and genetics of these disorders. We anticipate that an increased understanding of normal megakaryocyte differentiation will provide new insights into novel therapeutic approaches that will directly benefit patients. PMID:22018018

  13. Large mode radius resonators

    NASA Technical Reports Server (NTRS)

    Harris, Michael R.

    1987-01-01

    Resonator configurations permitting operation with large mode radius while maintaining good transverse mode discrimination are considered. Stable resonators incorporating an intracavity telescope and unstable resonator geometries utilizing an output coupler with a Gaussian reflectivity profile are shown to enable large radius single mode laser operation. Results of heterodyne studies of pulsed CO2 lasers with large (11mm e sup-2 radius) fundamental mode sizes are presented demonstrating minimal frequency sweeping in accordance with the theory of laser-induced medium perturbations.

  14. Patterned flattened modes.

    PubMed

    Messerly, Michael J; Pax, Paul H; Dawson, Jay W

    2013-09-01

    We show that field-flattened strands may be added to and arbitrarily positioned within a field-flattened shell to create patterned, flattened modes. Patterning does not alter the effective index or flatness of the flattened mode but does alter the characteristics of other modes; we show that it can improve a flattened mode's bend performance significantly. Patterning provides a new and potentially valuable waveguide design tool that may lead to higher-power transport and laser fibers. PMID:23988948

  15. Integrated mode converter for mode division multiplexing

    NASA Astrophysics Data System (ADS)

    Perez-Galacho, Diego; Alonso-Ramos, Carlos Alberto; Marris-Morini, Delphine; Vakarin, Vladyslav; Le Roux, Xavier; Ortega-Moñux, Alejandro; Wangüemert-Perez, Juan Gonzalo; Vivien, Laurent

    2016-05-01

    The ever growing demands of bandwidth in optical communication systems are making traditional Wavelength Division Multiplexing (WDM) based systems to reach its limit. In order to cope with future bandwidth demand is necessary to use new levels of orthogonality, such as the waveguide mode or the polarization state. Mode Division Multiplexing (MDM) has recently attracted attention as a possible solution to increase aggregate bandwidth. In this work we discuss the proposition a of mode converter that can cover the whole C-Band of optical communications. The Mode Converter is based on two Multimode Interference (MMI) couplers and a phase shifter. Insertion loss (IL) below 0.2 dB and Extinction ratio (ER) higher than 20 dB in a broad bandwidth range of 1.5 μm to 1.6 μm have been estimated. The total length of the device is less than 30 μm.

  16. Excitation of (2,1) neoclassical tearing modes by mode coupling with (1,1) internal mode in EAST

    NASA Astrophysics Data System (ADS)

    Shi, Tonghui; Wan, Baonian; Shen, Biao; Sun, Youwen; Qian, Jinping; Hu, Liqun; Gong, Xianzu; Liu, Guangjun; Luo, Zhengping; Zhong, Guoqiang; Xu, Liqing; Zhang, Jizong; Lin, Shiyao; Jie, Yinxian; Wang, Fudi; Lv, Bo; the EAST Team

    2013-05-01

    Neoclassical tearing modes (NTM) are observed in discharges with auxiliary heating LH+ICRF and LH only during H-mode in EAST. The m/n = 2/1 NTM is triggered by strongly coupling with an m/n = 1/1 internal mode. Here, LH and ICRF are the abbreviations of lower hybrid resonance heating and ion cyclotron resonance frequency heating, respectively. The mode number of the NTM is m/n = 2/1, where m is the poloidal mode number and n is the toroidal mode number. Just before the triggering of NTMs, an m/n = 1/1 internal mode appears in the soft x-ray emission at plasma centre when the intensity of hard x-ray (IHX) reaches a critical value. The mode, characterized by frequency chirping in the spectrum, may be related to suprathermal electrons produced by LH. The saturated magnetic island width wsat of the NTM is strongly correlated with poloidal βp. Normalized βN,onset and the magnetic island critical width wcrit increase with electron temperature Te.

  17. Landsat-5 bumper-mode geometric correction

    USGS Publications Warehouse

    Storey, J.C.; Choate, Michael J.

    2004-01-01

    The Landsat-5 Thematic Mapper (TM) scan mirror was switched from its primary operating mode to a backup mode in early 2002 in order to overcome internal synchronization problems arising from long-term wear of the scan mirror mechanism. The backup bumper mode of operation removes the constraints on scan start and stop angles enforced in the primary scan angle monitor operating mode, requiring additional geometric calibration effort to monitor the active scan angles. It also eliminates scan timing telemetry used to correct the TM scan geometry. These differences require changes to the geometric correction algorithms used to process TM data. A mathematical model of the scan mirror's behavior when operating in bumper mode was developed. This model includes a set of key timing parameters that characterize the time-varying behavior of the scan mirror bumpers. To simplify the implementation of the bumper-mode model, the bumper timing parameters were recast in terms of the calibration and telemetry data items used to process normal TM imagery. The resulting geometric performance, evaluated over 18 months of bumper-mode operations, though slightly reduced from that achievable in the primary operating mode, is still within the Landsat specifications when the data are processed with the most up-to-date calibration parameters.

  18. DISJUNCTIVE NORMAL SHAPE MODELS

    PubMed Central

    Ramesh, Nisha; Mesadi, Fitsum; Cetin, Mujdat; Tasdizen, Tolga

    2016-01-01

    A novel implicit parametric shape model is proposed for segmentation and analysis of medical images. Functions representing the shape of an object can be approximated as a union of N polytopes. Each polytope is obtained by the intersection of M half-spaces. The shape function can be approximated as a disjunction of conjunctions, using the disjunctive normal form. The shape model is initialized using seed points defined by the user. We define a cost function based on the Chan-Vese energy functional. The model is differentiable, hence, gradient based optimization algorithms are used to find the model parameters. PMID:27403233

  19. Normal black kidney

    PubMed Central

    Yarmohamadi, Aliasghar; Rezayat, Ali Reza Akhavan; Memar, Bahram; Rahimi, Hamid Reza; Cand, PhD

    2014-01-01

    A black kidney has 3 major differential diagnoses: hemosiderosis, lipofuscin pigment and melanotic renal cell carcinoma. Excluding lipofuscin, the other 2 are accompanied by an abnormal renal function. We report on a 25-year-old man who intended to donate a kidney to his cousin. On the operating room table when we incised the left flank region and exposed the kidney, we found a firm and black kidney so the operation was cancelled due to potential vascular injuries. Days after the incomplete procedure, we reviewed the donor’s biochemistry and imaging to reassess his renal function, but the results showed quite normal renal function again. The result of Ham test was also negative. Two weeks later, we began the operation, removed the same left kidney and found that it was in the same conditions as it was before. We took the opportunity to send needle biopsies of the kidney for histopathologic analysis. The analysis showed a melanotic kidney without pathological changes in glomeruli and interstitium and vessels. A black kidney may result in hemosiderin, lipofuscin or melanin deposits in the kidney, which can confirm the diagnosis; however, special tests for underlying disease and renal function should be considered. Some causes of black kidney lead to abnormal function, but our patients’s kidney returned to normal. PMID:24839502

  20. Wave modes facilitating fast magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Singh, N.

    2011-12-01

    Whistler and kinetic Alfven waves are often invoked to explain fast magnetic reconnection in collsionless plasmas. But how these wave modes facilitate the reconnection has remained unclear. An important unanswered question deals with the meaning of the wave frequency in the context of magnetic reconnection. New measurement on a fast explosive reconnection event in the Versatile Toroidal Facility (VTF) at MIT provides an interesting example of the meaning of the wave mode and the associated frequency directly related to the time scale of the impulsive reconnection. We examine the measurements in VTF in view of the whistler wave mode, showing that the explosive growth in the reconnection is related to the thinning of the current sheet to a few electron skin depths. We further demonstrate that the fastest measured time scale (~ 3 microseconds) and the largest normalized reconnection rate (~0.35) agree with those predicted from the whistler mode dispersion relation.

  1. Phase mixing and nonlinearity in geodesic acoustic modes

    SciTech Connect

    Hung, C. P.; Hassam, A. B.

    2013-09-15

    Phase mixing and nonlinear resonance detuning of geodesic acoustic modes in a tokamak plasma are examined. Geodesic acoustic modes (GAMs) are tokamak normal modes with oscillations in poloidal flow constrained to lie within flux surfaces. The mode frequency is sonic, dependent on the local flux surface temperature. Consequently, mode oscillations between flux surfaces get rapidly out of phase, resulting in enhanced damping from the phase mixing. Damping rates are shown to scale as the negative 1/3 power of the large viscous Reynolds number. The effect of convective nonlinearities on the normal modes is also studied. The system of nonlinear GAM equations is shown to resemble the Duffing oscillator, which predicts resonance detuning of the oscillator. Resonant amplification is shown to be suppressed nonlinearly. All analyses are verified by numerical simulation. The findings are applied to a recently proposed GAM excitation experiment on the DIII-D tokamak.

