Effects of Thermal Noise on the Transitional Dynamics of an Inextensible Elastic Filament in Stagnation Flow

PubMed Central

Deng, Mingge; Grinberg, Leopold; Caswell, Bruce

2015-01-01

We investigate the dynamics of a single inextensible elastic filament subject to anisotropic friction in a viscous stagnation-point flow, by employing both a continuum model represented by Langevin type stochastic partial differential equations (SPDEs) and a Dissipative Particle Dynamics (DPD) method. Unlike previous works1, the filament is free to rotate and the tension along the filament is determined by the local inextensible constraint. The kinematics of the filament is recorded and studied with normal modes analysis. The results show that the filament displays an instability induced by negative tension, which is analogous to Euler buckling of a beam. Symmetry breaking of normal modes dynamics and stretch-coil transitions are observed above the threshold of the buckling instability point. Furthermore, both temporal and spatial noise are amplified resulting from the interaction of thermal fluctuations and nonlinear filament dynamics. Specifically, the spatial noise is amplified with even normal modes being excited due to symmetry breaking, while the temporal noise is amplified with increasing time correlation length and variance. PMID:26023834

Dynamic Identification for Control of Large Space Structures

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.

1985-01-01

This is a compilation of reports by the one author on one subject. It consists of the following five journal articles: (1) A Parametric Study of the Ibrahim Time Domain Modal Identification Algorithm; (2) Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique; (3) Computation of Normal Modes from Identified Complex Modes; (4) Dynamic Modeling of Structural from Measured Complex Modes; and (5) Time Domain Quasi-Linear Identification of Nonlinear Dynamic Systems.

On the use of attachment modes in substructure coupling for dynamic analysis

NASA Technical Reports Server (NTRS)

Craig, R. R., Jr.; Chang, C.-J.

1977-01-01

Substructure coupling or component-mode synthesis may be employed in the solution of dynamics problems for complex structures. Although numerous substructure-coupling methods have been devised, little attention has been devoted to methods employing attachment modes. In the present paper the various mode sets (normal modes, constraint modes, attachment modes) are defined. A generalized substructure-coupling procedure is described. Those substructure-coupling methods which employ attachment modes are described in detail. One of these methods is shown to lead to results (e.g., system natural frequencies) comparable to or better than those obtained by the Hurty (1965) method.

Implementation of the block-Krylov boundary flexibility method of component synthesis

NASA Technical Reports Server (NTRS)

Carney, Kelly S.; Abdallah, Ayman A.; Hucklebridge, Arthur A.

1993-01-01

A method of dynamic substructuring is presented which utilizes a set of static Ritz vectors as a replacement for normal eigenvectors in component mode synthesis. This set of Ritz vectors is generated in a recurrence relationship, which has the form of a block-Krylov subspace. The initial seed to the recurrence algorithm is based on the boundary flexibility vectors of the component. This algorithm is not load-dependent, is applicable to both fixed and free-interface boundary components, and results in a general component model appropriate for any type of dynamic analysis. This methodology was implemented in the MSC/NASTRAN normal modes solution sequence using DMAP. The accuracy is found to be comparable to that of component synthesis based upon normal modes. The block-Krylov recurrence algorithm is a series of static solutions and so requires significantly less computation than solving the normal eigenspace problem.

Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis

PubMed Central

De Los Rios, Paolo; Cecconi, Fabio; Pretre, Anna; Dietler, Giovanni; Michielin, Olivier; Piazza, Francesco; Juanico, Brice

2005-01-01

Postsynaptic density-95/disks large/zonula occludens-1 (PDZ) domains are relatively small (80–120 residues) protein binding modules central in the organization of receptor clusters and in the association of cellular proteins. Their main function is to bind C-terminals of selected proteins that are recognized through specific amino acids in their carboxyl end. Binding is associated with a deformation of the PDZ native structure and is responsible for dynamical changes in regions not in direct contact with the target. We investigate how this deformation is related to the harmonic dynamics of the PDZ structure and show that one low-frequency collective normal mode, characterized by the concerted movements of different secondary structures, is involved in the binding process. Our results suggest that even minimal structural changes are responsible for communication between distant regions of the protein, in agreement with recent NMR experiments. Thus, PDZ domains are a very clear example of how collective normal modes are able to characterize the relation between function and dynamics of proteins, and to provide indications on the precursors of binding/unbinding events. PMID:15821164

Dynamical Principles of Emotion-Cognition Interaction: Mathematical Images of Mental Disorders

PubMed Central

Rabinovich, Mikhail I.; Muezzinoglu, Mehmet K.; Strigo, Irina; Bystritsky, Alexander

2010-01-01

The key contribution of this work is to introduce a mathematical framework to understand self-organized dynamics in the brain that can explain certain aspects of itinerant behavior. Specifically, we introduce a model based upon the coupling of generalized Lotka-Volterra systems. This coupling is based upon competition for common resources. The system can be regarded as a normal or canonical form for any distributed system that shows self-organized dynamics that entail winnerless competition. Crucially, we will show that some of the fundamental instabilities that arise in these coupled systems are remarkably similar to endogenous activity seen in the brain (using EEG and fMRI). Furthermore, by changing a small subset of the system's parameters we can produce bifurcations and metastable sequential dynamics changing, which bear a remarkable similarity to pathological brain states seen in psychiatry. In what follows, we will consider the coupling of two macroscopic modes of brain activity, which, in a purely descriptive fashion, we will label as cognitive and emotional modes. Our aim is to examine the dynamical structures that emerge when coupling these two modes and relate them tentatively to brain activity in normal and non-normal states. PMID:20877723

Dynamical principles of emotion-cognition interaction: mathematical images of mental disorders.

PubMed

Rabinovich, Mikhail I; Muezzinoglu, Mehmet K; Strigo, Irina; Bystritsky, Alexander

2010-09-21

The key contribution of this work is to introduce a mathematical framework to understand self-organized dynamics in the brain that can explain certain aspects of itinerant behavior. Specifically, we introduce a model based upon the coupling of generalized Lotka-Volterra systems. This coupling is based upon competition for common resources. The system can be regarded as a normal or canonical form for any distributed system that shows self-organized dynamics that entail winnerless competition. Crucially, we will show that some of the fundamental instabilities that arise in these coupled systems are remarkably similar to endogenous activity seen in the brain (using EEG and fMRI). Furthermore, by changing a small subset of the system's parameters we can produce bifurcations and metastable sequential dynamics changing, which bear a remarkable similarity to pathological brain states seen in psychiatry. In what follows, we will consider the coupling of two macroscopic modes of brain activity, which, in a purely descriptive fashion, we will label as cognitive and emotional modes. Our aim is to examine the dynamical structures that emerge when coupling these two modes and relate them tentatively to brain activity in normal and non-normal states.

Lattice dynamical and dielectric properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2006-08-01

We present the results of ab initio calculations of the lattice dynamical and dielectric properties of the L-amino acids L-alanine, L-leucine, and L-isoleucine. Normal-mode frequencies and dielectric permittivity tensors are obtained using density-functional perturbation theory implemented within the plane-wave pseudopotential approximation. IR spectra are calculated and are used to analyze the effects of intermolecular interactions and zwitterionization upon the lattice dynamics. It is found that vibronic modes associated with the carboxy and amino functional groups undergo modification from their free-molecule values due to the presence of hydrogen bonds. The role of macroscopic electric fields set up by zone-center normal modes in the lattice dynamics is investigated by analysis of the Born effective charge. Calculated permittivity tensors are found to be greater than would be obtained by a naive use of the isolated molecular values, indicating the role of intermolecular interactions in increasing molecular polarizability.

Alternation of regular and chaotic dynamics in a simple two-degree-of-freedom system with nonlinear inertial coupling.

PubMed

Sigalov, G; Gendelman, O V; AL-Shudeifat, M A; Manevitch, L I; Vakakis, A F; Bergman, L A

2012-03-01

We show that nonlinear inertial coupling between a linear oscillator and an eccentric rotator can lead to very interesting interchanges between regular and chaotic dynamical behavior. Indeed, we show that this model demonstrates rather unusual behavior from the viewpoint of nonlinear dynamics. Specifically, at a discrete set of values of the total energy, the Hamiltonian system exhibits non-conventional nonlinear normal modes, whose shape is determined by phase locking of rotatory and oscillatory motions of the rotator at integer ratios of characteristic frequencies. Considering the weakly damped system, resonance capture of the dynamics into the vicinity of these modes brings about regular motion of the system. For energy levels far from these discrete values, the motion of the system is chaotic. Thus, the succession of resonance captures and escapes by a discrete set of the normal modes causes a sequence of transitions between regular and chaotic behavior, provided that the damping is sufficiently small. We begin from the Hamiltonian system and present a series of Poincaré sections manifesting the complex structure of the phase space of the considered system with inertial nonlinear coupling. Then an approximate analytical description is presented for the non-conventional nonlinear normal modes. We confirm the analytical results by numerical simulation and demonstrate the alternate transitions between regular and chaotic dynamics mentioned above. The origin of the chaotic behavior is also discussed.

Boltzmann-conserving classical dynamics in quantum time-correlation functions: "Matsubara dynamics".

PubMed

Hele, Timothy J H; Willatt, Michael J; Muolo, Andrea; Althorpe, Stuart C

2015-04-07

We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or "classical Wigner approximation") results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e., a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads N → ∞, such that the lowest normal-mode frequencies take their "Matsubara" values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of ħ(2) at ħ(0) (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting "Matsubara" dynamics is inherently classical (since all terms O(ħ(2)) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.

Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor

NASA Astrophysics Data System (ADS)

Brooks, Bernard; Karplus, Martin

1983-11-01

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.

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.

Spent nuclear fuel system dynamic stability under normal conditions of transportation

DOE PAGES

Jiang, Hao; Wang, Jy-An John

2016-10-14

In a horizontal layout of a spent nuclear fuel (SNF) assembly under normal conditions of transportation (NCT), the fuel assembly’s skeleton formed by guide tubes and spacer grids is the primary load bearing structure for carrying and transferring the vibration loads within an SNF assembly. Therefore, the integrity of guide tubes and spacer grids will dictate the vibration amplitude/intensity of the fuel assembly during transport, and must be considered when designing multipurpose purpose canister (MPC) for safe SNF transport. This paper investigates the SNF assembly deformation dynamics during normal vibration mode, as well as the transient shock mode inside themore » cask during NCT. In conclusion, dynamic analyses were performed in the frequency domain to study frequency characteristic of the fuel assembly system and in the time domain to simulate the transient dynamic response of the fuel assembly.« less

Spent nuclear fuel system dynamic stability under normal conditions of transportation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Hao; Wang, Jy-An John

In a horizontal layout of a spent nuclear fuel (SNF) assembly under normal conditions of transportation (NCT), the fuel assembly’s skeleton formed by guide tubes and spacer grids is the primary load bearing structure for carrying and transferring the vibration loads within an SNF assembly. Therefore, the integrity of guide tubes and spacer grids will dictate the vibration amplitude/intensity of the fuel assembly during transport, and must be considered when designing multipurpose purpose canister (MPC) for safe SNF transport. This paper investigates the SNF assembly deformation dynamics during normal vibration mode, as well as the transient shock mode inside themore » cask during NCT. In conclusion, dynamic analyses were performed in the frequency domain to study frequency characteristic of the fuel assembly system and in the time domain to simulate the transient dynamic response of the fuel assembly.« less

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

PubMed

Tang, Ping-Han; Wu, Ten-Ming; Yen, Tsung-Wen; Lai, S K; Hsu, P J

2011-09-07

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat. © 2011 American Institute of Physics

Role of muscle mass and mode of contraction in circulatory responses to exercise

NASA Technical Reports Server (NTRS)

Lewis, S. F.; Snell, P. G.; Pettinger, W. A.; Blomqvist, C. G.; Taylor, W. F.; Hamra, M.; Graham, R. M.

1985-01-01

The roles of the mode of contraction (dynamic or static) and active muscle mass in determining the cardiovascular response to exercise has been investigated experimentally in six normal men. Exercise consisted of static handgrip and dynamic handgrip exercise, and static and dynamic knee extension for a period of six minutes. Observed increases in mean arterial pressure after exercise were similar for each mode of contraction, but larger for knee extension than handgrip exercise. Cardiac output increased more for dynamic than for static exercise and for each mode more for knee exercise than for handgrip exercise. Systemic resistance was found to be lower for dynamic than for static exercise, and to decrease from resisting levels by about one third during dynamic knee extension. It is shown that the magnitude of cardiovascular response is related to active muscle mass, but is independent of the contraction mode. Equalization of cardiovascular response was achieved by proportionately larger increases in cardiac output during dynamic exercise. The complete experimental results are given in a table.

