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.
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
The effective degeneracy of protein normal modes.
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
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.
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.
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 ...
Normal modes and continuous spectra
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.
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.
Normal Modes of Black Hole Accretion Disks
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.
Normal modes of confined cold ionic systems
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.
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.
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.
Electrostatic normal modes in nonneutral plasmas
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.
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.
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
Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach
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
Improving an all-atom force field.
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
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.
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.
Instantaneous normal modes and the protein glass transition.
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
Instantaneous Normal Modes and the Protein Glass Transition
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.
WEBnm@: a web application for normal mode analyses of proteins
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
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.
High-Frequency Normal Mode Propagation in Aluminum Cylinders
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.
Universal spectrum of normal modes in low-temperature glasses.
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
Universal spectrum of normal modes in low-temperature glasses
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
Normal modes of prion proteins: from native to infectious particle.
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
Refinement of protein dynamic structure: normal mode refinement.
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
Normal Modes of Prion Proteins: From Native to Infectious particle◊
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
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
Nonlinear normal modes modal interactions and isolated resonance curves
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
Nonlinear normal modes modal interactions and isolated resonance curves
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.
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.
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
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.
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).
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
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.
S-Wave Normal Mode Propagation in Aluminum Cylinders
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.
Normal-mode splitting with large collective cooperativity
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.
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
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.
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)
The normal modes of lattice vibrations of ice XI
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
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.
The normal modes of lattice vibrations of ice XI.
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
Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding
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.
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.
Antiport Mechanism for Cl−/H+ in ClC-ec1 from Normal-Mode Analysis
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
[Raman, FTIR spectra and normal mode analysis of acetanilide].
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
Generalized theory of helicon waves. I. Normal modes
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.}
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.
Vibrational dynamics of vocal folds using nonlinear normal modes.
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
iMODS: internal coordinates normal mode analysis server
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
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.
"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.
Antidepressants Normalize the Default Mode Network in Patients With Dysthymia
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
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
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.
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
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
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.
Prufer Transformations for the Normal Modes in Ocean Acoustics
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.
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.
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
Electromagnetic fluctuations and normal modes of a drifting relativistic plasma
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.
Echoes from anharmonic normal modes in model glasses.
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
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.
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
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.
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
An effective all-atom potential for proteins
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
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.
Normal forms for linear mode conversion and Landau-Zener transitions in one dimension
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.
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.
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.
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
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.
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.
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.
Isotope effect in normal-to-local transition of acetylene bending modes
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
Isotope effect in normal-to-local transition of acetylene bending modes
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.
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
Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes
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
Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes
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.
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.
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.
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.
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...
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.
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.
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.
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.
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.
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
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.
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.
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.
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
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
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.
High-frequency Born synthetic seismograms based on coupled normal modes
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).
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.
A brief study of quasi-normal modes in relativistic stars using algebraic computation
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.
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.
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.
Skin pigmentation and texture changes after hair removal with the normal-mode ruby laser.
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
Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes.
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
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.
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
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.
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.
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.
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.
Cavity quantum optomechanics of ultracold atoms in an optical lattice: Normal-mode splitting
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.
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.
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
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.
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
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.
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
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
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.
Variability in Diaphragm Motion During Normal Breathing, Assessed With B-Mode Ultrasound
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
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.
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.
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.
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.
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.
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.
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
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
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
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
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
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.
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.
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.
On the sensitivity of protein data bank normal mode analysis: an application to GH10 xylanases.
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
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).
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
Regional variation of inner core anisotropy from seismic normal mode observations.
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
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.
Anharmonicity and necessity of phonon eigenvectors in the phonon normal mode analysis
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.
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.
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.
Notch strengthening or weakening governed by transition of shear failure to normal mode fracture
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
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
Notch strengthening or weakening governed by transition of shear failure to normal mode fracture.
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
Dynamic and elastic properties of F-actin: a normal-modes analysis.
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
Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies.
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
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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
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.
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.
Normal mode analysis of macromolecular systems with the mobile block Hessian method
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.
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.
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
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.
Default mode network connectivity in patients with idiopathic normal pressure hydrocephalus.
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
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
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.
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.
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
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.
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.
Field evolution of the magnetic normal modes in elongated permalloy nanometric rings.
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
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.
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
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
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
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.
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
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.
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…
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.
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
Normal-Mode Splitting in the Coupled System of Hybridized Nuclear Magnons and Microwave Photons.
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
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.
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…
An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.
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
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.
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.
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.
Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.
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
An All-Atom Model of the Structure of Human Copper Transporter 1
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
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
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.
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
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.
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.
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.
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.
An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins
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
All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.
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
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
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
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.
All-Atom Molecular Dynamics of Virus Capsids as Drug Targets
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
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.
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.
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
Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
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
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.
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.
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
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
A Real-Time All-Atom Structural Search Engine for Proteins
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
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
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.
ALMOST: an all atom molecular simulation toolkit for protein structure determination.
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
Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.
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
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.
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.
Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.
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
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
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
All-atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling
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
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol
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
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.
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.
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
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.
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
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
On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.
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
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
Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.
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
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
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
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences
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
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
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
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
Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.
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
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.
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
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.
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.
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
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
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins
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
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