  2. Pornography, normalization, and empowerment.

    PubMed

    Weinberg, Martin S; Williams, Colin J; Kleiner, Sibyl; Irizarry, Yasmiyn

    2010-12-01

    Opponents and proponents of erotic representations (referred to hereafter as "pornography") have described the effects of pornography from their perspective. Little, however, has been done in the way of research to investigate these claims from the consumer's point of view. This especially has been so regarding the positive impact of such consumption on a person's sex life. Using a study group of 245 college students, we examined this question in a framework of scripting theory. We wanted to see whether viewing pornography appeared to expand sexual horizons through normalization and facilitate a willingness to explore new sexual behaviors and sexual relationships through empowerment. The data supported this viewpoint and further showed the effects to be mediated by gender and sexual preference identity. They suggested, however, that established scripts were extended rather than abandoned. We conclude with connections between our findings and the widespread viewing of pornography in contemporary society. PMID:20127507

  3. Normal Untreated Jurkat Cells

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Biomedical research offers hope for a variety of medical problems, from diabetes to the replacement of damaged bone and tissues. Bioreactors, which are used to grow cells and tissue cultures, play a major role in such research and production efforts. The objective of the research was to define a way to differentiate between effects due to microgravity and those due to possible stress from non-optimal spaceflight conditions. These Jurkat cells, a human acute T-cell leukemia was obtained to evaluate three types of potential experimental stressors: a) Temperature elevation; b) Serum starvation; and c) Centrifugal force. The data from previous spaceflight experiments showed that actin filaments and cell shape are significantly different for the control. These normal cells serve as the baseline for future spaceflight experiments.

  4. Acoustics measurements in normal jet impingement

    NASA Technical Reports Server (NTRS)

    Kleis, S. J.

    1977-01-01

    The dependence of far field acoustic measurements for a uniform jet on nozzle to plate spacing for small dimensionless spacings (h/d - 0.75 to 3.0) was investigated. Spectra from a real time analyzer were read and processed by an HP 2116 minicomputer in on-line mode. Similar data was generated for a fully developed pipe flow exit condition jet to compare with other investigations. The data base for normal jet impingement was extended to smaller values of nozzle to plate spacing. The effects of slight noise heating (30 deg rise) of the jet on the far field noise produced by the impinging jet are demonstrated.

  5. Dual-Mode Combustor

    NASA Technical Reports Server (NTRS)

    Trefny, Charles J (Inventor); Dippold, Vance F (Inventor)

    2013-01-01

    A new dual-mode ramjet combustor used for operation over a wide flight Mach number range is described. Subsonic combustion mode is usable to lower flight Mach numbers than current dual-mode scramjets. High speed mode is characterized by supersonic combustion in a free-jet that traverses the subsonic combustion chamber to a variable nozzle throat. Although a variable combustor exit aperture is required, the need for fuel staging to accommodate the combustion process is eliminated. Local heating from shock-boundary-layer interactions on combustor walls is also eliminated.

  6. Bartter Syndrome with Normal Aldosterone Level: An Unusual Presentation.

    PubMed

    Huque, S S; Rahman, M H; Khatun, S

    2016-04-01

    Bartter syndrome (BS) is a hereditary disease, with an autosomal recessive or autosomal dominant mode of transmission. It is characterized by salt wasting hypochloraemic, hypokalaemic metabolic alkalosis and hyperreninaemia with normal blood pressure. The primary defect is in the thick ascending limb of loop of Henle (TAL). Herein, we report a case that had typical features of BS like severe dehydration, severe hypokalaemia, metabolic alkalosis and failure to thrive but had normal aldosterone level which is very uncommon. PMID:27277374

  7. Nanosecond square pulse generation in fiber lasers with normal dispersion

    NASA Astrophysics Data System (ADS)

    Zhao, L. M.; Tang, D. Y.; Cheng, T. H.; Lu, C.

    2007-04-01

    We report on the generation of nanosecond square pulses in a passively mode-locked fiber ring laser made of purely normal dispersive fibers. Different to the noise-like pulse operation of the laser, the generated square pulses are stable and have no internal structures. We show that the formation of the square pulse is due to the combined action of the pulse peak clamping effect caused by the cavity and the almost linear pulse propagation in the normal dispersive fibers.

  8. A method for normalization of X-ray absorption spectra

    SciTech Connect

    Weng, T.-C.; Waldo, G.S.; Penner-Hahn, J.E.

    2010-07-20

    Accurate normalization of X-ray absorption data is essential for quantitative analysis of near-edge features. A method, implemented as the program MBACK, to normalize X-ray absorption data to tabulated mass absorption coefficients is described. Comparison of conventional normalization methods with MBACK demonstrates that the new normalization method is not sensitive to the shape of the background function, thus allowing accurate comparison of data collected in transmission mode with data collected using fluorescence ion chambers or solid-state fluorescence detectors. The new method is shown to have better reliability and consistency and smaller errors than conventional normalization methods. The sensitivity of the new normalization method is illustrated by analysis of data collected during an equilibrium titration.

  9. Role of the normal gut microbiota

    PubMed Central

    Jandhyala, Sai Manasa; Talukdar, Rupjyoti; Subramanyam, Chivkula; Vuyyuru, Harish; Sasikala, Mitnala; Reddy, D Nageshwar

    2015-01-01

    Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual’s life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool. PMID:26269668

  10. Role of the normal gut microbiota.

    PubMed

    Jandhyala, Sai Manasa; Talukdar, Rupjyoti; Subramanyam, Chivkula; Vuyyuru, Harish; Sasikala, Mitnala; Nageshwar Reddy, D

    2015-08-01

    Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual's life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool. PMID:26269668

  11. Normality, therapy, and enhancement.

    PubMed

    Giubilini, Alberto

    2015-07-01

    According to human enhancement advocates, it is morally permissible (and sometimes obligatory) to use biomedical means to modulate or select certain biological traits in order to increase people's welfare, even when there is no pathology to be treated or prevented. Some authors have recently proposed to extend the use of biomedical means to modulate lust, attraction, and attachment. I focus on some conceptual implications of this proposal, particularly with regard to bioconservatives' understanding of the notions of therapy and enhancement I first explain what makes the proposal of medicalizing love interesting and unique, compared to the other forms of bioenhancement usually advocated. I then discuss how the medicalization of love bears on the more general debate on human enhancement, particularly with regard to the key notion of "normality" that is commonly used to define the therapy-enhancement distinction. This analysis suggests that the medicalization of love, in virtue of its peculiarity, requires bioconservatives to reconsider their way of understanding and applying the notions of "therapy" and "enhancement." More in particular, I show that, because a non-arbitrary and value-free notion of "therapy" cannot be applied to the case of love, bioconservatives have the burden of either providing some new criterion that could be used for drawing a line between permissible and impermissible medicalization, or demonstrating that under no circumstances-including the cases in which love is already acknowledged to require medical intervention-can love fall within the domain of medicine. PMID:26059959

  12. [Normal aging and cognition].

    PubMed

    Ska, Bernadette; Joanette, Yves

    2006-03-01

    It is now well documented that normal aging modifies the cognitive functioning and most observations suggest that cognition evolves in the direction of deterioration. The more frequently impaired functions are memory, attention and visual-spatial abilities. On the other hand, some abilities seem to increase, such as vocabulary. Considering the aging effect on cognition, questions remain regarding directionality, universality and reversibility. A great variability in aged related impacts is observed among subjects and among cognitive domains. Some individuals evolved more rapidly than others. Some cognitive functions are more affected by aging than others. General and specific factors are hypothesized to explain the aged related cognitive decline. Among them, educational level, health, cognitive style, life style, personality, are likely to modulate the aged related cognitive evolution by influencing attentional resources and cerebral plasticity. Cognitive resources are essential to develop adaptative strategies. During the life span, resources are activated and increased by learning and training. Considering the role of cognitive resources, successful aging is dependent on several conditions : absence of disease leading to a loss of autonomy, maintenance of cognitive and physical activities, and active and social engaged lifestyle. PMID:16527210

  13. New Measurements of Radial Mode Eigenfrequencies

    NASA Astrophysics Data System (ADS)

    Laske, G.; Masters, G.; Dziewonski, A. M.

    2001-12-01

    Radial mode eigenfrequencies are commonly thought to be measured with great ease and precision. The reason for this is that these modes have no geographic pattern so one should be able to measure frequencies from a spectrum observed at any station in the world. Yet, radial modes often seem inconsistent with spherical Earth models that fit all other mode frequencies. It turns out that radial modes are sometimes strongly coupled. The strongest coupling is predicted to be with l=2 modes which is caused by the Earth's hydrostatic ellipticity and aspherical structure of harmonic degree 2. In such cases, mode-coupling due to ellipticity alone can cause a frequency shift for the radial modes by more than 4 microHz. Given that mode frequencies can be measured to within 0.1 microHz, this shift is significant, and some singlets of l=2 modes have indeed been misidentified as the radial mode in the past. Including the spectra of the June 23, 2001 Southern Peru Earthquake we have re-analyzed radial mode eigenfrequencies and present a mode dataset that is internally more consistent than previous ones. We construct spherical Earth models that are consistent with our new data, the Earth's mass and moment of inertia and the current best estimates of ``Reference Normal Mode Data'' (available on the Reference Earth Model web site: //mahi.ucsd.edu/Gabi/rem.html). We seek the smallest perturbation to PREM but update the Q-structure as well as the depths of the upper mantle discontinuities (418~km and 660~km as first order discontinuities; 520~km as change in gradient). The best fitting 1D model is transversely isotropic but we also show isotropic models that fit the data to within their errors. We show that the 220~km discontinuity is not required in the isotropic model but that there exists a trade-off between high shear-velocities in the lid and a low-density zone beneath it. We also investigate ways of truncating transverse isotropy without the 220.

  14. Institutionalizing Normal: Rethinking Composition's Precedence in Normal Schools

    ERIC Educational Resources Information Center

    Skinnell, Ryan

    2013-01-01

    Composition historians have recently worked to recover histories of composition in normal schools. This essay argues, however, that historians have inadvertently misconstrued the role of normal schools in American education by inaccurately comparing rhetorical education in normal schools to rhetorical education in colleges and universities.…

  15. Tearing Modes in Tokamaks

    NASA Astrophysics Data System (ADS)

    White, R. B.