Active vs. spectator modes in nonadiabatic photodissociation dynamics of the hydroxymethyl radical via the 22A(3s) Rydberg state

NASA Astrophysics Data System (ADS)

Xie, Changjian; Guo, Hua

2018-01-01

The choice of the active degrees of freedom (DOFs) is a pivotal issue in a reduced-dimensional model of quantum dynamics when a full-dimensional one is not feasible. Here, several five-dimensional (5D) models are used to investigate the nonadiabatic photodissociation dynamics of the hydroxymethyl (CH2OH) radical, which possesses nine internal DOFs, in its lowest absorption band. A normal-mode based scheme is used to identify the active and spectator modes, and its predictions are confirmed by 5D quantum dynamical calculations. Our results underscore the important role of the CO stretching mode in the photodissociation dynamics of CH2OH, originating from the photo-induced promotion of an electron from the half-occupied π*CO antibonding orbital to a carbon Rydberg orbital.

Collective dynamics of lysozyme in water: terahertz absorption spectroscopy and comparison with theory.

PubMed

Xu, Jing; Plaxco, Kevin W; Allen, S James

2006-11-30

To directly measure the low-frequency vibrational modes of proteins in biologically relevant water environment rather than previously explored dry or slightly hydrated phase, we have developed a broadband terahertz spectrometer suitable for strongly attenuating protein solutions. Radiation is provided by harmonic multipliers (up to 0.21 THz), a Gunn oscillator (at 0.139 THz), and the UCSB free-electron lasers (up to 4.8 THz). Our spectrometer combines these intense sources with a sensitive cryogenic detector and a variable path length sample cell to detect radiation after it is attenuated by more than 7 orders of magnitudes by the aqueous sample. Using this spectrometer, we have measured the molar extinction of solvated lysozyme between 0.075 and 3.72 THz (2.5-124 cm(-1)), and we made direct comparison to several published theoretical models based on molecular dynamics simulations and normal-mode analysis. We confirm the existence of dense, overlapping normal modes in the terahertz frequency range. Our observed spectrum, while in rough qualitative agreement with these models, differs in detail. Further, we observe a low-frequency cutoff in terahertz dynamics between 0.2 and 0.3 THz, and we see no evidence of a predicted normal mode at approximately 0.09 THz for the protein.

Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study

DOE PAGES

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; ...

2015-07-29

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

Multibody dynamics: Modeling component flexibility with fixed, free, loaded, constraint, and residual modes

NASA Technical Reports Server (NTRS)

Spanos, John T.; Tsuha, Walter S.

1989-01-01

The assumed-modes method in multibody dynamics allows the elastic deformation of each component in the system to be approximated by a sum of products of spatial and temporal functions commonly known as modes and modal coordinates respectively. The choice of component modes used to model articulating and non-articulating flexible multibody systems is examined. Attention is directed toward three classical Component Mode Synthesis (CMS) methods whereby component normal modes are generated by treating the component interface (I/F) as either fixed, free, or loaded with mass and stiffness contributions from the remaining components. The fixed and free I/F normal modes are augmented by static shape functions termed constraint and residual modes respectively. A mode selection procedure is outlined whereby component modes are selected from the Craig-Bampton (fixed I/F plus constraint), MacNeal-Rubin (free I/F plus residual), or Benfield-Hruda (loaded I/F) mode sets in accordance with a modal ordering scheme derived from balance realization theory. The success of the approach is judged by comparing the actuator-to-sensor frequency response of the reduced order system with that of the full order system over the frequency range of interest. A finite element model of the Galileo spacecraft serves as an example in demonstrating the effectiveness of the proposed mode selection method.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Large-amplitude nonlinear normal modes of the discrete sine lattices.

PubMed

Smirnov, Valeri V; Manevitch, Leonid I

2017-02-01

We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of π). Although this model has numerous applications in different fields of physics, it was studied earlier in the infinite limit only. The discrete chain with a finite length can be considered as a well analytical analog of the coarse-grain models of flexible polymers in the molecular dynamics simulations. The developed approach allows to find the dispersion relations for arbitrary amplitudes of the nonlinear normal modes. We emphasize that the long-wavelength approximation, which is described by well-known sine-Gordon equation, leads to an inadequate zone structure for the amplitudes of about π/2 even if the chain is long enough. An extremely complex zone structure at the large amplitudes corresponds to multiple resonances between nonlinear normal modes even with strongly different wave numbers. Due to the complexity of the dispersion relations the modes with shorter wavelengths may have smaller frequencies. The stability of the nonlinear normal modes under condition of the resonant interaction are discussed. It is shown that this interaction of the modes in the vicinity of the long wavelength edge of the spectrum leads to the localization of the oscillations. The thresholds of instability and localization are determined explicitly. The numerical simulation of the dynamics of a finite-length chain is in a good agreement with obtained analytical predictions.

Dynamics of Aqueous Foam Drops

NASA Technical Reports Server (NTRS)

Akhatov, Iskander; McDaniel, J. Gregory; Holt, R. Glynn

2001-01-01

We develop a model for the nonlinear oscillations of spherical drops composed of aqueous foam. Beginning with a simple mixture law, and utilizing a mass-conserving bubble-in-cell scheme, we obtain a Rayleigh-Plesset-like equation for the dynamics of bubbles in a foam mixture. The dispersion relation for sound waves in a bubbly liquid is then coupled with a normal modes expansion to derive expressions for the frequencies of eigenmodal oscillations. These eigenmodal (breathing plus higher-order shape modes) frequencies are elicited as a function of the void fraction of the foam. A Mathieu-like equation is obtained for the dynamics of the higher-order shape modes and their parametric coupling to the breathing mode. The proposed model is used to explain recently obtained experimental data.

Automatic control of the Skylab Astronaut Maneuvering Research Vehicle.

NASA Technical Reports Server (NTRS)

Murtagh, T. B.; Goodwin, M. A.; Greenlee, J. E.; Whitsett , C. E.

1973-01-01

The two automatic control modes of the Astronaut Maneuvering Research Vehicle (AMRV) are analyzed: the control moment gyro (CMG) and the rate gyro (RG). The AMRV is an autonomous maneuvering unit which translates and rotates the pilot by means of hand-controller input commands. The CMG normal operation, desaturation, and cage/lock dynamics are described in terms of a realistic AMRV mass property configuration. No propellant is used for normal operation in the CMG mode, and the maximum rotation rate is 5 deg/sec about each AMRV axis. The RG attitude maneuvering and limit cycle submode dynamic are described in terms of the same AMRV mass property configuration.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Liangjun; Zheng, Yujun, E-mail: yzheng@sdu.edu.cn

In the present study, the dynamical behaviors of tripartite entanglement of vibrations in triatomic molecules are studied based on the Lie algebraic models of molecules. The dynamical behaviors of tripartite entanglement of the local mode molecule H{sub 2}O and normal mode molecule NO{sub 2} are comparatively studied for different initial states by employing the general concurrence. Our results show that the dynamics of tripartite entanglement are relied on the dynamics of intramolecular energy distribution. The local mode molecule is more suitable to construct the tripartite entangled states. Also, the greater degree of tripartite entanglement can be obtained if the stretchingmore » vibration is first excited. These results shed new light on the understanding of quantum multipartite entanglement of vibrations in the polyatomic molecules.« less

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

DOE PAGES

Ma, Jianyi; Xu, Dingguo; Guo, Hua; ...

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

ΔΔPT: a comprehensive toolbox for the analysis of protein motion

PubMed Central

2013-01-01

Background Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies. Results ΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. Conclusions This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software. PMID:23758746

Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule.

PubMed

Matsumoto, Atsushi; Tobias, Irwin; Olson, Wilma K

2005-01-01

Fine structural and energetic details embedded in the DNA base sequence, such as intrinsic curvature, are important to the packaging and processing of the genetic material. Here we investigate the internal dynamics of a 200 bp closed circular molecule with natural curvature using a newly developed normal-mode treatment of DNA in terms of neighboring base-pair "step" parameters. The intrinsic curvature of the DNA is described by a 10 bp repeating pattern of bending distortions at successive base-pair steps. We vary the degree of intrinsic curvature and the superhelical stress on the molecule and consider the normal-mode fluctuations of both the circle and the stable figure-8 configuration under conditions where the energies of the two states are similar. To extract the properties due solely to curvature, we ignore other important features of the double helix, such as the extensibility of the chain, the anisotropy of local bending, and the coupling of step parameters. We compare the computed normal modes of the curved DNA model with the corresponding dynamical features of a covalently closed duplex of the same chain length constructed from naturally straight DNA and with the theoretically predicted dynamical properties of a naturally circular, inextensible elastic rod, i.e., an O-ring. The cyclic molecules with intrinsic curvature are found to be more deformable under superhelical stress than rings formed from naturally straight DNA. As superhelical stress is accumulated in the DNA, the frequency, i.e., energy, of the dominant bending mode decreases in value, and if the imposed stress is sufficiently large, a global configurational rearrangement of the circle to the figure-8 form takes place. We combine energy minimization with normal-mode calculations of the two states to decipher the configurational pathway between the two states. We also describe and make use of a general analytical treatment of the thermal fluctuations of an elastic rod to characterize the motions of the minicircle as a whole from knowledge of the full set of normal modes. The remarkable agreement between computed and theoretically predicted values of the average deviation and dispersion of the writhe of the circular configuration adds to the reliability in the computational approach. Application of the new formalism to the computed modes of the figure-8 provides insights into macromolecular motions which are beyond the scope of current theoretical treatments.

Normal mode-guided transition pathway generation in proteins

PubMed Central

Lee, Byung Ho; Seo, Sangjae; Kim, Min Hyeok; Kim, Youngjin; Jo, Soojin; Choi, Moon-ki; Lee, Hoomin; Choi, Jae Boong

2017-01-01

The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this. PMID:29020017

Characterization of Ventilatory Modes in Dragonfly Nymph

NASA Astrophysics Data System (ADS)

Roh, Chris; Saxton-Fox, Theresa; Gharib, Morteza

2013-11-01

A dragonfly nymph's highly modified hindgut has multiple ventilatory modes: hyperventilation (i.e. jet propulsion), gulping ventilation (extended expiratory phase) and normal ventilation. Each mode involves dynamic manipulation of the exit diameter and pressure. To study the different fluid dynamics associated with the three modes, Anisopteran larvae of the family Aeshnidae were tethered onto a rod for flow visualization. The result showed distinct flow structures. The hyperventilation showed a highly turbulent and powerful jet that occurred at high frequency. The gulping ventilation produced a single vortex at a moderate frequency. The normal ventilation showed two distinct vortices, a low-Reynolds number vortex, followed by a high-Reynolds number vortex. Furthermore, a correlation of the formation of the vortices with the movement of the sternum showed that the dragonfly is actively controlling the timing and the speed of the vortices to have them at equal distance from the jet exit at the onset of inspiration. This behavior prevents inspiration of the oxygen deficient expirated water, resulting in the maximization of the oxygen intake. Supported by NSF GRFP.

Upper-Level Waves of Synoptic Scale at Midlatitudes

NASA Astrophysics Data System (ADS)

Rivest, Chantal

1990-01-01

Upper-level waves of synoptic scale are important dynamical entities at midlatitudes. They often induce surface cyclogenesis (cf. Peterssen and Smebye, 1971), and their life duration is typically longer than time scales for disruption by the ambient shear (Sanders, 1988). The objectives of the present thesis are to explain the maintenance and genesis of upper-level synoptic-scale waves in the midlatitude flow. We develop an analytical model of waves on generalized Eady basic states that have uniform tropospheric and stratospheric potential vorticity, but allow for the decay of density with height. The Eady basic state represents the limiting case of infinite stratospheric stability and constant density. We find that the Eady normal mode characteristics hold in the presence of realistic tropopause and stratosphere. In particular, the basic states studied support at the synoptic scale upper-level normal modes. These modes provide simple models for the dynamics of upper-level synoptic-scale waves, as waves supported by the large latitudinal gradients of potential vorticity at the tropopause. In the presence of infinitesimal positive tropospheric gradients of potential vorticity, the upper-level normal mode solutions no longer exist, as was demonstrated in Green (1960). Disappearance of the normal mode solution when a parameter changes slightly represents a dilemma that we seek to understand. We examine what happens to the upper-level normal modes in the presence of tropospheric gradients of potential vorticity in a series of initial -value experiments. Our results show that the normal modes become slowly decaying quasi-modes. Mathematically the quasi-modes consist of a superposition of singular modes sharply peaked in the phase speed domain, and their decay proceeds as the modes interfere with one another. We repeat these experiments in basic states with a smooth tropopause in the presence of tropospheric and stratospheric gradients, and similar results are obtained. Basic states with positive tropospheric and stratospheric gradients of potential vorticity are found to support upper-level synoptic-scale waves for time scales consistent with observations. Following Farrell (1989), we then identify a class of near optimal initial conditions for the excitation of upper-level waves. The initial conditions consist of upper -tropospheric disturbances that lean against the shear. They strongly excite upper-level waves not only in the absence of tropospheric potential vorticity gradients, but also in their presence. This result demonstrates that quasi -modes are as likely to emerge from favorably configured initial conditions as real normal modes, although their excitation is followed by a slow decay. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.).