    2008-05-01

    This lecture gives a basic introduction to magnetic £elds, magnetic surface destruction, toroidal equilibrium and tearing modes in a tokamak, including the linear and nonlinear development of these modes and their modi£cation by current drive and bootstrap current, and sawtooth oscillations and disruptions.

  16. Mode decomposition evolution equations

    PubMed Central

    Wang, Yang; Wei, Guo-Wei; Yang, Siyang

    2011-01-01

    Partial differential equation (PDE) based methods have become some of the most powerful tools for exploring the fundamental problems in signal processing, image processing, computer vision, machine vision and artificial intelligence in the past two decades. The advantages of PDE based approaches are that they can be made fully automatic, robust for the analysis of images, videos and high dimensional data. A fundamental question is whether one can use PDEs to perform all the basic tasks in the image processing. If one can devise PDEs to perform full-scale mode decomposition for signals and images, the modes thus generated would be very useful for secondary processing to meet the needs in various types of signal and image processing. Despite of great progress in PDE based image analysis in the past two decades, the basic roles of PDEs in image/signal analysis are only limited to PDE based low-pass filters, and their applications to noise removal, edge detection, segmentation, etc. At present, it is not clear how to construct PDE based methods for full-scale mode decomposition. The above-mentioned limitation of most current PDE based image/signal processing methods is addressed in the proposed work, in which we introduce a family of mode decomposition evolution equations (MoDEEs) for a vast variety of applications. The MoDEEs are constructed as an extension of a PDE based high-pass filter (Europhys. Lett., 59(6): 814, 2002) by using arbitrarily high order PDE based low-pass filters introduced by Wei (IEEE Signal Process. Lett., 6(7): 165, 1999). The use of arbitrarily high order PDEs is essential to the frequency localization in the mode decomposition. Similar to the wavelet transform, the present MoDEEs have a controllable time-frequency localization and allow a perfect reconstruction of the original function. Therefore, the MoDEE operation is also called a PDE transform. However, modes generated from the present approach are in the spatial or time domain and can be

  17. Zero-mode waveguides

    DOEpatents

    Levene, Michael J.; Korlach, Jonas; Turner, Stephen W.; Craighead, Harold G.; Webb, Watt W.

    2007-02-20

    The present invention is directed to a method and an apparatus for analysis of an analyte. The method involves providing a zero-mode waveguide which includes a cladding surrounding a core where the cladding is configured to preclude propagation of electromagnetic energy of a frequency less than a cutoff frequency longitudinally through the core of the zero-mode waveguide. The analyte is positioned in the core of the zero-mode waveguide and is then subjected, in the core of the zero-mode waveguide, to activating electromagnetic radiation of a frequency less than the cut-off frequency under conditions effective to permit analysis of the analyte in an effective observation volume which is more compact than if the analysis were carried out in the absence of the zero-mode waveguide.

  18. Excursions through KK modes

    NASA Astrophysics Data System (ADS)

    Furuuchi, Kazuyuki

    2016-07-01

    In this article we study Kaluza-Klein (KK) dimensional reduction of massive Abelian gauge theories with charged matter fields on a circle. Since local gauge transformations change position dependence of the charged fields, the decomposition of the charged matter fields into KK modes is gauge dependent. While whole KK mass spectrum is independent of the gauge choice, the mode number depends on the gauge. The masses of the KK modes also depend on the field value of the zero-mode of the extra dimensional component of the gauge field. In particular, one of the KK modes in the KK tower of each massless 5D charged field becomes massless at particular values of the extra-dimensional component of the gauge field. When the extra-dimensional component of the gauge field is identified with the inflaton, this structure leads to recursive cosmological particle productions.

  19. A review of time-domain and frequency-domain component mode synthesis method

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.

    1985-01-01

    Hurty (1965) has conducted a dynamic analysis of structural systems using component modes. The component mode synthesis (CMS) procedure considered by him represents a form of substructure coupling analysis which is often utilized in structural dynamics. Time-domain CMS methods employing real modes are discussed, taking into account real component modes, normal modes, redundant constraint modes, rigid-body modes, attachment modes, inertia-relief modes, statically-complete interface mode sets, dynamic component mode supersets, component modal models, the coupling of components, and the classification of methods. Attention is also given to the experimental determination of component mode synthesis parameters, time-domain CMS methods for damped systems, and frequency-domain CMS methods for damped systems.

  20. Is My Child's Appetite Normal?

    MedlinePlus

    ... normal way, not overeat. That is a good habit for lifelong health. Provided by NIBBLES FOR HEALTH 17 Nutrition Newsletters for Parents of Young Children, USDA, Food and Nutrition Service Is My Child’s Appetite Normal? ...

  1. Multipole moments of stellar oscillation modes

    NASA Technical Reports Server (NTRS)

    Reisenegger, Andreas

    1994-01-01

    The oscillating mass 2(exp l)-pole moment, M(sub nl), of a star in a given (normalized) oscillation mode determines the energy that can be absorbed by the mode in a tidal interaction and the power radiated by the mode in gravitational waves, both of which are proportional to (absolute value of M(sub nl))(exp 2). The coefficients in the expansion of the vector fields del(r(exp l)Y(sub lm)(theta, phi)) in terms of the displacement fields of modes of given l and m are proportional to M(sub nl). This expansion leads to a sum rule sum over n(absolute value of M(sub nl))(exp 2) = constant. For stars of weak to moderate central condensation (such as neutron stars), the f-mode is well approximated by the vector field being expanded, and therefore it takes the lion's share of the sum. Thus the multipole moments of all other modes must be small. In there numerical evaluation, it is necessary to know the shape of the eigenfunctions quite precisly, since a small f-mode contamination can significantly increase the obtained values. This contamination occurs in some `hybrid' numerical computations of neutron star oscillations with relativistic equilibrium stars and Newtonian dynamics (e.g., McDermott et al. 1988). In this case, it is due to a slight inconsistency in the models and leads to a large overestimate of the power radiated in gravitational waves by modes other than the f-mode, although their oscillation periods are nearly unaffected.

  2. Robust fiber optic flexure sensor exploiting mode coupling in few-mode fiber

    NASA Astrophysics Data System (ADS)

    Nelsen, Bryan; Rudek, Florian; Taudt, Christopher; Baselt, Tobias; Hartmann, Peter

    2015-05-01

    Few-mode fiber (FMF) has become very popular for use in multiplexing telecommunications data over fiber optics. The simplicity of producing FMF and the relative robustness of the optical modes, coupled with the simplicity of reading out the information make this fiber a natural choice for communications. However, little work has been done to take advantage of this type of fiber for sensors. Here, we demonstrate the feasibility of using FMF properties as a mechanism for detecting flexure by exploiting mode coupling between modes when the cylindrical symmetry of the fiber is perturbed. The theoretical calculations shown here are used to understand the coupling between the lowest order linearly polarized mode (LP01) and the next higher mode (LP11x or LP11y) under the action of bending. Twisting is also evaluated as a means to detect flexure and was determined to be the most reliable and effective method when observing the LP21 mode. Experimental results of twisted fiber and observations of the LP21 mode are presented here. These types of fiber flexure sensors are practical in high voltage, high magnetic field, or high temperature medical or industrial environments where typical electronic flexure sensors would normally fail. Other types of flexure measurement systems that utilize fiber, such as Rayleigh back-scattering [1], are complicated and expensive and often provide a higher-than necessary sensitivity for the task at hand.

  3. Onset and Saturation of a Non-resonant Internal Mode in NSTX and Implications For AT Modes in ITER

    SciTech Connect

    J.A. Breslau, M.S. Chance, J. Chen, G.Y. Fu, S,. Gerhardt, N. Gorelenkov, S.C. Jardin and J. Manickam

    2011-08-01

    Motivated by experimental observations of apparently triggerless tearing modes, we have performed linear and nonlinear MHD analysis showing that a non-resonant mode with toroidal mode number n = 1 can develop in the National Spherical Torus eXperiment (NSTX) at moderate normalized βN when the shear is low and the central safety factor q0 is close to but greater than one. This mode, which is related to previously identified ‘infernal’ modes, will saturate and persist, and can develop poloidal mode number m = 2 magnetic islands in agreement with experiments. We have also extended this analysis by performing a free-boundary transport simulation of an entire discharge and showing that, with reasonable assumptions, we can predict the time of mode onset. __________________________________________________

  4. Dementia and the default mode.

    PubMed

    Beason-Held, L L

    2011-06-01

    Changes in regional activity levels and network connectivity occur across the lifespan within the default mode network (DMN) of resting brain function. Changes with age are noted in most components of the DMN, especially in medial frontal/anterior cingulate and posterior cingulate/precuneus regions. Individuals with age-related disease such as mild cognitive impairment (MCI) and Alzheimer's disease (AD) demonstrate additional default-related changes particularly in posterior cingulate/precuneus and hippocampal regions. As these regions are areas of known pathologic change in both normal aging and age-related disease, examining DMN activity may allow future studies to more fully assess the relationship between pathology and function in these regions. The ability to form this structure-function link could allow us to determine critical factors involved in the decline or preservation of function in the presence of age-related neuropathology. PMID:21222595

  5. Impregnation mode in wood plastic composite

    NASA Astrophysics Data System (ADS)

    Mozaffar Husain, M.; Khan, Mubarak A.; Azam Ali, M.; Idriss Ali, K. M.; Mustafa, A. I.

    1996-12-01

    Bulk monomer MMA was impregnated into simul, a fuel wood of Bangladesh, under vacuum and under normal temperature and pressure conditions in order to compare the mode of impregnation and its effect on various characteristic parameters of wood plastic composites. Methanol (MeOH) was used as the swelling solvent with methylmethacrylate (MMA) at MMA: MeOH = 70:30, v/v. Impregnation of the bulk monomer was very high under vacuum compared to that at normal condition; but the difference of grafting of MMA to the wood cellulose under these two impregnating conditions was much lower as compared to that of the uptakes of impregnating solution MMA + MeOH under these two modes of impregnation. Incorporation of additives to MMA + MeOH has substantially enhanced grafting, tensile strength, bending strength and compression strength of thcomposite of such an extent that there is virtually very little difference between vacuum impregnation and normal impregnation. Considering the available data it is suggested that the impregnation under normal condition is preferable beacuse different substrates of various sizes and shapes can be suitably impregnated under normal condition while vacuum impregnation has several limitations in this respect.

  6. WMAP normalization of inflationary cosmologies

    SciTech Connect

    Liddle, Andrew R.; Parkinson, David; Mukherjee, Pia; Leach, Samuel M.

    2006-10-15

    We use the three-year WMAP observations to determine the normalization of the matter power spectrum in inflationary cosmologies. In this context, the quantity of interest is not the normalization marginalized over all parameters, but rather the normalization as a function of the inflationary parameters n{sub S} and r with marginalization over the remaining cosmological parameters. We compute this normalization and provide an accurate fitting function. The statistical uncertainty in the normalization is 3%, roughly half that achieved by COBE. We use the k-l relation for the standard cosmological model to identify the pivot scale for the WMAP normalization. We also quote the inflationary energy scale corresponding to the WMAP normalization.

  7. Spin waves in ferromagnetic insulators coupled via a normal metal

    NASA Astrophysics Data System (ADS)

    Skarsvâg, Hans; Kapelrud, André; Brataas, Arne

    2014-09-01

    Herein, we study spin-wave dispersion and dissipation in a ferromagnetic insulator-normal metal-ferromagnetic insulator system. Long-range dynamic coupling because of spin pumping and spin transfer lead to collective magnetic excitations in the two thin-film ferromagnets. In addition, the dynamic dipolar field contributes to the interlayer coupling. By solving the Landau-Lifshitz-Gilbert-Slonczewski equation for macrospin excitations and the exchange-dipole volume as well as surface spin waves, we compute the effect of the dynamic coupling on the resonance frequencies and linewidths of the various modes. The long-wavelength modes may couple acoustically or optically. In the absence of spin-memory loss in the normal metal, the spin-pumping-induced Gilbert damping enhancement of the acoustic mode vanishes, whereas the optical mode acquires a significant Gilbert damping enhancement, comparable to that of a system attached to a perfect spin sink. The dynamic coupling is reduced for short-wavelength spin waves, and there is no synchronization. For intermediate wavelengths, the coupling can be increased by the dipolar field such that the modes in the two ferromagnetic insulators can couple despite possible small frequency asymmetries. The surface waves induced by an easy-axis surface anisotropy exhibit much greater Gilbert damping enhancement. These modes also may acoustically or optically couple, but they are unaffected by thickness asymmetries.

  8. Chiral Surface Modes in Three-Dimensional Topological Insulators

    NASA Astrophysics Data System (ADS)

    Hattori, Kiminori; Okamoto, Hiroaki

    2016-05-01

    Where chiral modes should appear is an essential question for the quantum anomalous Hall (QAH) effect in three-dimensional topological insulators (3DTIs). In this letter, we show that in a slab of ferromagnetic 3DTI subjected to a uniform exchange field normal to its top and bottom surfaces, the QAH effect creates a single chiral surface mode delocalized on the side faces. In a nonmagnetic 3DTI, analogously, delocalized helical modes consisting of a pair of oppositely propagating chiral surface modes are produced by the quantum spin Hall effect.

  9. Edge chlorination of hexa-peri-hexabenzocoronene investigated by density functional theory and vibrational spectroscopy† †Electronic supplementary information (ESI) available: Description and animations of the vibrational normal modes of HBC and HBC-Cl discussed in the text. See DOI: 10.1039/c5cp07755a Click here for additional data file. Click here for additional data file.

    PubMed Central

    Maghsoumi, Ali; Narita, Akimitsu; Dong, Renhao; Feng, Xinliang; Castiglioni, Chiara

    2016-01-01

    We investigate the molecular structure and vibrational properties of perchlorinated hexa-peri-hexabenzocoronene (HBC-Cl) by density functional theory (DFT) calculations and IR and Raman spectroscopy, in comparison to the parent HBC. The theoretical and experimental IR and Raman spectra demonstrated very good agreement, elucidating a number of vibrational modes corresponding to the observed peaks. Compared with the parent HBC, the edge chlorination significantly alters the planarity of the molecule. Nevertheless, the results indicated that such structural distortion does not significantly impair the π-conjugation of such polycyclic aromatic hydrocarbons. PMID:26912311

  10. Mode II fatigue crack propagation.

    NASA Technical Reports Server (NTRS)

    Roberts, R.; Kibler, J. J.

    1971-01-01

    Fatigue crack propagation rates were obtained for 2024-T3 bare aluminum plates subjected to in-plane, mode I, extensional loads and transverse, mode II, bending loads. These results were compared to the results of Iida and Kobayashi for in-plane mode I-mode II extensional loads. The engineering significance of mode I-mode II fatigue crack growth is considered in view of the present results. A fatigue crack growth equation for handling mode I-mode II fatigue crack growth rates from existing mode I data is also discussed.

  11. Single mode thermal emission.

    PubMed

    Fohrmann, Lena Simone; Petrov, Alexander Yu; Lang, Slawa; Jalas, Dirk; Krauss, Thomas F; Eich, Manfred

    2015-10-19

    We report on the properties of a thermal emitter which radiates into a single mode waveguide. We show that the maximal power of thermal radiation into a propagating single mode is limited only by the temperature of the thermal emitter and does not depend on other parameters of the waveguide. Furthermore, we show that the power of the thermal emitter cannot be increased by resonant coupling. For a given temperature, the enhancement of the total emitted power is only possible if the number of excited modes is increased. Either a narrowband or a broadband thermal excitation of the mode is possible, depending on the properties of the emitter. We finally discuss an example system, namely a thermal source for silicon photonics. PMID:26480429

  12. The use of normal forms for analysing nonlinear mechanical vibrations

    PubMed Central

    Neild, Simon A.; Champneys, Alan R.; Wagg, David J.; Hill, Thomas L.; Cammarano, Andrea

    2015-01-01

    A historical introduction is given of the theory of normal forms for simplifying nonlinear dynamical systems close to resonances or bifurcation points. The specific focus is on mechanical vibration problems, described by finite degree-of-freedom second-order-in-time differential equations. A recent variant of the normal form method, that respects the specific structure of such models, is recalled. It is shown how this method can be placed within the context of the general theory of normal forms provided the damping and forcing terms are treated as unfolding parameters. The approach is contrasted to the alternative theory of nonlinear normal modes (NNMs) which is argued to be problematic in the presence of damping. The efficacy of the normal form method is illustrated on a model of the vibration of a taut cable, which is geometrically nonlinear. It is shown how the method is able to accurately predict NNM shapes and their bifurcations. PMID:26303917

  13. The use of normal forms for analysing nonlinear mechanical vibrations.

    PubMed

    Neild, Simon A; Champneys, Alan R; Wagg, David J; Hill, Thomas L; Cammarano, Andrea

    2015-09-28

    A historical introduction is given of the theory of normal forms for simplifying nonlinear dynamical systems close to resonances or bifurcation points. The specific focus is on mechanical vibration problems, described by finite degree-of-freedom second-order-in-time differential equations. A recent variant of the normal form method, that respects the specific structure of such models, is recalled. It is shown how this method can be placed within the context of the general theory of normal forms provided the damping and forcing terms are treated as unfolding parameters. The approach is contrasted to the alternative theory of nonlinear normal modes (NNMs) which is argued to be problematic in the presence of damping. The efficacy of the normal form method is illustrated on a model of the vibration of a taut cable, which is geometrically nonlinear. It is shown how the method is able to accurately predict NNM shapes and their bifurcations. PMID:26303917

  14. Normal forces of magnetorheological fluids under oscillatory shear

    NASA Astrophysics Data System (ADS)

    Guo, Chaoyang; Gong, Xinglong; Xuan, Shouhu; Zong, Luhang; Peng, Chao

    2012-03-01

    The normal forces of magnetorheological fluids under oscillatory shear are investigated by a commercial magneto-rheometer with plate-plate geometry. At the constant strain amplitude and frequency, the normal forces almost keep a steady value with the testing time if the strain amplitude is smaller than the critical value. When a larger strain is applied, they will fluctuate periodically. Under the strain sweep mode, the relationships between normal forces and strain amplitude can be divided into three regions: linear viscoelastic region, nonlinear viscoelastic region and the viscoplastic region. Under the frequency sweep method, it is found that the angular frequency show little influence on the normal forces. At last, the normal forces increase with increasing of the temperature under a low magnetic field, while they decrease under a high magnetic field.

  15. Supersymmetric mode converters

    NASA Astrophysics Data System (ADS)

    Heinrich, Matthias; Miri, Mohammad-Ali; Stützer, Simon; Nolte, Stefan; Szameit, Alexander; Christodoulides, Demetrios N.