Normal Mode Analysis on the Relaxation of AN Excited Nitromethane Molecule in Argon Bath

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Wagner, Albert F.

2017-06-01

In our previous work [Rivera-Rivera et al. J. Chem. Phys. 142, 014303 (2015).] classical molecular dynamics simulations followed, in an Ar bath, the relaxation of nitromethane (CH_3NO_2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm. Both rotational and vibrational energies exhibited multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997).], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH_3NO_2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. In addition to mode-specificity, the results show disruption of IVR with increasing pressure.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry I.; Kasimov, Aslan R.

2018-03-01

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

Characteristic Exponent of Normal and Oblique Rolls in Homeotropically Aligned Nematic Liquid Crystal

NASA Astrophysics Data System (ADS)

Saraswati, V.; Nugroho, F.

2018-04-01

Soft-mode turbulence (SMT) is one of an experimental example of spatiotemporal chaos, observed in electroconvection system of homeotropically aligned nematic liquid crystal (NLC), due to a non-linear interaction between Nambu-Goldstone mode denoted by the C(r)- director and the convective mode q(r). There are two types of stripe patterns in the SMT, namely normal rolls (NR) and oblique rolls (OR) which separated by a point of applied frequency, called the Lifshitz frequency (f L ). We report a study of the phase transition from normal to oblique rolls by observing the patterns with an applied frequency below and beyond of fL . The temporal fluctuations of the pattern images had been analyzed using autocorrelation function. It fits with Kohlrausch Williams Watts (KWW) function, showing there is a dynamical glass-forming liquid in the transition of NR-OR regime. Also, we found a new type of defect in the NR regime which never been reported before, a dynamic defect which takes the shape of a ring first to a spot in the end.

Multivariate frequency domain analysis of protein dynamics

NASA Astrophysics Data System (ADS)

Matsunaga, Yasuhiro; Fuchigami, Sotaro; Kidera, Akinori

2009-03-01

Multivariate frequency domain analysis (MFDA) is proposed to characterize collective vibrational dynamics of protein obtained by a molecular dynamics (MD) simulation. MFDA performs principal component analysis (PCA) for a bandpass filtered multivariate time series using the multitaper method of spectral estimation. By applying MFDA to MD trajectories of bovine pancreatic trypsin inhibitor, we determined the collective vibrational modes in the frequency domain, which were identified by their vibrational frequencies and eigenvectors. At near zero temperature, the vibrational modes determined by MFDA agreed well with those calculated by normal mode analysis. At 300 K, the vibrational modes exhibited characteristic features that were considerably different from the principal modes of the static distribution given by the standard PCA. The influences of aqueous environments were discussed based on two different sets of vibrational modes, one derived from a MD simulation in water and the other from a simulation in vacuum. Using the varimax rotation, an algorithm of the multivariate statistical analysis, the representative orthogonal set of eigenmodes was determined at each vibrational frequency.

Transition from normal to ballistic diffusion in a one-dimensional impact system

NASA Astrophysics Data System (ADS)

Livorati, André L. P.; Kroetz, Tiago; Dettmann, Carl P.; Caldas, Iberê L.; Leonel, Edson D.

2018-03-01

We characterize a transition from normal to ballistic diffusion in a bouncing ball dynamics. The system is composed of a particle, or an ensemble of noninteracting particles, experiencing elastic collisions with a heavy and periodically moving wall under the influence of a constant gravitational field. The dynamics lead to a mixed phase space where chaotic orbits have a free path to move along the velocity axis, presenting a normal diffusion behavior. Depending on the control parameter, one can observe the presence of featured resonances, known as accelerator modes, that lead to a ballistic growth of velocity. Through statistical and numerical analysis of the velocity of the particle, we are able to characterize a transition between the two regimes, where transport properties were used to characterize the scenario of the ballistic regime. Also, in an analysis of the probability of an orbit to reach an accelerator mode as a function of the velocity, we observe a competition between the normal and ballistic transport in the midrange velocity.

Transition from normal to ballistic diffusion in a one-dimensional impact system.

PubMed

Livorati, André L P; Kroetz, Tiago; Dettmann, Carl P; Caldas, Iberê L; Leonel, Edson D

2018-03-01

We characterize a transition from normal to ballistic diffusion in a bouncing ball dynamics. The system is composed of a particle, or an ensemble of noninteracting particles, experiencing elastic collisions with a heavy and periodically moving wall under the influence of a constant gravitational field. The dynamics lead to a mixed phase space where chaotic orbits have a free path to move along the velocity axis, presenting a normal diffusion behavior. Depending on the control parameter, one can observe the presence of featured resonances, known as accelerator modes, that lead to a ballistic growth of velocity. Through statistical and numerical analysis of the velocity of the particle, we are able to characterize a transition between the two regimes, where transport properties were used to characterize the scenario of the ballistic regime. Also, in an analysis of the probability of an orbit to reach an accelerator mode as a function of the velocity, we observe a competition between the normal and ballistic transport in the midrange velocity.

Dynamics of active sites in biological macromolecules using a Green-function approach: An application to heme vibrational dynamics in myoglobin

NASA Astrophysics Data System (ADS)

Rai, Brajesh; Prohofsky, Earl

2003-03-01

Dynamics of functionally active regions of biological macromolecules can be studied using a Green-function technique. This approach uses the fact that in most cases one has a good set of force constants for active sites, and rather poorly defined force field parameters for other regions of the macromolecule. The Green-function method is applied to study the iron vibrational modes of the heme active site in myoglobin. In this approach, the heme active site is viewed as a system interacting with surrounding globin, which acts as an excitation bath. The normal modes of heme and globin are separately calculated using the best available force fields for the two entities. The iron vibrational spectrum of myoglobin is then obtained using the solutions of the heme and globin, and by considering physically meaningful interactions between the two units. The refinement of the Green-function calculations to the experimental data from an x-ray synchrotron-based Nuclear Resonance Vibrational Spectroscopy provides important insights into the character of iron normal modes of myoglobin.

Upper-Tropospheric Synoptic-Scale Waves. Part II: Maintenance and Excitation of Quasi Modes.

NASA Astrophysics Data System (ADS)

Rivest, Chantal; Farrell, Brian F.

1992-11-01

In a preceding paper a simple dynamical model for the maintenance of upper-tropospheric waves was proposed: the upper-level Eady normal modes. In this paper it is shown that these modes have counterparts in basic states with positive tropospheric gradients of potential vorticity, and that these counterparts can be maintained and excited on time scales consistent with observations.In the presence of infinitesimal positive tropospheric gradients of potential vorticity, the upper-level normal-mode solutions no longer exist. That the normal-mode solution disappears when gradients are infinitesimal represents an apparent singularity and challenges the interpretation of upper-level synoptic-scale waves as related to the upper-level Eady normal modes. What happens to the upper-level modal solution in the presence of tropospheric gradients of potential vorticity is examined in a series of initial-value experiments. Our results show that they become slowly decaying quasi modes. Mathematically the quasi modes consist of a superposition of singular modes sharply peaked in the phase speed domain, and their decay proceeds as the modes interfere with one another. We repeat these experiments in basic states with a smooth tropopause in the presence of tropospheric and stratospheric gradients, and similar results are obtained.Following a previous study by Farrell, a class of near-optimal initial conditions for the excitation of upper-level waves is identified. The initial conditions consist of upper-tropospheric disturbances that lean against the shear. They strongly excite upper-level waves not only in the absence of tropospheric potential vorticity gradients, but also in their presence. This result is important mathematically since it suggests that quasi modes are as likely to emerge from favorably configured initial disturbances as true normal modes, although the excitation is followed by a slow decay.

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Oscillatory Dynamics of One-Dimensional Homogeneous Granular Chains

NASA Astrophysics Data System (ADS)

Starosvetsky, Yuli; Jayaprakash, K. R.; Hasan, Md. Arif; Vakakis, Alexander F.

The acoustics of the homogeneous granular chains has been studied extensively both numerically and experimentally in the references cited in the previous chapters. This chapter focuses on the oscillatory behavior of finite dimensional homogeneous granular chains. It is well known that normal vibration modes are the building blocks of the vibrations of linear systems due to the applicability of the principle of superposition. One the other hand, nonlinear theory is deprived of such a general superposition principle (although special cases of nonlinear superpositions do exist), but nonlinear normal modes ‒ NNMs still play an important role in the forced and resonance dynamics of these systems. In their basic definition [1], NNMs were defined as time-periodic nonlinear oscillations of discrete or continuous dynamical systems where all coordinates (degrees-of-freedom) oscillate in-unison with the same frequency; further extensions of this definition have been considered to account for NNMs of systems with internal resonances [2]...

2 Gbit/s 0.5 μm complementary metal-oxide semiconductor optical transceiver with event-driven dynamic power-on capability

NASA Astrophysics Data System (ADS)

Wang, Xingle; Kiamilev, Fouad; Gui, Ping; Wang, Xiaoqing; Ekman, Jeremy; Zuo, Yongrong; Blankenberg, Jason; Haney, Michael

2006-06-01

A 2 Gb/s0.5 μm complementary metal-oxide semiconductor optical transceiver designed for board- or backplane level power-efficient interconnections is presented. The transceiver supports optical wake-on-link (OWL), an event-driven dynamic power-on technique. Depending on external events, the transceiver resides in either the active mode or the sleep mode and switches accordingly. The active-to-sleep transition shuts off the normal, gigabit link and turns on dedicated circuits to establish a low-power (~1.8 mW), low data rate (less than 100 Mbits/s) link. In contrast the normal, gigabit link consumes over 100 mW. Similarly the sleep-to-active transition shuts off the low-power link and turns on the normal, gigabit link. The low-power link, sharing the same optical channel with the normal, gigabit link, is used to achieve transmitter/receiver pair power-on synchronization and greatly reduces the power consumption of the transceiver. A free-space optical platform was built to evaluate the transceiver performance. The experiment successfully demonstrated the event-driven dynamic power-on operation. To our knowledge, this is the first time a dynamic power-on scheme has been implemented for optical interconnects. The areas of the circuits that implement the low-power link are approximately one-tenth of the areas of the gigabit link circuits.

Evaluation of Geometrically Nonlinear Reduced Order Models with Nonlinear Normal Modes

DOE PAGES

Kuether, Robert J.; Deaner, Brandon J.; Hollkamp, Joseph J.; ...

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

Design, development and manufacture of a breadboard radio frequency mass gauging system

NASA Technical Reports Server (NTRS)

1975-01-01

The feasibility of the RF gauging mode, counting technique was demonstrated for gauging liquid hydrogen and liquid oxygen under all attitude conditions. With LH2, it was also demonstrated under dynamic fluid conditions, in which the fluid assumes ever changing positions within the tank, that the RF gauging technique on the average provides a very good indication of mass. It is significant that the distribution of the mode count data at each fill level during dynamic LH2 and LOX orientation testing does approach a statistical normal distribution. Multiple space-diversity probes provide better coupling to the resonant modes than utilization of a single probe element. The variable sweep rate generator technique provides a more uniform mode versus time distribution for processing.

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

PubMed

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

2013-05-28

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.

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.

Application of attachment modes in the control of large space structures

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.

1989-01-01

Various ways are examined to obtain reduced order mathematical models of structures for use in dynamic response analyses and in controller design studies. Attachment modes are deflection shapes of a structure subjected to specified unit load distributions. Attachment modes are frequently employed to supplement free-interface normal modes to improve the modeling of components (structures) employed in component mode synthesis analyses. Deflection shapes of structures subjected to generalized loads of some specified distribution and of unit magnitude can also be considered to be attachment modes. Several papers which were written under this contract are summarized herein.

Modeling and simulation performance of photovoltaic system integration battery and supercapacitor paralellization of MPPT prototipe for solar vehicle

NASA Astrophysics Data System (ADS)

Ajiatmo, Dwi; Robandi, Imam

2017-03-01

This paper proposes a control scheme photovoltaic, battery and super capacitor connected in parallel for use in a solar vehicle. Based on the features of battery charging, the control scheme consists of three modes, namely, mode dynamic irradian, constant load mode and constant voltage charging mode. The shift of the three modes can be realized by controlling the duty cycle of the mosffet Boost converter system. Meanwhile, the high voltage which is more suitable for the application can be obtained. Compared with normal charging method with parallel connected current limiting detention and charging method with dynamic irradian mode, constant load mode and constant voltage charging mode, the control scheme is proposed to shorten the charging time and increase the use of power generated from the PV array. From the simulation results and analysis conducted to determine the performance of the system in state transient and steady-state by using simulation software Matlab / Simulink. Response simulation results demonstrate the suitability of the proposed concept.

Metastable states and energy flow pathway in square graphene resonators

NASA Astrophysics Data System (ADS)

Wang, Yisen; Zhu, Zhigang; Zhang, Yong; Huang, Liang

2018-01-01

Nonlinear interaction between flexural modes is critical to heat conductivity and mechanical vibration of two-dimensional materials such as graphene. Much effort has been devoted to understand the underlying mechanism. In this paper, we examine solely the out-of-plane flexural modes and identify their energy flow pathway during thermalization process. The key is the development of a universal scheme that numerically characterizes the strength of nonlinear interactions between normal modes. In particular, for our square graphene system, the modes are grouped into four classes by their distinct symmetries. The couplings are significantly larger within a class than between classes. As a result, the equations for the normal modes in the same class as the initially excited one can be approximated by driven harmonic oscillators, therefore, they get energy almost instantaneously. Because of the hierarchical organization of the mode coupling, the energy distribution among the modes will arrive at a stable profile, where most of the energy is localized on a few modes, leading to the formation of "natural package" and metastable states. The dynamics for modes in other symmetry classes follows a Mathieu type of equation, thus, interclass energy flow, when the initial excitation energy is small, starts typically when there is a mode that lies in the unstable region in the parameter space of Mathieu equation. Due to strong coupling of the modes inside the class, the whole class will get energy and be lifted up by the unstable mode. This characterizes the energy flow pathway of the system. These results bring fundamental understandings to the Fermi-Pasta-Ulam problem in two-dimensional systems with complex potentials, and reveal clearly the physical picture of dynamical interactions between the flexural modes, which will be crucial to the understanding of their abnormal contribution to heat conduction and nonlinear mechanical vibrations.

Analytical and experimental investigation of a 1/8-scale dynamic model of the shuttle orbiter. Volume 3B: Supporting data

NASA Technical Reports Server (NTRS)

Mason, P. W.; Harris, H. G.; Zalesak, J.; Bernstein, M.

1974-01-01

The NASA Structural Analysis System (NASTRAN) Model 1 finite element idealization, input data, and detailed analytical results are presented. The data presented include: substructuring analysis for normal modes, plots of member data, plots of symmetric free-free modes, plots of antisymmetric free-free modes, analysis of the wing, analysis of the cargo doors, analysis of the payload, and analysis of the orbiter.

Mid-IR Microresonator-Based Optical Frequency Combs

DTIC Science & Technology

2015-09-01

theoretical treatment of Kerr comb amplitude and phase fluctuation dynamics. Determine which set of requirements must be met in order to obtain mode...Use this detection apparatus to measure the mid-IR Kerr comb coherence and study phase locking of the comb harmonics. Characterize the amplitude and...to all microresonator modes, j is the central frequency of the j th mode, h is Planck’s constant, F is the normalized pump laser amplitude , and

Optimal geometry for a quartz multipurpose SPM sensor.

PubMed

Stirling, Julian

2013-01-01

We propose a geometry for a piezoelectric SPM sensor that can be used for combined AFM/LFM/STM. The sensor utilises symmetry to provide a lateral mode without the need to excite torsional modes. The symmetry allows normal and lateral motion to be completely isolated, even when introducing large tips to tune the dynamic properties to optimal values.

Quantum control of the normal modes of benzene with ultrafast laser pulses

NASA Astrophysics Data System (ADS)

Sauer, Petra; Dou, Yusheng; Torralva, Ben; Allen, Roland

2005-03-01

Remarkable innovations in laser technology have made it possible to create laser pulses with ultrashort durations (below 100 femtoseconds) and ultrahigh intensities (above 1 terawatt per cm^2). To understand the behavior of complex molecules and materials in this new regime of physics, chemistry, biology, and materials science requires innovative techniques which complement experiment and standard theory, and which can treat situations in which conventional approximations like the Born- Oppenheimer approximation, the Franck-Condon principle, and Fermi's golden rule are no longer valid. In this talk we describe a method that we are developing, semiclassical electron-radiation-ion dyanmics (SERID), which can be used to perform simulations of the coupled dynamics of electrons and nuclei in an intense radiation field. We have employed this technique in studying the normal modes of benzene, and the possibility of controlling these modes by optimizing the laser pulses that are applied to the molecule. Animations will be shown of particular normal modes, including the breathing and beating modes, illustrating their symmetries and other properties, and of the photodissociation of benzene when the laser pulse exceeds a threshold intensity.

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations - Part 2: Quasi-geostrophic Rossby modes

NASA Astrophysics Data System (ADS)

Konor, Celal S.; Randall, David A.

2018-05-01

We use a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the quasi-geostrophic anelastic baroclinic and barotropic Rossby modes on a midlatitude β plane. The dispersion equations are derived for the linearized anelastic system, discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of various horizontal grid spacings and vertical wavenumbers are discussed. A companion paper, Part 1, discusses the impacts of the discretization on the inertia-gravity modes on a midlatitude f plane.The results of our normal-mode analyses for the Rossby waves overall support the conclusions of the previous studies obtained with the shallow-water equations. We identify an area of disagreement with the E-grid solution.

Microphysics of liquid complex plasmas in equilibrium and non-equilibrium systems

NASA Astrophysics Data System (ADS)

Piel, Alexander; Block, Dietmar; Melzer, André; Mulsow, Matthias; Schablinski, Jan; Schella, André; Wieben, Frank; Wilms, Jochen

2018-05-01

The dynamic evolution of the microscopic structure of solid and liquid phases of complex plasmas is studied experimentally and by means of molecular dynamics (MD) simulations. In small finite systems, the cooperative motion can be described in terms of discrete modes. These modes are studied with different experimental approaches. Using diffuse scattered laser light, applying laser tweezer forces to individual particles, and periodic laser pulses, the excitation of modes is investigated. The instantaneous normal mode analysis of experimental data from two-dimensional liquid clusters gives access to the local dynamics of the liquid phase. Our investigations shed light on the role of compressional and shear modes as well as the determination of diffusion constants and melting temperatures in finite systems. Special attention is paid to hydrodynamic situations with a stationary inhomogeneous dust flow. MD simulations allow to study the collective motion in the shell of nearest neighbors, which can be linked to smooth and sudden changes of the macroscopic flow. Finally, the observed micro-motion in all situations above allows to shed light on the preference of shear-like over compressional motion in terms of a minimized potential energy and a dynamic incompressibility.

Modeling of human operator dynamics in simple manual control utilizing time series analysis. [tracking (position)

NASA Technical Reports Server (NTRS)

Agarwal, G. C.; Osafo-Charles, F.; Oneill, W. D.; Gottlieb, G. L.

1982-01-01

Time series analysis is applied to model human operator dynamics in pursuit and compensatory tracking modes. The normalized residual criterion is used as a one-step analytical tool to encompass the processes of identification, estimation, and diagnostic checking. A parameter constraining technique is introduced to develop more reliable models of human operator dynamics. The human operator is adequately modeled by a second order dynamic system both in pursuit and compensatory tracking modes. In comparing the data sampling rates, 100 msec between samples is adequate and is shown to provide better results than 200 msec sampling. The residual power spectrum and eigenvalue analysis show that the human operator is not a generator of periodic characteristics.

Improvements in Block-Krylov Ritz Vectors and the Boundary Flexibility Method of Component Synthesis

NASA Technical Reports Server (NTRS)

Carney, Kelly Scott

1997-01-01

A method of dynamic substructuring is presented which utilizes a set of static Ritz vectors as a replacement for normal eigenvectors in component mode synthesis. This set of Ritz vectors is generated in a recurrence relationship, proposed by Wilson, which has the form of a block-Krylov subspace. The initial seed to the recurrence algorithm is based upon the boundary flexibility vectors of the component. Improvements have been made in the formulation of the initial seed to the Krylov sequence, through the use of block-filtering. A method to shift the Krylov sequence to create Ritz vectors that will represent the dynamic behavior of the component at target frequencies, the target frequency being determined by the applied forcing functions, has been developed. A method to terminate the Krylov sequence has also been developed. Various orthonormalization schemes have been developed and evaluated, including the Cholesky/QR method. Several auxiliary theorems and proofs which illustrate issues in component mode synthesis and loss of orthogonality in the Krylov sequence have also been presented. The resulting methodology is applicable to both fixed and free- interface boundary components, and results in a general component model appropriate for any type of dynamic analysis. The accuracy is found to be comparable to that of component synthesis based upon normal modes, using fewer generalized coordinates. In addition, the block-Krylov recurrence algorithm is a series of static solutions and so requires significantly less computation than solving the normal eigenspace problem. The requirement for less vectors to form the component, coupled with the lower computational expense of calculating these Ritz vectors, combine to create a method more efficient than traditional component mode synthesis.

Dynamics and structure of planetary rings

NASA Technical Reports Server (NTRS)

French, R. G.

1991-01-01

Recent research efforts were directed towards sharpening the understanding of kinematical and dynamical properties of the Uranian rings, with the combination of Earth-based and Voyager observations, and in obtaining and interpreting new observations of the Saturn system from the remarkable stellar occultation of 3 Jul. 1989. Some of the highlights studied include: (1) a detailed comparison of structure and dynamics of the Uranus rings from joint analysis of high quality Earth-based data and the complete set of Voyager occultation measurements; (2) a comprehensive search for weak normal modes excited in the Uranian rings, analogous to the m = 2 and m = 0 normal modes previously identified for the delta and gamma rings; (3) an ongoing search for faint rings and ring arcs of Uranus, using both Voyager images of the rings and Earth-based and spacecraft stellar occultation data; (4) a comparison of upper stratospheric temperatures of Uranus inferred from Voyager ultraviolet occultations with results of ground-based occultation observations; and (5) observations of the 3 Jul. 1989 Saturn occultation of 28 Sgr.

Attitude control of an orbiting space vehicle.

NASA Technical Reports Server (NTRS)

Sutherlin, D. W.; Boland, J. S. , III; Borelli, M. T.

1971-01-01

Study of the normal and clamped modes of operation and dynamic response characteristics of the gimbaled control moment gyro (CMG) designed to fulfill the stringent pointing requirements of the Skylab telescope mount when the spacecraft is under the influence of both external and internal torques. The results indicate that the clamped mode of operation provides a feasible approach for significantly improving the system characteristics.

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

Normal Modes Expose Active Sites in Enzymes

PubMed Central

Glantz-Gashai, Yitav; Samson, Abraham O.

2016-01-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations - Part 1: Nonhydrostatic inertia-gravity modes

NASA Astrophysics Data System (ADS)

Konor, Celal S.; Randall, David A.

2018-05-01

We have used a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the nonhydrostatic anelastic inertia-gravity modes on a midlatitude f plane. The dispersion equations are derived from the linearized anelastic equations that are discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of both horizontal grid spacing and vertical wavenumber are analyzed, and the role of nonhydrostatic effects is discussed. We also compare the results of the normal-mode analyses with numerical solutions obtained by running linearized numerical models based on the various horizontal grids. The sources and behaviors of the computational modes in the numerical simulations are also examined.Our normal-mode analyses with the Z, C, D, A, E and B grids generally confirm the conclusions of previous shallow-water studies for the cyclone-resolving scales (with low horizontal wavenumbers). We conclude that, aided by nonhydrostatic effects, the Z and C grids become overall more accurate for cloud-resolving resolutions (with high horizontal wavenumbers) than for the cyclone-resolving scales.A companion paper, Part 2, discusses the impacts of the discretization on the Rossby modes on a midlatitude β plane.

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

PubMed

Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

2011-10-14

Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

The Shock and Vibration Bulletin. Part 2. Model Test and Analysis, Testing Techniques, Machinery Dynamics, Isolation and Damping, Structural Dynamics

DTIC Science & Technology

1986-08-01

each subsystem wist include more than a set of rigid body and normal modes to properly represent the dynamics of the entire system. Various types of...MCM 1 AUGMENTATION HETNO-MrifaOII FIELD TflACKER »f Tl BASIC EXPERIMENT Figure 3. Dynamics augmentation experiment. i i mnc...Villeurbanne - France Today the dynamic behavior of rotors must be predicted with the greatest care. This work deals with the influence of disc flexi

Normal modes of synchronous rotation

NASA Astrophysics Data System (ADS)

Varadi, Ferenc; Musotto, Susanna; Moore, William; Schubert, Gerald

2005-07-01

The dynamics of synchronous rotation and physical librations are revisited in order to establish a conceptually simple and general theoretical framework applicable to a variety of problems. Our motivation comes from disagreements between the results of numerical simulations and those of previous theoretical studies, and also because different theoretical studies disagree on basic features of the dynamics. We approach the problem by decomposing the orientation matrix of the body into perfectly synchronous rotation and deviation from the equilibrium state. The normal modes of the linearized equations are computed in the case of a circular satellite orbit, yielding both the periods and the eigenspaces of three librations. Libration in longitude decouples from the other two, vertical modes. There is a fast vertical mode with a period very close to the average rotational period. It corresponds to tilting the body around a horizontal axis while retaining nearly principal-axis rotation. In the inertial frame, this mode appears as nutation and free precession. The other vertical mode, a slow one, is the free wobble. The effects of the nodal precession of the orbit are investigated from the point of view of Cassini states. We test our theory using numerical simulations of the full equations of the dynamics and discuss the disagreements among our study and previous ones. The numerical simulations also reveal that in the case of eccentric orbits large departures from principal-axis rotation are possible due to a resonance between free precession and wobble. We also revisit the history of the Moon's rotational state and show that it switched from one Cassini state to another when it was at 46.2 Earth radii. This number disagrees with the value 34.2 derived in a previous study.