    2015-08-01

    In recent years, the ever-increasing demand for high-capacity transmission systems has driven remarkable advances in technologies that encode information on an optical signal. Mode-division multiplexing makes use of individual modes supported by an optical waveguide as mutually orthogonal channels. The key requirement in this approach is the capability to selectively populate and extract specific modes. Optical supersymmetry (SUSY) has recently been proposed as a particularly elegant way to resolve this design challenge in a manner that is inherently scalable, and at the same time maintains compatibility with existing multiplexing strategies. Supersymmetric partners of multimode waveguides are characterized by the fact that they share all of their effective indices with the original waveguide. The crucial exception is the fundamental mode, which is absent from the spectrum of the partner waveguide. Here, we demonstrate experimentally how this global phase-matching property can be exploited for efficient mode conversion. Multimode structures and their superpartners are experimentally realized in coupled networks of femtosecond laser-written waveguides, and the corresponding light dynamics are directly observed by means of fluorescence microscopy. We show that SUSY transformations can readily facilitate the removal of the fundamental mode from multimode optical structures. In turn, hierarchical sequences of such SUSY partners naturally implement the conversion between modes of adjacent order. Our experiments illustrate just one of the many possibilities of how SUSY may serve as a building block for integrated mode-division multiplexing arrangements. Supersymmetric notions may enrich and expand integrated photonics by versatile optical components and desirable, yet previously unattainable, functionalities.

  16. On the use of attachment modes in substructure coupling for dynamic analysis

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.; Chang, C.-J.

    1977-01-01

    Substructure coupling or component-mode synthesis may be employed in the solution of dynamics problems for complex structures. Although numerous substructure-coupling methods have been devised, little attention has been devoted to methods employing attachment modes. In the present paper the various mode sets (normal modes, constraint modes, attachment modes) are defined. A generalized substructure-coupling procedure is described. Those substructure-coupling methods which employ attachment modes are described in detail. One of these methods is shown to lead to results (e.g., system natural frequencies) comparable to or better than those obtained by the Hurty (1965) method.

  17. Analysis of nonlinear structures via mode synthesis

    NASA Technical Reports Server (NTRS)

    Gieseke, R. K.

    1975-01-01

    An effective procedure for NASTRAN was developed that permits any number of substructures of any size to be synthesized for the purpose of developing normal modes of vibration of the complete structural system. The technique is extended to permit modal transient analysis of the subdivided system. This latter procedure permits the use of NASTRAN's ability to include nonlinear forces in the problem. The five-phase process is accomplished using standard NASTRAN rigid formats with problem-independent alter packages and DMAP sequences.

  18. Mode-dependent vibrational autoionization in aniline

    SciTech Connect

    Raptis, C. A.; Pratt, S. T.

    2000-09-08

    High-resolution photoelectron spectroscopy is used to study the branching ratios for vibrational autoionization of Rydberg states of aniline (C{sub 6}H{sub 5}NH{sub 2}) converging to the ground electronic state of the ion. By using two-color double-resonance excitation, it is possible to prepare autoionizing resonances in which two different vibrational modes are excited. Determination of the vibrational state distribution in the product ion provides information on the relative rates of autoionization for the two modes. It is found that some normal modes appear to be especially effective at promoting vibrational autoionization, while others appear to be completely ineffective. (c) 2000 American Institute of Physics.

  19. Quantum dynamics of two-optical modes and a single mechanical mode optomechanical system: Selective energy exchange

    NASA Astrophysics Data System (ADS)

    Aggarwal, Neha; Bhattacherjee, Aranya B.

    2014-01-01

    We study the quantum dynamics of an optomechanical setup comprising two optical modes and one mechanical mode. We show that the same system can undergo a dynamical phase transition analogous to Dicke-Hepp-Lieb superradiant type phase transition. We found that the coupling between the momentum quadratures of the two optical fields gives rise to a new dynamical critical point. We show that selective energy exchange between any two modes is possible by coherent control of the coupling parameters. In addition we also demonstrate the occurrence of normal mode splitting (NMS) in the mechanical displacement spectrum.

  20. Forest canopy interactions with nucleation mode particles

    NASA Astrophysics Data System (ADS)

    Pryor, S. C.; Hornsby, K. E.; Novick, K. A.

    2014-11-01

    Ultrafine particle size distributions through a deciduous forest canopy indicate that nucleation mode particle concentrations decline with depth into the canopy, such that number concentrations at the bottom of the canopy are an average of 16% lower than those at the top. However, growth rates of nucleation mode particles (diameters 6-30 nm) are invariant with height within the canopy, which implies that the semi-volatile gases contributing to their growth are comparatively well-mixed through the canopy. Growth rates of nucleation mode particles during a meteorological drought year (2012) were substantially lower than during a meteorologically normal year with high soil water potential (2013). This may reflect suppression of actual biogenic volatile organic compound (BVOC) emissions by drought and thus a reduction in the production of condensable products during the drought-affected vegetation season. This hypothesis is supported by evidence that growth rates during the normal year exhibit a positive correlation with emissions of BVOC modeled on observed forest composition, leaf area index, temperature and photosynthetically active radiation (PAR), but particle growth rates during the drought-affected vegetation season are not correlated with modeled BVOC emissions. These data thus provide indirect evidence that drought stress in forests may reduce BVOC emissions and limit growth of nucleation mode particles to climate-relevant sizes.

  1. Quantum Mechanical Investigation of Mode-Specific Tunneling upon Fundamental Excitation in Malonaldehyde.

    PubMed

    Wu, Feng

    2016-06-01

    We present a quantum mechanical study of mode-specific tunneling upon fundamental excitation in malonaldehyde with a multidimensional theory that utilizes the saddle-point normal coordinates. We find that a ring-deformation normal mode is as essential as the well-known imaginary-frequency normal mode in the multidimensional investigation. The changes in tunneling splittings upon fundamental excitation are calculated. The results are competitive with those from a recently developed mixed classical-quantum method. Moreover, the results are qualitatively consistent with experiment for about half of all the modes. PMID:27192182

  2. Group normalization for genomic data.

    PubMed

    Ghandi, Mahmoud; Beer, Michael A

    2012-01-01

    Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets. PMID:22912661

  3. Ductile fracture in HY100 steel under mixed mode I/mode II loading

    SciTech Connect

    Bhattacharjee, D. . Dept. of Materials Science and Metallurgy); Knott, J.F. . School of Metallurgy and Materials)

    1994-05-01

    A number of criteria have been proposed which predict the direction of cracking under mixed Mode 1/Mode 2 loading. All have been evaluated for brittle materials, in which a crack subjected to tension and shear propagates normal to the maximum tensile stress (i.e. fracture is of the Mode 1 type). In a ductile material, however, a notch subjected to mixed Mode 1/Mode 2 loading may initiate a crack in the direction of maximum shear. This paper shows that the profile of the notch tip changes with increasing mixed mode load in such a way that one side of the tip blunts while the other sharpens. Various specimens, subjected to the same mixed mode ratio, were unloaded from different points on the load-displacement curves to study the change in notch-tip profile. Studies under the Scanning Electron Microscope (SEM) have shown that cracks initiate at the sharpened end, along a microscopic shear band. Using a dislocation pile-up model for decohesion of the carbide-matrix interface, a micromechanical model has been proposed for crack initiation in the shear band. It is shown that a theoretical prediction of the shear strain required for decohesion gives a result that is, of magnitude, similar to that of the shear strain at crack initiation measured in the experiments.

  4. Measurement of the wave-normal vector of proton whistlers on Ogo 6.

    NASA Technical Reports Server (NTRS)

    Chan, K. W.; Burton, R. K.; Holzer, R. E.; Smith, E. J.

    1972-01-01

    Description of the first experimental determination of the wave-normal vector of proton whistlers in the ionosphere. Between the crossover frequency and the proton gyrofrequency, both right-hand and left-hand modes of propagation can occur for upgoing waves. Theoretically, the amount of energy in the respective modes depends on theta, the angle between the wave normal and the magnetic field. For proton whistlers with only left-hand mode energy between the crossover and proton gyrofrequency, theta ranged from 36 to 51 deg. For proton whistlers with strong right-hand and left-hand mode signals, theta ranged from 24 to 29 deg. The result is in good agreement with Wang's (1971) collisionless mode-coupling model. The angle between the wave normal and the vertical is found to increase with increasing altitude.

  5. Unidirectional dissipative soliton operation in an all-normal-dispersion Yb-doped fiber laser without an isolator.

    PubMed

    Li, Daojing; Shen, Deyuan; Li, Lei; Chen, Hao; Tang, Dingyuan; Zhao, Luming

    2015-09-10

    We demonstrate self-started unidirectional dissipative soliton operation and noise-like pulse operation in an all-normal-dispersion bidirectional Yb-doped fiber laser mode-locked by nonlinear polarization rotation. The laser works unidirectionally once mode-locking is achieved due to the cavity directional nonlinearity asymmetry along with the nonlinear polarization rotation mode-locking mechanism. PMID:26368963

  6. Normalizing Catastrophe: An Educational Response

    ERIC Educational Resources Information Center

    Jickling, Bob

    2013-01-01

    Processes of normalizing assumptions and values have been the subjects of theoretical framing and critique for several decades now. Critique has often been tied to issues of environmental sustainability and social justice. Now, in an era of global warming, there is a rising concern that the results of normalizing of present values could be…

  7. Whispering Bloch modes

    PubMed Central

    Craster, R. V.

    2016-01-01

    We investigate eigenvalue problems for the planar Helmholtz equation in open systems with a high order of rotational symmetry. The resulting solutions have similarities with the whispering gallery modes exploited in photonic micro-resonators and elsewhere, but unlike these do not necessarily require a surrounding material boundary, with confinement instead resulting from the geometry of a series of inclusions arranged in a ring. The corresponding fields exhibit angular quasi-periodicity reminiscent of Bloch waves, and hence we refer to them as whispering Bloch modes (WBMs). We show that if the geometry of the system is slightly perturbed such that the rotational symmetry is broken, modes with asymmetric field patterns can be observed, resulting in field enhancement and other potentially desirable effects. We investigate the WBMs of two specific geometries first using expansion methods and then by applying a two-scale asymptotic scheme. PMID:27493564

  8. The nonlinear tearing mode

    NASA Technical Reports Server (NTRS)

    Van Hoven, G.; Steinolfson, R. S.

    1984-01-01

    A series of nonlinear computations of tearing-mode development have been performed which achieve higher values of the magnetic Reynolds number and larger wavelengths than previously considered. A prime candidate for the realization of dynamic reconnection is the resistive magnetic tearing mode, a spontaneous instability of a stressed magnetic field. Typical simulations are described for a magnetic Lundquist number S of 10 to the 4th and wavelength parameters alpha from 0.05 to 0.5. In all cases, the nonlinear mode initially evolves at the linear growth rate, followed by a period of reduced growth. Another common feature is the formation of secondary flow vortices, near the tearing surface, which are opposite in direction to the initial linear vortices.

  9. Violin plate modes.

    PubMed

    Gough, Colin

    2015-01-01

    As the first step toward developing a generic model for the acoustically radiating vibrational modes of the violin and related instruments, the modes of both freely supported and edge-constrained top and back plates have been investigated as functions of shape, arching height, elastic anisotropy, the f-holes and associated island area, thickness graduations, and the additional boundary constraints of the ribs, soundpost, and bass-bar present in the assembled instrument. Comsol shell structure finite element software has been used as a quasi-experimental tool, with physical and geometric properties varied smoothly, often over several orders of magnitude, allowing the development of the plate modes to be followed continuously from those of an initially square plate to those of doubly-arched, guitar-shaped, orthotropic plates and their dependence on all the above factors. PMID:25618046

  10. Competing stability modes in vortex structure formation

    NASA Astrophysics Data System (ADS)

    Garrett, Stephen; Gostelow, J. Paul; Rona, Aldo; McMullan, W. Andrew

    2015-11-01

    Nose cones and turbine blades have rotating components and represent very practical geometries for which the behavior of vortex structures is not completely understood. These two different physical cases demonstrate a common theme of competition between mode and vortex types. The literature concerning boundary-layer transition over rotating cones presents clear evidence of an alternative instability mode leading to counter-rotating vortex pairs, consistent with a centrifugal instability. This is in contrast to co-rotating vortices present over rotating disks that arise from crossflow effects. It is demonstrated analytically that this mode competes with the crossflow mode and is dominant only over slender cones. Predictions are aligned with experimental measurements over slender cones. Concurrent experimental work on the flow over swept cylinders shows that organized fine-scale streamwise vorticity occurs more frequently on convex surfaces than is appreciated. The conventional view of purely two-dimensional laminar boundary layers following blunt leading edges is not realistic and such boundary layers need to be treated three-dimensionally, particularly when sweep is present. The vortical structures are counter-rotating for normal cylinders and co-rotating under high sweep conditions. Crossflow instabilities may have a major role to play in the transition process but the streamline curvature mode is still present, and seemingly unchanged, when the boundary layer becomes turbulent.

  11. Three distinct reversing modes in the geodynamo

    NASA Astrophysics Data System (ADS)

    Gallet, Y.; Pavlov, V. E.

    2016-03-01

    The data that describe the long-term reversing behavior of the geodynamo show strong and sudden changes in magnetic reversal frequency. This concerns both the onset and the end of superchrons and most probably the occurrence of episodes characterized by extreme geomagnetic reversal frequency (>10-15 rev./Myr). To account for the complexity observed in geomagnetic reversal frequency evolution, we propose a simple scenario in which the geodynamo operates in three distinct reversing modes: i—a "normal" reversing mode generating geomagnetic polarity reversals according to a stationary random process, with on average a reversal rate of ˜3 rev./Myr; ii—a non-reversing "superchron" mode characterizing long time intervals without reversal; iii—a hyper-active reversing mode characterized by an extreme geomagnetic reversal frequency. The transitions between the different reversing modes would be sudden, i.e., on the Myr time scale. Following previous studies, we suggest that in the past, the occurrence of these transitions has been modulated by thermal conditions at the core-mantle boundary governed by mantle dynamics. It might also be possible that they were more frequent during the Precambrian, before the nucleation of the inner core, because of a stronger influence on geodynamo activity of the thermal conditions at the core-mantle boundary.

  12. ROTATIONAL SPLITTING OF PULSATION MODES

    SciTech Connect

    Deupree, Robert G.; Beslin, Wilfried

    2010-10-01

    Mode splittings produced by uniform rotation and a particular form of differential rotation are computed for two-dimensional rotating 10 M{sub sun} zero-age main sequence stellar models. The change in the character of the mode splitting is traced as a function of uniform rotation rate, and it is found that only relatively slow rotation rates are required before the mode splitting becomes asymmetric about the azimuthally symmetric (m = 0) mode. Increased rotation produces a progressively altered pattern of the individual modes with respect to each other. Large mode splittings begin to overlap with the mode splittings produced by different radial and latitudinal modes at relatively low rotation rates. The mode-splitting pattern for the differentially rotating stars we model is different than that for uniformly rotating stars, making the mode splitting a possible discriminant of the internal angular momentum distribution if one assumes that the formidable challenge of mode identification can be overcome.

  13. Managing incontinence: women's normalizing strategies.

    PubMed

    Skoner, M M; Haylor, M J

    1993-01-01

    Women's strategies for managing urinary incontinence were examined in a grounded-theory study. The women's basic social concern was dealing with incontinence in a manner that enabled them to feel normal. Feeling normal meant being able to do what they wanted to do and needed to do to have a normal life-style as they perceived it. This goal was accomplished by normalizing incontinence and its management. Normalization was achieved by directing its course through self-management, accounting for it in terms of personal history and life experiences, and delaying medical counsel. These strategies are described. The findings provide fresh insights about women's response to incontinence and their practice of self-managing its consequences. PMID:8138472

  14. Effects of magnetosonic perturbations on electron temperature gradient driven modes and the stability of skin depth sized electron ballooning modes

    SciTech Connect

    Joiner, N.; Hirose, A.

    2007-11-15

    The effect of the magnetosonic perturbation {delta}B{sub parallel} on the growth of electron temperature gradient driven (ETG) modes and electron temperature gradient driven ballooning modes [Hirose, Plasma Phys. Control. Fusion 49, 145 (2007)] is investigated using local gyrokinetic analysis and numerical solution, with supporting simulations from the initial value code GS2 [Kotschenreuther, et al., Comp. Phys. Commun. 88, 128 (1996)]. The effect of {delta}B{sub parallel} on the ETG mode is found to depend on the competition between two physical processes related to magnetosonic compression. Local analysis of the ballooning mode appears to significantly overestimate growth rates of this instability. The electron temperature gradient driven ballooning mode has been observed in GS2 simulations. However, this work supports the conclusion that this instability will be subdominant to the ETG mode in normal tokamak regimes.

  15. Multi-mode horn

    NASA Technical Reports Server (NTRS)

    Neilson, Jeffrey M. (Inventor)

    2002-01-01

    A horn has an input aperture and an output aperture, and comprises a conductive inner surface formed by rotating a curve about a central axis. The curve comprises a first arc having an input aperture end and a transition end, and a second arc having a transition end and an output aperture end. When rotated about the central axis, the first arc input aperture end forms an input aperture, and the second arc output aperture end forms an output aperture. The curve is then optimized to provide a mode conversion which maximizes the power transfer of input energy to the Gaussian mode at the output aperture.

  16. A physical interpretation of elastic guided-wave reflection from normal ends of a waveguide.

    PubMed

    Bian, Hongxin; Rose, Joseph L

    2004-07-01

    Studied in this paper are two-dimensional guided wave reflections from normal boundaries in an isotropic elastic media. By making use of the transverse resonance concept, the reflections of the waveguide modes from normal interfaces are interrogated. A general condition is obtained under which the guided waves in an isotropic medium will undergo no mode conversion when interaction occurs with a normal traction free or fixed end. Under some circumstances, similarities are obtained between waveguide modes and bulk-wave modes, for example, doubling of the displacement field at a free end and doubling of the stress field at a fixed end. The results obtained are applicable to all two-dimensional, guided-wave modes, along one waveguide direction with lossless boundaries on the surface(s) parallel to the waveguide direction, including all possible guided-wave modes, propagating and nonpropagating, in plates, one half space, interface of two different half spaces, layers on a half space, multilayer structures, and all axisymmetric modes in cylindrical structures. In addition, the function of displacement potentials is analyzed in the course of guided-wave mode conversion at a normal end. PMID:15301003

  17. Axisymmetric toroidal modes of general relativistic magnetized neutron star models

    SciTech Connect

    Asai, Hidetaka; Lee, Umin E-mail: lee@astr.tohoku.ac.jp

    2014-07-20

    We calculate axisymmetric toroidal modes of magnetized neutron stars with a solid crust in the general relativistic Cowling approximation. We assume that the interior of the star is threaded by a poloidal magnetic field, which is continuous at the surface with an outside dipole field. We examine the cases of the field strength B{sub S} ∼ 10{sup 16} G at the surface. Since separation of variables is not possible for the oscillations of magnetized stars, we employ finite series expansions for the perturbations using spherical harmonic functions. We find discrete normal toroidal modes of odd parity, but no toroidal modes of even parity are found. The frequencies of the toroidal modes form distinct mode sequences and the frequency in a given mode sequence gradually decreases as the number of radial nodes of the eigenfunction increases. From the frequency spectra computed for neutron stars of different masses, we find that the frequency is almost exactly proportional to B{sub S} and is well represented by a linear function of R/M for a given B{sub S}, where M and R are the mass and radius of the star. The toroidal mode frequencies for B{sub S} ∼ 10{sup 15} G are in the frequency range of the quasi-periodic oscillations (QPOs) detected in the soft-gamma-ray repeaters, but we find that the toroidal normal modes cannot explain all the detected QPO frequencies.