Hybrid experimental/analytical models of structural dynamics - Creation and use for predictions

NASA Technical Reports Server (NTRS)

Balmes, Etienne

1993-01-01

An original complete methodology for the construction of predictive models of damped structural vibrations is introduced. A consistent definition of normal and complex modes is given which leads to an original method to accurately identify non-proportionally damped normal mode models. A new method to create predictive hybrid experimental/analytical models of damped structures is introduced, and the ability of hybrid models to predict the response to system configuration changes is discussed. Finally a critical review of the overall methodology is made by application to the case of the MIT/SERC interferometer testbed.

Normal-mode-based analysis of electron plasma waves with second-order Hermitian formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramos, J. J.; White, R. L.

The classic problem of the dynamic evolution and Landau damping of linear Langmuir electron waves in a collisionless plasma with Maxwellian background is cast as a second-order, self-adjoint problem with a continuum spectrum of real and positive squared frequencies. The corresponding complete basis of singular normal modes is obtained, along with their orthogonality relation. This yields easily the general expression of the time-reversal-invariant solution for any initial-value problem. Examples are then given for specific initial conditions that illustrate different behaviors of the Landau-damped macroscopic moments of the perturbations.

Normal-mode-based analysis of electron plasma waves with second-order Hermitian formalism

DOE PAGES

Ramos, J. J.; White, R. L.

2018-03-01

The classic problem of the dynamic evolution and Landau damping of linear Langmuir electron waves in a collisionless plasma with Maxwellian background is cast as a second-order, self-adjoint problem with a continuum spectrum of real and positive squared frequencies. The corresponding complete basis of singular normal modes is obtained, along with their orthogonality relation. This yields easily the general expression of the time-reversal-invariant solution for any initial-value problem. Examples are then given for specific initial conditions that illustrate different behaviors of the Landau-damped macroscopic moments of the perturbations.

Dynamics of crystalline acetanilide: Analysis using neutron scattering and computer simulation

NASA Astrophysics Data System (ADS)

Hayward, R. L.; Middendorf, H. D.; Wanderlingh, U.; Smith, J. C.

1995-04-01

The unusual temperature dependence of several optical spectroscopic vibrational bands in crystalline acetanilide has been interpreted as providing evidence for dynamic localization. Here we examine the vibrational dynamics of crystalline acetanilide over a spectral range of ˜20-4000 cm-1 using incoherent neutron scattering experiments, phonon normal mode calculations and molecular dynamics simulations. A molecular mechanics energy function is parametrized and used to perform the normal mode analyses in the full configurational space of the crystal i.e., including the intramolecular and intermolecular degrees of freedom. One- and multiphonon incoherent inelastic neutron scattering intensities are calculated from harmonic analyses in the first Brillouin zone and compared with the experimental data presented here. Phonon dispersion relations and mean-square atomic displacements are derived from the harmonic model and compared with data derived from coherent inelastic neutron scattering and neutron and x-ray diffraction. To examine the temperature effects on the vibrations the full, anharmonic potential function is used in molecular dynamics simulations of the crystal at 80, 140, and 300 K. Several, but not all, of the spectral features calculated from the molecular dynamics simulations exhibit temperature-dependent behavior in agreement with experiment. The significance of the results for the interpretation of the optical spectroscopic results and possible improvements to the model are discussed.

Broken Detailed Balance of Filament Dynamics in Active Networks

NASA Astrophysics Data System (ADS)

Schmidt, Christoph F.; Gladrow, Jannes; Fakhri, Nikta; Mackintosh, Fred C.; Broedersz, Chase

Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single- walled carbon nanotubes can be used as novel tools to noninvasively track equilibrium and nonequilibrium fluctuations in biopolymer networks. We analytically calculated shape fluctuations of semi- flexible probe filaments in a viscoelastic environment, driven out of equilibrium by motor activity. Transverse bending fluctuations of the probe filaments can be decomposed into dynamic normal modes. We find that these modes no longer evolve independently under non-equilibrium driving. This effective mode coupling results in nonzero circulatory currents in a conformational phase space, reflecting a violation of detailed balance. We present predictions for the characteristic frequencies associated with these currents and investigate how the temporal signatures of motor activity determine mode correlations, which we find to be consistent with recent experiments on microtubules embedded in cytoskeletal networks.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Energy-efficient orthogonal frequency division multiplexing-based passive optical network based on adaptive sleep-mode control and dynamic bandwidth allocation

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Xiao, Nengwu; Chen, Chen; Yuan, Weicheng; Qiu, Kun

2016-02-01

We propose an energy-efficient orthogonal frequency division multiplexing-based passive optical network (OFDM-PON) using adaptive sleep-mode control and dynamic bandwidth allocation. In this scheme, a bidirectional-centralized algorithm named the receiver and transmitter accurate sleep control and dynamic bandwidth allocation (RTASC-DBA), which has an overall bandwidth scheduling policy, is employed to enhance the energy efficiency of the OFDM-PON. The RTASC-DBA algorithm is used in an optical line terminal (OLT) to control the sleep mode of an optical network unit (ONU) sleep and guarantee the quality of service of different services of the OFDM-PON. The obtained results show that, by using the proposed scheme, the average power consumption of the ONU is reduced by ˜40% when the normalized ONU load is less than 80%, compared with the average power consumption without using the proposed scheme.

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations

PubMed Central

Sagnella, Diane E.; Straub, John E.; Jackson, Timothy A.; Lim, Manho; Anfinrud, Philip A.

1999-01-01

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the δ- and ɛ-tautomers of the distal His-64. Vibrational population relaxation times of 335 ± 115 ps for the δ-tautomer and 640 ± 185 ps for the ɛ-tautomer were estimated by using the Landau–Teller model. Normal mode analysis was used to identify those protein residues that act as the primary “doorway” modes in the vibrational relaxation of the oscillator. Although the CO relaxation rates in both the ɛ- and δ-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the δ-tautomer with the distal His playing an important role in the energy relaxation mechanism. Time-resolved mid-IR absorbance measurements were performed on photolyzed carbonmonoxy hemoglobin (Hb13CO). From these measurements, a T1 time of 600 ± 150 ps was determined. The simulation and experimental estimates are compared and discussed. PMID:10588704

The interplay of protein and solvent picosecond dynamics: Experimental and theoretical studies

NASA Astrophysics Data System (ADS)

He, Yunfen

Terahertz gap is located between microwaves and infrared. THz-TDS is based on the generation of subpicosecond terahertz pulses using ultrashort laser pulses with pulse durations of a few femtoseconds. From the spectroscopic point of view terahertz radiation excites the low frequency vibrations of molecules. Terahertz spectroscopy provides a new way to study protein dynamics in this critical frequency range. The strong temperature dependence of molecular flexibility near 200 K for proteins and polynucleotides hydrated above 30% by weight, dynamical transition, is one of the most significant phenomena of biomolecular dynamics. Measurements of the dynamical transition were performed for native, fully denatured and unstructured polypeptides using THz-TDS. The results reveal that the dynamical transition is independent of either tertiary or secondary structure. The transition are also found for shorter chain alanine peptides down to penta-alanine, which indicates that a quantitative predictive theory for the temperature dependence lies in the understanding of the interaction of the side chains of the poly peptide or poly nucleotide with the biological water. The far infrared vibrational modes can be calculated using harmonic or anharmonic normal mode analysis, and the resulting Density of States (DOS) strongly resembles the measured absorbance. A large contrast in the terahertz dielectric response between oxidized and reduced cytochrome c has lready been observed experimentally. This large contrast has been associated with a change in the collective structural motions that related to protein flexibility. Molecular simulation results from quasiharmonic analysis and dipole-dipole correlation analysis are compared with the measurements to determine the relative contribution of correlated motions and diffusive motions to the measured dielectric response. The measured hydration dependence is reproduced by hydration dependence of quasiharmonic normal modes, but these modes calculations do not reproduce the oxidation dependence. Whereas dipole-dipole correlation analysis reproduces the oxidation dependence at the lowest hydration level, but surprisingly do not capture the hydration dependence. These results suggest that the hydration dependence in the THz response does in fact arise from changes in the vibrational modes, and the oxidation dependence arises from relaxational motions.

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations – Part 2: Quasi-geostrophic Rossby modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konor, Celal S.; Randall, David A.

We use a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the quasi-geostrophic anelastic baroclinic and barotropic Rossby modes on a midlatitude β plane. The dispersion equations are derived for the linearized anelastic system, discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of various horizontal grid spacings and vertical wavenumbers are discussed. A companion paper, Part 1, discusses the impacts of the discretization on the inertia–gravity modes on a midlatitude f plane.The results of our normal-modemore » analyses for the Rossby waves overall support the conclusions of the previous studies obtained with the shallow-water equations. We identify an area of disagreement with the E-grid solution.« less

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations – Part 2: Quasi-geostrophic Rossby modes

DOE PAGES

Konor, Celal S.; Randall, David A.

2018-05-08

We use a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the quasi-geostrophic anelastic baroclinic and barotropic Rossby modes on a midlatitude β plane. The dispersion equations are derived for the linearized anelastic system, discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of various horizontal grid spacings and vertical wavenumbers are discussed. A companion paper, Part 1, discusses the impacts of the discretization on the inertia–gravity modes on a midlatitude f plane.The results of our normal-modemore » analyses for the Rossby waves overall support the conclusions of the previous studies obtained with the shallow-water equations. We identify an area of disagreement with the E-grid solution.« less

Normal mode analysis on the relaxation of an excited nitromethane molecule in argon bath

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis; Wagner, Albert

In our previous work [J. Chem. Phys. 142, 014303 (2015)] classical molecular dynamics simulations followed in an Ar bath the relaxation of nitromethane (CH3NO2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm, a range spanning the breakdown of the isolated binary collision approximation. Both rotational and vibrational energies exhibit multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997)], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH3NO2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. Increasing pressure can be shown to increasingly interfere with post-collision IVR. The work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

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)

Time-dependent local-to-normal mode transition in triatomic molecules

NASA Astrophysics Data System (ADS)

Cruz, Hans; Bermúdez-Montaña, Marisol; Lemus, Renato

2018-01-01

Time-evolution of the vibrational states of two interacting harmonic oscillators in the local mode scheme is presented. A local-to-normal mode transition (LNT) is identified and studied from temporal perspective through time-dependent frequencies of the oscillators. The LNT is established as a polyad-breaking phenomenon from the local standpoint for the stretching degrees of freedom in a triatomic molecule. This study is carried out in the algebraic representation of bosonic operators. The dynamics of the states are determined via the solutions of the corresponding nonlinear Ermakov equation and a local time-dependent polyad is obtained as a tool to identify the LNT. Applications of this formalism to H2O, CO2, O3 and NO2 molecules in the adiabatic, sudden and linear regime are considered.

Dynamic radioactive particle source

DOEpatents

Moore, Murray E; Gauss, Adam Benjamin; Justus, Alan Lawrence

2012-06-26

A method and apparatus for providing a timed, synchronized dynamic alpha or beta particle source for testing the response of continuous air monitors (CAMs) for airborne alpha or beta emitters is provided. The method includes providing a radioactive source; placing the radioactive source inside the detection volume of a CAM; and introducing an alpha or beta-emitting isotope while the CAM is in a normal functioning mode.

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations – Part 1: Nonhydrostatic inertia–gravity modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konor, Celal S.; Randall, David A.

We have used a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the nonhydrostatic anelastic inertia–gravity modes on a midlatitude f plane. The dispersion equations are derived from the linearized anelastic equations that are discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of both horizontal grid spacing and vertical wavenumber are analyzed, and the role of nonhydrostatic effects is discussed. We also compare the results of the normal-mode analyses with numerical solutions obtained by runningmore » linearized numerical models based on the various horizontal grids. The sources and behaviors of the computational modes in the numerical simulations are also examined.Our normal-mode analyses with the Z, C, D, A, E and B grids generally confirm the conclusions of previous shallow-water studies for the cyclone-resolving scales (with low horizontal wavenumbers). We conclude that, aided by nonhydrostatic effects, the Z and C grids become overall more accurate for cloud-resolving resolutions (with high horizontal wavenumbers) than for the cyclone-resolving scales.A companion paper, Part 2, discusses the impacts of the discretization on the Rossby modes on a midlatitude β plane.« less

Impacts of the horizontal and vertical grids on the numerical solutions of the dynamical equations – Part 1: Nonhydrostatic inertia–gravity modes

DOE PAGES

Konor, Celal S.; Randall, David A.

2018-05-08

We have used a normal-mode analysis to investigate the impacts of the horizontal and vertical discretizations on the numerical solutions of the nonhydrostatic anelastic inertia–gravity modes on a midlatitude f plane. The dispersion equations are derived from the linearized anelastic equations that are discretized on the Z, C, D, CD, (DC), A, E and B horizontal grids, and on the L and CP vertical grids. The effects of both horizontal grid spacing and vertical wavenumber are analyzed, and the role of nonhydrostatic effects is discussed. We also compare the results of the normal-mode analyses with numerical solutions obtained by runningmore » linearized numerical models based on the various horizontal grids. The sources and behaviors of the computational modes in the numerical simulations are also examined.Our normal-mode analyses with the Z, C, D, A, E and B grids generally confirm the conclusions of previous shallow-water studies for the cyclone-resolving scales (with low horizontal wavenumbers). We conclude that, aided by nonhydrostatic effects, the Z and C grids become overall more accurate for cloud-resolving resolutions (with high horizontal wavenumbers) than for the cyclone-resolving scales.A companion paper, Part 2, discusses the impacts of the discretization on the Rossby modes on a midlatitude β plane.« less

Relationships between nonlinear normal modes and response to random inputs

NASA Astrophysics Data System (ADS)

Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

2017-02-01

The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). This work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing. Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.

Bushes of vibrational modes for Fermi-Pasta-Ulam chains

NASA Astrophysics Data System (ADS)

Chechin, G. M.; Novikova, N. V.; Abramenko, A. A.

2002-06-01

Some exact solutions and multimode invariant submanifolds were found for the Fermi-Pasta-Ulam (FPU)- β model by Poggi and Ruffo [Physica D 103 (1997) 251]. In the present paper we demonstrate how results of such a type can be obtained for an arbitraryN-particle chain with periodic boundary conditions with the aid of our group-theoretical approach [Physica D 117 (1998) 43] based on the concept of bushes of normal modes in mechanical systems with discrete symmetry. The integro-differential equation describing the FPU- α dynamics in the modal space is derived. The loss of stability of the bushes of modes for the FPU- α model, in particular, for the limiting case N→∞ for the dynamical regime with displacement pattern having period twice the lattice spacing ( π-mode) is studied. Our results for the FPU- α chain are compared with those by Poggi and Ruffo for the FPU- β chain.

Broken Detailed Balance of Filament Dynamics in Active Networks

NASA Astrophysics Data System (ADS)

Gladrow, J.; Fakhri, N.; MacKintosh, F. C.; Schmidt, C. F.; Broedersz, C. P.

2016-06-01

Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel tools to noninvasively track equilibrium and nonequilibrium fluctuations in such biopolymer networks. Here, we analytically calculate shape fluctuations of semiflexible probe filaments in a viscoelastic environment, driven out of equilibrium by motor activity. Transverse bending fluctuations of the probe filaments can be decomposed into dynamic normal modes. We find that these modes no longer evolve independently under nonequilibrium driving. This effective mode coupling results in nonzero circulatory currents in a conformational phase space, reflecting a violation of detailed balance. We present predictions for the characteristic frequencies associated with these currents and investigate how the temporal signatures of motor activity determine mode correlations, which we find to be consistent with recent experiments on microtubules embedded in cytoskeletal networks.

Volume Dynamics Propulsion System Modeling for Supersonics Vehicle Research

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; Paxson, Daniel E.; Ma, Peter

2010-01-01

Under the NASA Fundamental Aeronautics Program the Supersonics Project is working to overcome the obstacles to supersonic commercial flight. The proposed vehicles are long slim body aircraft with pronounced aero-servo-elastic modes. These modes can potentially couple with propulsion system dynamics; leading to performance challenges such as aircraft ride quality and stability. Other disturbances upstream of the engine generated from atmospheric wind gusts, angle of attack, and yaw can have similar effects. In addition, for optimal propulsion system performance, normal inlet-engine operations are required to be closer to compressor stall and inlet unstart. To study these phenomena an integrated model is needed that includes both airframe structural dynamics as well as the propulsion system dynamics. This paper covers the propulsion system component volume dynamics modeling of a turbojet engine that will be used for an integrated vehicle Aero-Propulso-Servo-Elastic model and for propulsion efficiency studies.

Volume Dynamics Propulsion System Modeling for Supersonics Vehicle Research

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; Paxson, Daniel E.; Ma, Peter

2008-01-01

Under the NASA Fundamental Aeronautics Program, the Supersonics Project is working to overcome the obstacles to supersonic commercial flight. The proposed vehicles are long slim body aircraft with pronounced aero-servo-elastic modes. These modes can potentially couple with propulsion system dynamics; leading to performance challenges such as aircraft ride quality and stability. Other disturbances upstream of the engine generated from atmospheric wind gusts, angle of attack, and yaw can have similar effects. In addition, for optimal propulsion system performance, normal inlet-engine operations are required to be closer to compressor stall and inlet unstart. To study these phenomena an integrated model is needed that includes both airframe structural dynamics as well as the propulsion system dynamics. This paper covers the propulsion system component volume dynamics modeling of a turbojet engine that will be used for an integrated vehicle Aero-Propulso-Servo-Elastic model and for propulsion efficiency studies.

Volume Dynamics Propulsion System Modeling for Supersonics Vehicle Research

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; Paxson, Daniel E.; Ma, Peter

2008-01-01

Under the NASA Fundamental Aeronautics Program the Supersonics Project is working to overcome the obstacles to supersonic commercial flight. The proposed vehicles are long slim body aircraft with pronounced aero-servo-elastic modes. These modes can potentially couple with propulsion system dynamics; leading to performance challenges such as aircraft ride quality and stability. Other disturbances upstream of the engine generated from atmospheric wind gusts, angle of attack, and yaw can have similar effects. In addition, for optimal propulsion system performance, normal inlet-engine operations are required to be closer to compressor stall and inlet unstart. To study these phenomena an integrated model is needed that includes both airframe structural dynamics as well as the propulsion system dynamics. This paper covers the propulsion system component volume dynamics modeling of a turbojet engine that will be used for an integrated vehicle Aero- Propulso-Servo-Elastic model and for propulsion efficiency studies.

Dynamic modeling and Super-Twisting Sliding Mode Control for Tethered Space Robot

NASA Astrophysics Data System (ADS)

Zhao, Yakun; Huang, Panfeng; Zhang, Fan

2018-02-01

Recent years, tethered space capturing systems have been considered as one of the most promising solutions for active space debris removal due to the increasing threat of space debris to spacecraft and astronauts. In this paper, one of the tethered space capturing systems, Tethered Space Robot (TSR), is investigated. TSR includes a space platform, a space tether, and a gripper as the terminal device. Based on the assumptions that the platform and the gripper are point masses and the tether is rigid, inextensible and remaining straight, the dynamic model of TSR is presented, in which the disturbances from space environment is considered. According to the previous study, the in-plane and out-of-plane angles of the tether oscillate periodically although the tether is released to the desired length. A super-twisting adaptive sliding mode control scheme is designed for TSR to eliminate the vibration of the tether to assure a successful capture in station-keeping phase. Both uncontrolled and controlled situations are simulated. The simulation results show that the proposed controller is effective. Additionally, after comparing with normal sliding mode control algorithm, it is verified that the proposed control scheme can avoid the chattering of normal sliding mode control and is robust for unknown boundary perturbations.

Normal modes and frequencies from covariances in molecular dynamics or Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Strachan, Alejandro

2004-01-01

We propose a simple method to obtain normal modes (NMs) and their characteristic frequencies from molecular dynamics or Monte Carlo simulations at any temperature. The resulting NM are consistent with the vibrational density of states (DOS) (every feature of the DOS can be attributed to one or few NMs). At low temperatures they coincide with the ones obtained from the Hessian matrix. We define the NMs (ρi) by imposing the condition that their velocities be uncorrelated to each other: <ρ˙i(t)ρ˙j(t)>∝δij, where < > denotes time average and δij is Kronecker's delta. With this definition the modes are the eigenvectors of the matrix Kijv=1/2<√mimj vivj> [i, j=1,…,3N (N being the number of atoms); m are masses and v atomic velocities]. The eigenvalues of Kijv, λiv, represent the kinetic energy in each NM. The ratio between the eigenvalues (λiv) and those obtained using positions (λir), accelerations (λia) in Kijv instead of velocities are a very good approximation to the mode frequencies: 2πνi˜(λiv/λix)(1/2)˜(λia/λix)(1/4). We demonstrate the new method using with two cases: an isolated water molecule and a crystalline polymer.

Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

2018-06-01

Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆G binding  = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation ability, drug release and further development of novel liposome-based pH-responsive nano-drug delivery system with refined structural and chemical features of potential lipid molecule for formulation development.

Modal coupling procedures adapted to NASTRAN analysis of the 1/8-scale shuttle structural dynamics model. Volume 1: Technical report

NASA Technical Reports Server (NTRS)

Zalesak, J.

1975-01-01

A dynamic substructuring analysis, utilizing the component modes technique, of the 1/8 scale space shuttle orbiter finite element model is presented. The analysis was accomplished in 3 phases, using NASTRAN RIGID FORMAT 3, with appropriate Alters, on the IBM 360-370. The orbiter was divided into 5 substructures, each of which was reduced to interface degrees of freedom and generalized normal modes. The reduced substructures were coupled to yield the first 23 symmetric free-free orbiter modes, and the eigenvectors in the original grid point degree of freedom lineup were recovered. A comparison was made with an analysis which was performed with the same model using the direct coordinate elimination approach. Eigenvalues were extracted using the inverse power method.

The mathematical cell model reconstructed from interference microscopy data

NASA Astrophysics Data System (ADS)

Rogotnev, A. A.; Nikitiuk, A. S.; Naimark, O. B.; Nebogatikov, V. O.; Grishko, V. V.

2017-09-01

The mathematical model of cell dynamics is developed to link the dynamics of the phase cell thickness with the signs of the oncological pathology. The measurements of irregular oscillations of cancer cells phase thickness were made with laser interference microscope MIM-340 in order to substantiate this model. These data related to the dynamics of phase thickness for different cross-sections of cells (nuclei, nucleolus, and cytoplasm) allow the reconstruction of the attractor of dynamic system. The attractor can be associated with specific types of collective modes of phase thickness responsible for the normal and cancerous cell dynamics. Specific type of evolution operator was determined using an algorithm of designing of the mathematical cell model and temporal phase thickness data for cancerous and normal cells. Qualitative correspondence of attractor types to the cell states was analyzed in terms of morphological signs associated with maximum value of mean square irregular oscillations of phase thickness dynamics.

Nonlinear cellular dynamics of keratinocytes in normal and psoriatic epidermis under action of UV radiation

NASA Astrophysics Data System (ADS)

Stolnitz, Mikhail M.; Medvedev, Boris A.; Gribko, Tatyana V.

2004-05-01

The semi-phenomenological model of epidermal cell dynamics is submitted. The model takes into account three types of basal layer keratinocytes (stem, transient amplifying, terminally differentiated), distribution of first two types cells on mitotic cycle stages and resting states, keratinocytes-lymphocytes interactions that provide a positive feedback loop, influence of more differentiated cells on their progenitors that provide a negative feedback loop. Simplified model are developed and its stationary solutions are received. The opportunity of interpretation of some received modes as corresponding to various stages of psoriasis is discussed. Influence of UV-radiation on transitions between various modes of epidermis functioning is qualitatively analyzed.

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

NASA Technical Reports Server (NTRS)

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

1975-01-01

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

Stiffness-generated rigid-body mode shapes for Lanczos eigensolution with SUPORT DOF by way of a MSC/NASTRAN DMAP alter

NASA Technical Reports Server (NTRS)

Abdallah, Ayman A.; Barnett, Alan R.; Widrick, Timothy W.; Manella, Richard T.; Miller, Robert P.

1994-01-01

When using all MSC/NASTRAN eigensolution methods except Lanczos, the analyst can replace the coupled system rigid-body modes calculated within DMAP module READ with mass orthogonalized and normalized rigid-body modes generated from the system stiffness. This option is invoked by defining MSC/NASTRAN r-set degrees of freedom via the SUPORT bulk data card. The newly calculated modes are required if the rigid-body modes calculated by the eigensolver are not 'clean' due to numerical roundoffs in the solution. When performing transient structural dynamic load analysis, the numerical roundoffs can result in inaccurate rigid-body accelerations which affect steady-state responses. Unfortunately, when using the Lanczos method and defining r-set degrees of freedom, the rigid-body modes calculated within DMAP module REIGL are retained. To overcome this limitation and to allow MSC/NASTRAN to handle SUPORT degrees of freedom identically for all eigensolvers, a DMAP Alter has been written which replaces Lanczos-calculated rigid-body modes with stiffness-generated rigid-body modes. The newly generated rigid-body modes are normalized with respect to the system mass and orthogonalized using the Gram-Schmidt technique. This algorithm has been implemented as an enhancement to an existing coupled loads methodology.