  18. The Middeck 0-gravity Dynamics Experiment (MODE)

    NASA Technical Reports Server (NTRS)

    Crawley, Edward F.; Deluis, Javier

    1992-01-01

    Viewgraphs on the middeck 0-gravity dynamics experiment (MODE) are presented. Topics covered include: MODE flight hardware elements; MODE science objectives; MODE team; flight operations; and summary.

  19. Thermodynamics of Radiation Modes

    ERIC Educational Resources Information Center

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  20. Two Modes of Sexuality.

    ERIC Educational Resources Information Center

    Firestone, Robert W.

    This paper describes the essential difference between two modes of sexual relating: (1) a personal, outward style of interaction that is the natural extension of affection, tenderness, and companionship between two people; and (2) an impersonal, inward, more masturbatory expression in which sex is used primarily as a narcotic. The origins of…

  1. Theories and Modes

    ERIC Educational Resources Information Center

    Apsche, Jack A.

    2005-01-01

    In his work on the Theory of Modes, Beck (1996) suggested that there were flaws with his cognitive theory. He suggested that though there are shortcomings to his cognitive theory, there were not similar shortcomings to the practice of Cognitive Therapy. The author suggests that if there are shortcomings to cognitive theory the same shortcomings…

  2. Synthesize Modes and Correlate

    2005-10-01

    SMAC is an automated experimental modal parameter extraction package which determines the natural frequencies of vibration, viscous damping ratios and mode shapes from experimental accelerance frequency response functions (FRFs). It is written in the MATLAB interpretive matrix language and has a graphical user interface.

  3. Mode conversion in ITER

    NASA Astrophysics Data System (ADS)

    Jaeger, E. F.; Berry, L. A.; Myra, J. R.

    2006-10-01

    Fast magnetosonic waves in the ion cyclotron range of frequencies (ICRF) can convert to much shorter wavelength modes such as ion Bernstein waves (IBW) and ion cyclotron waves (ICW) [1]. These modes are potentially useful for plasma control through the generation of localized currents and sheared flows. As part of the SciDAC Center for Simulation of Wave-Plasma Interactions project, the AORSA global-wave solver [2] has been ported to the new, dual-core Cray XT-3 (Jaguar) at ORNL where it demonstrates excellent scaling with the number of processors. Preliminary calculations using 4096 processors have allowed the first full-wave simulations of mode conversion in ITER. Mode conversion from the fast wave to the ICW is observed in mixtures of deuterium, tritium and helium3 at 53 MHz. The resulting flow velocity and electric field shear will be calculated. [1] F.W. Perkins, Nucl. Fusion 17, 1197 (1977). [2] E.F. Jaeger, L.A. Berry, J.R. Myra, et al., Phys. Rev. Lett. 90, 195001-1 (2003).

  4. Modes of Communication

    ERIC Educational Resources Information Center

    Dewatripont, Mathias; Tirole, Jean

    2005-01-01

    The paper develops a theory of costly communication in which the sender's and receiver's motivations and abilities endogenously determine the communication mode and the transfer of knowledge. Communication is modeled as a problem of moral hazard in teams, in which the sender and receiver select persuasion and message elaboration efforts. The model…

  5. Forest canopy interactions with nucleation mode particles

    NASA Astrophysics Data System (ADS)

    Pryor, S. C.; Hornsby, K. E.; Novick, K. A.

    2014-07-01

    Forests play a key role in removal of particles from the atmosphere but may also significantly contribute to formation and growth of ultrafine particles. Ultrafine particle size distributions through a deciduous forest canopy indicate substantial capture of nucleation mode particles by the foliage. Concentrations decline with depth into the canopy, such that nucleation mode number concentrations at the bottom of the canopy are an average of 16% lower than those at the top. However, growth rates of nucleation mode particles (diameters 6-30 nm) are invariant with height within the canopy, which implies that the semi-volatile gases contributing to their growth are comparatively well-mixed through the canopy. Growth rates of nucleation mode particles during a meteorological drought year (2012) were substantially lower than during a meteorologically normal year with high soil water potential (2013). This may reflect suppression of actual BVOC emissions by drought and thus reduced production of condensable products (and thus particle growth) during the drought-affected vegetation season. This hypothesis is supported by evidence that growth rates during the normal year exhibit a positive correlation with emissions of biogenic volatile organic compounds (BVOC) modeled based on observed forest composition, leaf area index, temperature and PAR, but particle growth rates during the drought-affected vegetation season are not correlated with modeled BVOC emissions. These data thus provide direct evidence for the importance of canopy capture in atmospheric particle budgets and indirect evidence that drought-stress in forests may reduce BVOC emissions and limit growth of nucleation mode particles to climate-relevant sizes.

  6. Higgs amplitude mode in massless Dirac fermion systems

    NASA Astrophysics Data System (ADS)

    Lu, Ming; Liu, Haiwen; Wang, Pei; Xie, X. C.

    2016-02-01

    The Higgs amplitude mode in superconductors is the condensed-matter analogy of Higgs bosons in particle physics. We investigate the time evolution of Higgs amplitude mode in massless Dirac systems induced by a weak quench of an attractive interaction. We find that the Higgs amplitude mode in the half-filled honeycomb lattice has a logarithmic decaying behavior, qualitatively different from the 1 /√{t } decay in the normal superconductors. Our study is also extended to the doped cases in honeycomb lattices. As for the three-dimensional Dirac semimetal at half filling, we obtain an undamped oscillation of the amplitude mode. Our finding is not only an important supplement to the previous theoretical studies on normal fermion systems but also provides an experimental signature to characterize the superconductivity in two- or three-dimensional Dirac systems.

  7. Nonlinear modes of clarinet-like musical instruments

    NASA Astrophysics Data System (ADS)

    Noreland, Daniel; Bellizzi, Sergio; Vergez, Christophe; Bouc, Robert

    2009-07-01

    The concept of nonlinear modes is applied in order to analyze the behavior of a model of woodwind reed instruments. Using a modal expansion of the impedance of the instrument, and by projecting the equation for the acoustic pressure on the normal modes of the air column, a system of second-order ordinary differential equations is obtained. The equations are coupled through the nonlinear relation describing the volume flow of air through the reed channel in response to the pressure difference across the reed. The system is treated using an amplitude-phase formulation for nonlinear modes, where the frequency and damping functions, as well as the invariant manifolds in the phase space, are unknowns to be determined. The formulation gives, without explicit integration of the underlying ordinary differential equation, access to the transient, the limit cycle, its period and stability. The process is illustrated for a model reduced to three normal modes of the air column.

  8. THz time domain spectroscopy of biomolecular conformational modes.

    PubMed

    Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

    2002-11-01

    We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm(-1) range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules. PMID:12452570

  9. Cladding-mode obtained by core-offset structure and applied in fiber Bragg grating sensor

    NASA Astrophysics Data System (ADS)

    Zhang, Xinpu; Peng, Wei; Liu, Yun; Li, Hong; Jing, Zhenguo; Yu, Qi; Zhou, Xinlei; Yao, Wenjuan; Wang, Yanjie; Liang, Yuzhang

    2011-12-01

    Comparing to core-modes of optical fibers, some cladding-modes are more sensitive to the surroundings which are very valuable to sensing application; recently, a novel type of FBG sensor with core-offset structure attracts more and more interests. Normally, the forward core-mode is not only reflected and coupled to the backward core mode by the Fiber Bragg Grating in the step-type photosensitive single mode fiber, but also coupled to the backward cladding-modes and the radiation modes, eventually they will leak or be absorbed by the high refraction index coating layer. These backward cladding-modes can also be used for sensing analysis. In this paper, we propose and develop a core-offset structure to obtain the backward core-mode and backward cladding-modes by using the wavelength shift of the backward core-mode and the power of the backward cladding-modes in Fiber Bragg Grating sensor, and the power of the backward cladding-modes are independent from temperature variation. We develop a mode coupling sensor model between the forward core-mode and the backward cladding-modes, and demonstrate two coupling methods in the core-offset structure experimentally. The sensor is fabricated and demonstrated for refractive index monitoring. Some specific works are under investigation now, more analysis and fabrication will be done to improve this cladding-mode based sensor design for applicable sensing technology.

  10. Wave normal analysis of chorus at Saturn

    NASA Astrophysics Data System (ADS)

    Hospodarsky, G. B.; Averkamp, T. F.; Kurth, W. S.; Gurnett, D. A.; Dougherty, M. K.