Dynamics of streaming instability with quantum correction

NASA Astrophysics Data System (ADS)

Goutam, H. P.; Karmakar, P. K.

2017-05-01

A modified quantum hydrodynamic model (m-QHD) is herein proposed on the basis of the Thomas-Fermi (TF) theory of many fermionic quantum systems to investigate the dynamics of electrostatic streaming instability modes in a complex (dusty) quantum plasma system. The newly formulated m-QHD, as an amelioration over the existing usual QHD, employs a dimensionality-dependent Bohmian quantum correction prefactor, γ = [(D-2)/3D], in the electron quantum dynamics, where D symbolizing the problem dimensionality under consideration. The normal mode analysis of the coupled structure equations reveals the excitation of two distinct streaming modes associated with the flowing ions (against electrons and dust) and the flowing dust particulates (against the electrons and ions). It is mainly shown that the γ-factor introduces a new source of stability and dispersive effects to the ion-streaming instability solely; but not to the dust counterparts. A non-trivial application of our investigation in electrostatic beam-plasma (flow-driven) coupled dynamics leading to the development of self-sustained intense electric current, and hence, of strong magnetic field in compact astrophysical objects (in dwarf-family stars) is summarily indicated.

Relationships between nonlinear normal modes and response to random inputs

DOE PAGES

Schoneman, Joseph D.; Allen, Matthew S.; Kuether, Robert J.

2016-07-25

The ability to model nonlinear structures subject to random excitation is of key importance in designing hypersonic aircraft and other advanced aerospace vehicles. When a structure is linear, superposition can be used to construct its response to a known spectrum in terms of its linear modes. Superposition does not hold for a nonlinear system, but several works have shown that a system's dynamics can still be understood qualitatively in terms of its nonlinear normal modes (NNMs). Here, this work investigates the connection between a structure's undamped nonlinear normal modes and the spectrum of its response to high amplitude random forcing.more » Two examples are investigated: a spring-mass system and a clamped-clamped beam modeled within a geometrically nonlinear finite element package. In both cases, an intimate connection is observed between the smeared peaks in the response spectrum and the frequency-energy dependence of the nonlinear normal modes. In order to understand the role of coupling between the underlying linear modes, reduced order models with and without modal coupling terms are used to separate the effect of each NNM's backbone from the nonlinear couplings that give rise to internal resonances. In the cases shown here, uncoupled, single-degree-of-freedom nonlinear models are found to predict major features in the response with reasonable accuracy; a highly inexpensive approximation such as this could be useful in design and optimization studies. More importantly, the results show that a reduced order model can be expected to give accurate results only if it is also capable of accurately predicting the frequency-energy dependence of the nonlinear modes that are excited.« less

Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit.

PubMed

Skjaerven, Lars; Martinez, Aurora; Reuter, Nathalie

2011-01-01

Principal component analysis (PCA) and normal mode analysis (NMA) have emerged as two invaluable tools for studying conformational changes in proteins. To compare these approaches for studying protein dynamics, we have used a subunit of the GroEL chaperone, whose dynamics is well characterized. We first show that both PCA on trajectories from molecular dynamics (MD) simulations and NMA reveal a general dynamical behavior in agreement with what has previously been described for GroEL. We thus compare the reproducibility of PCA on independent MD runs and subsequently investigate the influence of the length of the MD simulations. We show that there is a relatively poor one-to-one correspondence between eigenvectors obtained from two independent runs and conclude that caution should be taken when analyzing principal components individually. We also observe that increasing the simulation length does not improve the agreement with the experimental structural difference. In fact, relatively short MD simulations are sufficient for this purpose. We observe a rapid convergence of the eigenvectors (after ca. 6 ns). Although there is not always a clear one-to-one correspondence, there is a qualitatively good agreement between the movements described by the first five modes obtained with the three different approaches; PCA, all-atoms NMA, and coarse-grained NMA. It is particularly interesting to relate this to the computational cost of the three methods. The results we obtain on the GroEL subunit contribute to the generalization of robust and reproducible strategies for the study of protein dynamics, using either NMA or PCA of trajectories from MD simulations. © 2010 Wiley-Liss, Inc.

Global Dynamics of Proteins: Bridging Between Structure and Function

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781

Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.

Evaluation of left ventricular performance during supine exercise by transoesophageal M-mode echocardiography in normal subjects.

PubMed Central

Matsumoto, M; Hanrath, P; Kremer, P; Tams, C; Langenstein, B A; Schlüter, M; Weiter, R; Bleifeld, W

1982-01-01

In order to evaluate left ventricular function during dynamic exercise transoesophageal M-mode recordings of the left ventricle were carried out with a newly developed transducer gastroscope system. Twelve healthy subjects performed a graded supine bicycle exercise test. Stable and good quality images of the left ventricle at rest and during exercise at different steps up to a maximum workload of 100 watts were obtained in all patients. Isotonic maximum exercise resulted in a significant increase in fractional shortening of the left ventricle, peak shortening rate, and peak lengthening rate of the left ventricular minor axis. Left ventricular end-diastolic dimension decreased significantly. With increasing workload the pressure rate product increased significantly. It is concluded that transoesophageal M-mode echocardiography is a useful method of evaluating left ventricular performance during dynamic exercise. Images PMID:7082515

Nonlinear Wave Propagation

DTIC Science & Technology

2009-02-09

grey) soliton , to a nearly linear wavetrain at the front moving with its group velocity ; like KdV the NLS DSW has two speeds. The 1-D NLS theory was...studies of wave phenomena in nonlinear optics include ultrashort pulse dynamics in mode- locked lasers, dynamics and perturbations of dark solitons ...nonlinear Kerr response and has a large normal group - velocity dispersion (GVD). This requires a set of prisms and/or mirrors specially designed to have

Performance evaluation of a dynamic telepathology system (Panoptiq™) in the morphologic assessment of peripheral blood film abnormalities.

PubMed

Goswami, R; Pi, D; Pal, J; Cheng, K; Hudoba De Badyn, M

2015-06-01

The study evaluated the performance of a dynamic imaging telepathology system (Panoptiq(™) ) as a diagnostic aid to the identification of peripheral blood film (PBF) abnormalities. The study assumed a laboratory personnel working in a clinical laboratory were operating the telepathology system to seek diagnostic opinion from an external consulting hematopathologist. The study examined 100 blood films, encompassing 23 different hematological diseases, reactive or normal cases. The study revealed that with real-time image transmission in live scanning mode of operation, the telepathology system was able to aid reviewers in achieving excellent accuracy, that is correct interpretation of morphologic abnormalities obtained in 83/84 of the hematologic diseases and 12/12 of the reactive/normal conditions (Sensitivity: 0.99; Specificity: 1.00). In contrast, when only saved static images in digital capture mode of operation were reviewed remotely, interpretative omissions occurred in 8/84 of the hematologic diseases and 0/12 of the reactive/normal conditions (Sensitivity: 0.91; Specificity: 1.00). It is hypothesized that real-time operator-reviewer communication during live scanning played an important role in the identification of key morphologic abnormalities for review. Our study showed the Panoptiq system can be adopted reliably as a dynamic telepathology tool in aiding community laboratories in the triage of PBF cases for external diagnostic consultation. © 2014 John Wiley & Sons Ltd.

Improved dynamic analysis method using load-dependent Ritz vectors

NASA Technical Reports Server (NTRS)

Escobedo-Torres, J.; Ricles, J. M.

1993-01-01

The dynamic analysis of large space structures is important in order to predict their behavior under operating conditions. Computer models of large space structures are characterized by having a large number of degrees of freedom, and the computational effort required to carry out the analysis is very large. Conventional methods of solution utilize a subset of the eigenvectors of the system, but for systems with many degrees of freedom, the solution of the eigenproblem is in many cases the most costly phase of the analysis. For this reason, alternate solution methods need to be considered. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. The load dependent Ritz vector method is presented as an alternative to the classical normal mode methods for obtaining dynamic responses of large space structures. A simplified model of a space station is used to compare results. Results show that the load dependent Ritz vector method predicts the dynamic response better than the classical normal mode method. Even though this alternate method is very promising, further studies are necessary to fully understand its attributes and limitations.

A Generalized Framework for Reduced-Order Modeling of a Wind Turbine Wake

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, Nicholas; Viggiano, Bianca; Calaf, Marc

A reduced-order model for a wind turbine wake is sought from large eddy simulation data. Fluctuating velocity fields are combined in the correlation tensor to form the kernel of the proper orthogonal decomposition (POD). Proper orthogonal decomposition modes resulting from the decomposition represent the spatially coherent turbulence structures in the wind turbine wake; eigenvalues delineate the relative amount of turbulent kinetic energy associated with each mode. Back-projecting the POD modes onto the velocity snapshots produces dynamic coefficients that express the amplitude of each mode in time. A reduced-order model of the wind turbine wake (wakeROM) is defined through a seriesmore » of polynomial parameters that quantify mode interaction and the evolution of each POD mode coefficients. The resulting system of ordinary differential equations models the wind turbine wake composed only of the large-scale turbulent dynamics identified by the POD. Tikhonov regularization is used to recalibrate the dynamical system by adding additional constraints to the minimization seeking polynomial parameters, reducing error in the modeled mode coefficients. The wakeROM is periodically reinitialized with new initial conditions found by relating the incoming turbulent velocity to the POD mode coefficients through a series of open-loop transfer functions. The wakeROM reproduces mode coefficients to within 25.2%, quantified through the normalized root-mean-square error. A high-level view of the modeling approach is provided as a platform to discuss promising research directions, alternate processes that could benefit stability and efficiency, and desired extensions of the wakeROM.« less

Resistive wall instabilities and tearing mode dynamics in the EXTRAP T2R thin shell reversed-field pinch

NASA Astrophysics Data System (ADS)

Malmberg, J.-A.; Brunsell, P. R.

2002-01-01

Observations of resistive wall instabilities and tearing mode dynamics in the EXTRAP T2R thin shell (τw=6 ms) reversed field pinch are described. A nonresonant mode (m=1,n=-10) with the same handedness as the internal field grows nearly exponentially with an average growth time of about 2.6 ms (less than 1/2 of the shell time) consistent with linear stability theory. The externally nonresonant unstable modes (m=1,n>0), predicted by linear stability theory, are observed to have only low amplitudes (in the normal low-Θ operation mode of the device). The radial field of the dominant internally resonant tearing modes (m=1,n=-15 to n=-12) remain low due to spontaneous fast mode rotation, corresponding to angular phase velocities up to 280 krad/s. Phase aligned mode structures are observed to rotate toroidally with an average angular velocity of 40 krad/s, in the opposite direction of the plasma current. Toward the end of the discharge, the radial field of the internally resonant modes grows as the modes slow down and become wall-locked, in agreement with nonlinear computations. Fast rotation of the internally resonant modes has been observed only recently and is attributed to a change of the front-end system (vacuum vessel, shell, and TF coil) of the device.

Blade loss transient dynamics analysis with flexible bladed disk

NASA Technical Reports Server (NTRS)

Gallardo, V. C.; Black, G.; Bach, L.; Cline, S.; Storace, A.

1983-01-01

The transient dynamic response of a flexible bladed disk on a flexible rotor in a two rotor system is formulated by modal synthesis and a Lagrangian approach. Only the nonequilibrated one diameter flexible mode is considered for the flexible bladed disk, while the two flexible rotors are represented by their normal modes. The flexible bladed disk motion is modeled as a combination of two one diameter standing waves, and is coupled inertially and gyroscopically to the flexible rotors. Application to a two rotor model shows that a flexible bladed disk on one rotor can be driven into resonance by an unbalance in the other rotor, and at a frequency equal to the difference in the rotor speeds.

Kinetic theory of nonlinear diffusion in a weakly disordered nonlinear Schrödinger chain in the regime of homogeneous chaos.

PubMed

Basko, D M

2014-02-01

We study the discrete nonlinear Schröinger equation with weak disorder, focusing on the regime when the nonlinearity is, on the one hand, weak enough for the normal modes of the linear problem to remain well resolved but, on the other, strong enough for the dynamics of the normal mode amplitudes to be chaotic for almost all modes. We show that in this regime and in the limit of high temperature, the macroscopic density ρ satisfies the nonlinear diffusion equation with a density-dependent diffusion coefficient, D(ρ) = D(0)ρ(2). An explicit expression for D(0) is obtained in terms of the eigenfunctions and eigenvalues of the linear problem, which is then evaluated numerically. The role of the second conserved quantity (energy) in the transport is also quantitatively discussed.