    2006-05-01

    Whistler mode chorus has been detected by the Radio and Plasma Wave Science (RPWS) instrument during most of Cassini's first 21 orbits of Saturn. The emission is detected primarily between L shells of 5 to 8 and the occurrence of the emission shows no correlation with Saturn latitude or local time. High resolution wideband measurements from the Wideband Receiver (WBR) shows fine structure in the chorus similar to fine structure of chorus observed at the Earth, but on a longer time scale. Wave normal and Poynting vector analysis using the simultaneous waveforms of the two-axis electric antenna and the three-axis magnetic search coil obtained by the RPWS Five-Channel Waveform Receiver (WFR) has been performed on the chorus emission. This analysis shows that the chorus propagates away from the Saturnian magnetic equator, similar to chorus propagation at the Earth, suggesting a source region near the magnetic equator. The variation of the wave normal angle with location of the spacecraft will be presented.

  11. Normal evaporation of binary alloys

    NASA Technical Reports Server (NTRS)

    Li, C. H.

    1972-01-01

    In the study of normal evaporation, it is assumed that the evaporating alloy is homogeneous, that the vapor is instantly removed, and that the alloy follows Raoult's law. The differential equation of normal evaporation relating the evaporating time to the final solute concentration is given and solved for several important special cases. Uses of the derived equations are exemplified with a Ni-Al alloy and some binary iron alloys. The accuracy of the predicted results are checked by analyses of actual experimental data on Fe-Ni and Ni-Cr alloys evaporated at 1600 C, and also on the vacuum purification of beryllium. These analyses suggest that the normal evaporation equations presented here give satisfactory results that are accurate to within an order of magnitude of the correct values, even for some highly concentrated solutions. Limited diffusion and the resultant surface solute depletion or enrichment appear important in the extension of this normal evaporation approach.

  12. Normal, nearsightedness, and farsightedness (image)

    MedlinePlus

    ... it. A person with normal vision can see objects clearly near and faraway. Nearsightedness results in blurred ... or contact lenses. A nearsighted person sees near objects clearly, while objects in the distance are blurred. ...

  13. COBE DMR-normalized open inflation cold dark matter cosmogony

    NASA Technical Reports Server (NTRS)

    Gorski, Krzysztof M.; Ratra, Bharat; Sugiyama, Naoshi; Banday, Anthony J.

    1995-01-01

    A cut-sky orthogonal mode analysis of the 2 year COBE DMR 53 and 90 GHz sky maps (in Galactic coordinates) is used to determine the normalization of an open inflation model based on the cold dark matter (CDM) scenario. The normalized model is compared to measures of large-scale structure in the universe. Although the DMR data alone does not provide sufficient discriminative power to prefer a particular value of the mass density parameter, the open model appears to be reasonably consistent with observations when Omega(sub 0) is approximately 0.3-0.4 and merits further study.

  14. Characterization of Ventilatory Modes in Dragonfly Nymph

    NASA Astrophysics Data System (ADS)

    Roh, Chris; Saxton-Fox, Theresa; Gharib, Morteza

    2013-11-01

    A dragonfly nymph's highly modified hindgut has multiple ventilatory modes: hyperventilation (i.e. jet propulsion), gulping ventilation (extended expiratory phase) and normal ventilation. Each mode involves dynamic manipulation of the exit diameter and pressure. To study the different fluid dynamics associated with the three modes, Anisopteran larvae of the family Aeshnidae were tethered onto a rod for flow visualization. The result showed distinct flow structures. The hyperventilation showed a highly turbulent and powerful jet that occurred at high frequency. The gulping ventilation produced a single vortex at a moderate frequency. The normal ventilation showed two distinct vortices, a low-Reynolds number vortex, followed by a high-Reynolds number vortex. Furthermore, a correlation of the formation of the vortices with the movement of the sternum showed that the dragonfly is actively controlling the timing and the speed of the vortices to have them at equal distance from the jet exit at the onset of inspiration. This behavior prevents inspiration of the oxygen deficient expirated water, resulting in the maximization of the oxygen intake. Supported by NSF GRFP.

  15. High Power Tests of Normal Conducting Single-Cell Structures

    SciTech Connect

    Dolgashev, V.A.; Tantawi, S.G.; Nantista, C.D.; Higashi, Y.; Higo, T.; /KEK, Tsukuba

    2007-11-07

    We report the results of the first high power tests of single-cell traveling-wave and standing-wave structures. These tests are part of an experimental and theoretical study of rf breakdown in normal conducting structures at 11.4 GHz. The goal of this study is to determine the gradient potential of normal-conducting rf-powered particle beam accelerators. The test setup consists of reusable mode converters and short test structures and is powered by SLAC's XL-4 klystron. This setup was created for economical testing of different cell geometries, cell materials and preparation techniques with short turn-around time. The mode launchers and structures were manufactured at SLAC and KEK and tested in the SLAC Klystron Test Lab.

  16. Dancing bunches as Van Kampen modes

    SciTech Connect

    Burov, A.; /Fermilab

    2011-03-01

    Van Kampen modes are eigen-modes of Jeans-Vlasov equation [1-3]. Their spectrum consists of continuous and, possibly, discrete parts. Onset of a discrete van Kampen mode means emergence of a coherent mode without any Landau damping; thus, even a tiny couple-bunch wake is sufficient to drive instability. Longitudinal instabilities observed at Tevatron [4], RHIC [5] and SPS [6] can be explained as loss of Landau damping (LLD), which is shown here to happen at fairly low impedances. For repulsive wakes and single-harmonic RF, LLD is found to be extremely sensitive to steepness of the bunch distribution function at small amplitudes. Based on that, a method of beam stabilization is suggested. Emergence of a discrete van Kampen mode means either loss of Landau damping or instability. Longitudinal bunch stability is analysed in weak head-tail approximation for inductive impedance and single-harmonic RF. The LLD threshold intensities are found to be rather low: for cases under study all of them do not exceed a few percent of the zero-amplitude incoherent synchrotron frequency shift, strongly decreasing for shorter bunches. Because of that, LLD can explain longitudinal instabilities happened at fairly low impedances at Tevatron [4], and possibly for RHIC [5] and SPS [6], being in that sense an alternative to the soliton explanation [5, 20]. Although LLD itself results in many cases in emergence of a mode with zero growth rate, any couple-bunch (and sometimes multi-turn) wake would drive instability for that mode, however small this wake is. LLD is similar to a loss of immune system of a living cell, when any microbe becomes fatal for it. The emerging discrete mode is normally very different from the rigid-bunch motion; thus the rigid-mode model significantly overestimates the LLD threshold. The power low of LLD predicted in Ref. [17] agrees with results of this paper. However, the numerical factor in that scaling low strongly depends on the bunch distribution function

  17. Modes of Learning.

    ERIC Educational Resources Information Center

    Partridge, Susan

    This literature review is divided into two parts. The first part is a survey of materials in the William S. Gray Collection at the University of Chicago that deal with modes of learning. The studies reviewed range from the 1930s to the 1960s. The second part of the paper extends the review to studies published during the 1970s. Each section of the…

  18. Single mode cavity laser

    SciTech Connect

    Martin, D.W.; Levy, J.L.

    1984-01-17

    This external cavity laser utilizes an unstable resonator in conjuction with a high reflectivity stripe end mirror which is oriented substantially parallel to the plane of the maximum divergence of the laser diode output beam and whose axis is substantially parallel to the plane of the junction of the laser diode. This configuration operates with high efficiency to select only the fundamental mode of the laser diode with a minimal divergence in the output beam.

  19. Cell proliferation in normal epidermis

    SciTech Connect

    Weinstein, G.D.; McCullough, J.L.; Ross, P.

    1984-06-01

    A detailed examination of cell proliferation kinetics in normal human epidermis is presented. Using tritiated thymidine with autoradiographic techniques, proliferative and differentiated cell kinetics are defined and interrelated. The proliferative compartment of normal epidermis has a cell cycle duration (Tc) of 311 h derived from 3 components: the germinative labeling index (LI), the duration of DNA synthesis (ts), and the growth fraction (GF). The germinative LI is 2.7% +/- 1.2 and ts is 14 h, the latter obtained from a composite fraction of labeled mitoses curve obtained from 11 normal subjects. The GF obtained from the literature and from human skin xenografts to nude mice is estimated to be 60%. Normal-appearing epidermis from patients with psoriasis appears to have a higher proliferation rate. The mean LI is 4.2% +/- 0.9, approximately 50% greater than in normal epidermis. Absolute cell kinetic values for this tissue, however, cannot yet be calculated for lack of other information on ts and GF. A kinetic model for epidermal cell renewal in normal epidermis is described that interrelates the rate of birth/entry, transit, and/or loss of keratinocytes in the 3 epidermal compartments: proliferative, viable differentiated (stratum malpighii), and stratum corneum. Expected kinetic homeostasis in the epidermis is confirmed by the very similar ''turnover'' rates in each of the compartments that are, respectively, 1246, 1417, and 1490 cells/day/mm2 surface area. The mean epidermal turnover time of the entire tissue is 39 days. The Tc of 311 h in normal cells in 8-fold longer than the psoriatic Tc of 36 h and is necessary for understanding the hyperproliferative pathophysiologic process in psoriasis.

  20. Cluster Features of Normal-, Super- and Hyperdeformed nuclei

    SciTech Connect

    Adamian, G.G.; Antonenko, N.V.; Kuklin, S.N.

    2005-11-21

    It is shown that an important mode of nuclear excitations in different processes like as cluster radioactivity, parity splitting in normal deformed bands, decay out phenomenon of the yrast superdeformed states in the heavy nuclei and formation of super- and hyper-deformed states in induced fission and heavy ion reactions is related to the motion in charge (mass) asymmetry coordinate. With the suggested cluster model one can try to unify all phenomena mentioned above.