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

NASA Astrophysics Data System (ADS)

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

1994-12-01

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

Chromophore-Dependent Intramolecular Exciton-Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics.

PubMed

Padula, Daniele; Lee, Myeong H; Claridge, Kirsten; Troisi, Alessandro

2017-11-02

In this paper, we adopt an approach suitable for monitoring the time evolution of the intramolecular contribution to the spectral density of a set of identical chromophores embedded in their respective environments. We apply the proposed method to the Fenna-Matthews-Olson (FMO) complex, with the objective to quantify the differences among site-dependent spectral densities and the impact of such differences on the exciton dynamics of the system. Our approach takes advantage of the vertical gradient approximation to reduce the computational demands of the normal modes analysis. We show that the region of the spectral density that is believed to strongly influence the exciton dynamics changes significantly in the timescale of tens of nanoseconds. We then studied the impact of the intramolecular vibrations on the exciton dynamics by considering a model of FMO in a vibronic basis and neglecting the interaction with the environment to isolate the role of the intramolecular exciton-vibration coupling. In agreement with the assumptions in the literature, we demonstrate that high frequency modes at energy much larger than the excitonic energy splitting have negligible influence on exciton dynamics despite the large exciton-vibration coupling. We also find that the impact of including the site-dependent spectral densities on exciton dynamics is not very significant, indicating that it may be acceptable to apply the same spectral density on all sites. However, care needs to be taken for the description of the exciton-vibrational coupling in the low frequency part of intramolecular modes because exciton dynamics is more susceptible to low frequency modes despite their small Huang-Rhys factors.

Structural dynamic model obtained from flight use with piloted simulation and handling qualities analysis

NASA Technical Reports Server (NTRS)

Powers, Bruce G.

1996-01-01

The ability to use flight data to determine an aircraft model with structural dynamic effects suitable for piloted simulation. and handling qualities analysis has been developed. This technique was demonstrated using SR-71 flight test data. For the SR-71 aircraft, the most significant structural response is the longitudinal first-bending mode. This mode was modeled as a second-order system, and the other higher order modes were modeled as a time delay. The distribution of the modal response at various fuselage locations was developed using a uniform beam solution, which can be calibrated using flight data. This approach was compared to the mode shape obtained from the ground vibration test, and the general form of the uniform beam solution was found to be a good representation of the mode shape in the areas of interest. To calibrate the solution, pitch-rate and normal-acceleration instrumentation is required for at least two locations. With the resulting structural model incorporated into the simulation, a good representation of the flight characteristics was provided for handling qualities analysis and piloted simulation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Comandi, G.L.; Chiofalo, M.L.; Toncelli, R.

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

Interactions of the Salience Network and Its Subsystems with the Default-Mode and the Central-Executive Networks in Normal Aging and Mild Cognitive Impairment.

PubMed

Chand, Ganesh B; Wu, Junjie; Hajjar, Ihab; Qiu, Deqiang

2017-09-01

Previous functional magnetic resonance imaging (fMRI) investigations suggest that the intrinsically organized large-scale networks and the interaction between them might be crucial for cognitive activities. A triple network model, which consists of the default-mode network, salience network, and central-executive network, has been recently used to understand the connectivity patterns of the cognitively normal brains versus the brains with disorders. This model suggests that the salience network dynamically controls the default-mode and central-executive networks in healthy young individuals. However, the patterns of interactions have remained largely unknown in healthy aging or those with cognitive decline. In this study, we assess the patterns of interactions between the three networks using dynamical causal modeling in resting state fMRI data and compare them between subjects with normal cognition and mild cognitive impairment (MCI). In healthy elderly subjects, our analysis showed that the salience network, especially its dorsal subnetwork, modulates the interaction between the default-mode network and the central-executive network (Mann-Whitney U test; p < 0.05), which was consistent with the pattern of interaction reported in young adults. In contrast, this pattern of modulation by salience network was disrupted in MCI (p < 0.05). Furthermore, the degree of disruption in salience network control correlated significantly with lower overall cognitive performance measured by Montreal Cognitive Assessment (r = 0.295; p < 0.05). This study suggests that a disruption of the salience network control, especially the dorsal salience network, over other networks provides a neuronal basis for cognitive decline and may be a candidate neuroimaging biomarker of cognitive impairment.

Magnetic energy storage and the nightside magnetosphere-ionosphere coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horton, W.; Pekker, M.; Doxas, I.

1998-05-01

The change m in the magnetic energy stored m in the Earth`s magnetotail as a function of the solar wind, BIF conditions are investigated using an empirical magnetic field model. The results are used to calculate the two normal modes contained m in the low-dimensional global model called WINDMI for the solar wind driven magnetosphere-ionosphere system. The coupling of the magnetosphere-ionosphere (MI) through the nightside region 1 current loop transfers power to the ionosphere through two modes: a fast (period of minutes) oscillation and a slow (period of one hour) geotail cavity mode. The solar wind drives both modes mmore » in the substorm dynamics.« less

Extensions to the instantaneous normal mode analysis of cluster dynamics: Diffusion constants and the role of rotations in clusters

NASA Astrophysics Data System (ADS)

Adams, John E.; Stratt, Richard M.

1990-08-01

For the instantaneous normal mode analysis method to be generally useful in studying the dynamics of clusters of arbitrary size, it ought to yield values of atomic self-diffusion constants which agree with those derived directly from molecular dynamics calculations. The present study proposes that such agreement indeed can be obtained if a sufficiently sophisticated formalism for computing the diffusion constant is adopted, such as the one suggested by Madan, Keyes, and Seeley [J. Chem. Phys. 92, 7565 (1990)]. In order to implement this particular formalism, however, we have found it necessary to pay particular attention to the removal from the computed spectra of spurious rotational contributions. The utility of the formalism is demonstrated via a study of small argon clusters, for which numerous results generated using other approaches are available. We find the same temperature dependence of the Ar13 self-diffusion constant that Beck and Marchioro [J. Chem. Phys. 93, 1347 (1990)] do from their direct calculation of the velocity autocorrelation function: The diffusion constant rises quickly from zero to a liquid-like value as the cluster goes through (the finite-size equivalent of) the melting transition.

Numerical Analysis of Stochastic Dynamical Systems in the Medium-Frequency Range

DTIC Science & Technology

2003-02-01

frequency vibration analysis such as the statistical energy analysis (SEA), the traditional modal analysis (well-suited for high and low: frequency...that the first few structural normal modes primarily constitute the total response. In the higher frequency range, the statistical energy analysis (SEA

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

NASA Astrophysics Data System (ADS)

Ehrhardt, David A.; Allen, Matthew S.

2016-08-01

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

Non-Linear Structural Dynamics Characterization using a Scanning Laser Vibrometer

NASA Technical Reports Server (NTRS)

Pai, P. F.; Lee, S.-Y.

2003-01-01

This paper presents the use of a scanning laser vibrometer and a signal decomposition method to characterize non-linear dynamics of highly flexible structures. A Polytec PI PSV-200 scanning laser vibrometer is used to measure transverse velocities of points on a structure subjected to a harmonic excitation. Velocity profiles at different times are constructed using the measured velocities, and then each velocity profile is decomposed using the first four linear mode shapes and a least-squares curve-fitting method. From the variations of the obtained modal \\ielocities with time we search for possible non-linear phenomena. A cantilevered titanium alloy beam subjected to harmonic base-excitations around the second. third, and fourth natural frequencies are examined in detail. Influences of the fixture mass. gravity. mass centers of mode shapes. and non-linearities are evaluated. Geometrically exact equations governing the planar, harmonic large-amplitude vibrations of beams are solved for operational deflection shapes using the multiple shooting method. Experimental results show the existence of 1:3 and 1:2:3 external and internal resonances. energy transfer from high-frequency modes to the first mode. and amplitude- and phase- modulation among several modes. Moreover, the existence of non-linear normal modes is found to be questionable.

Noncircular features in Saturn's rings III: The Cassini Division

NASA Astrophysics Data System (ADS)

French, Richard G.; Nicholson, Philip D.; McGhee-French, Colleen A.; Lonergan, Katherine; Sepersky, Talia; Hedman, Mathew M.; Marouf, Essam A.; Colwell, Joshua E.

2016-08-01

We have conducted a comprehensive survey of 22 sharp-edged ringlets and gaps in the Cassini Division of Saturn's rings, making use of nearly 200 high-SNR stellar and radio occultation chords obtained by the Cassini VIMS, UVIS, and RSS instruments between 2005 and 2013. We measure eccentricities from as small as ae = 80 m to nearly 30 km, free normal modes with amplitudes from ∼ 0.1 to 4.1 km, and detectable inclinations as small as asini = 0.2 km. Throughout the entire region, the Mimas 2.1 ILR (inner Lindblad resonance) produces systematic forced m = 2 distortions that quantitatively match the expected amplitudes, phases, and pattern speed. The narrow Russell, Jeffreys, Kuiper, Bessel, and Barnard gaps are simplest, and do not contain dense ringlets. Their outer edges are generally quite sharp and four of them are circular to within ∼0.25 km, whereas most of the inner gap edges have significant eccentricities. Three gaps are more complex, containing one or more isolated ringlets. First among these is the 361 km-wide Huygens gap, containing two ringlets. The wider Huygens ringlet has nearly identical eccentricities on the two edges, in addition to OLR-type (outer Lindblad resonance) normal modes on the inner edge and ILR-type modes on the outer edge. A secondary m = 1 (eccentric) mode is present on the outer edge of the ringlet, with a pattern speed similar to that of the B ring's outer edge. Variations in the ringlet's width are complex, but are statistically consistent with the expected magnitudes resulting from the random superposition of the multiple normal modes on the two edges. Also present in the Huygens gap is the very narrow so-called Strange ringlet, with a substantial eccentricity and inclination, as well as both ILR- and OLR-type normal modes. The 100 km-wide Herschel gap's inner edge is highly eccentric, with at least seven ILR-type normal modes. The outer gap edge is also eccentric, and hosts four OLR-type normal modes, and a secondary m = 1 mode with a pattern speed quite close to that of the B ring's outer edge. The Herschel ringlet itself is eccentric and inclined, but neither the pericenters nor the nodes are well-aligned. The third of the complex gaps is the 241 km-wide Laplace gap, containing the Laplace ringlet. Both gap edges are eccentric, with very similar pericenter longitudes and apsidal precession rates, in spite of their large radial separation. The Laplace ringlet has eccentric edges and an abundance of normal modes. Like the Herschel ringlet, the Laplace ringlet does not precess rigidly and does not conform to the usual dynamical picture of an eccentric ringlet. Normal modes are abundant in the Cassini Division. Consistently, we find free ILR-type normal modes (m > 0) at the outer edges of ringlets and the inner edges of gaps, and free OLR-type normal modes (m ≤ 0) at inner ringlet edges and outer edges of gaps, as expected from the resonant cavity model of normal modes. We estimate the surface density of ring features from the resonance locations of the normal modes. The Cassini Division exhibits apsidal precession rates that are anomalously large, compared to the predicted values based on Saturn's zonal gravity field. The overall radial trend matches the secular contribution expected from the nearby B ring, assuming a surface mass density of Σ = 100 gm cm-2. However, the outer edges of the Huygens and Laplace gaps, and the outer edge of the Laplace ringlet, have conspicuously large residuals, exceeding their predicted precession rates by more than 0 .03∘d-1 . These patterns are probably the result of forcing by nearby ring material, but at present we cannot account for them in detail.

Macroscopic response in active nonlinear photonic crystals.

PubMed

Alagappan, Gandhi; John, Sajeev; Li, Er Ping

2013-09-15

We derive macroscopic equations of motion for the slowly varying electric field amplitude in three-dimensional active nonlinear optical nanostructures. We show that the microscopic Maxwell equations and polarization dynamics can be simplified to a macroscopic one-dimensional problem in the direction of group velocity. For a three-level active material, we derive the steady-state equations for normal mode frequency, threshold pumping, nonlinear Bloch mode amplitude, and lasing in photonic crystals. Our analytical results accurately recapture the results of exact numerical methods.

A practical method to avoid zero-point leak in molecular dynamics calculations: application to the water dimer.

PubMed

Czakó, Gábor; Kaledin, Alexey L; Bowman, Joel M

2010-04-28

We report the implementation of a previously suggested method to constrain a molecular system to have mode-specific vibrational energy greater than or equal to the zero-point energy in quasiclassical trajectory calculations [J. M. Bowman et al., J. Chem. Phys. 91, 2859 (1989); W. H. Miller et al., J. Chem. Phys. 91, 2863 (1989)]. The implementation is made practical by using a technique described recently [G. Czako and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], where a normal-mode analysis is performed during the course of a trajectory and which gives only real-valued frequencies. The method is applied to the water dimer, where its effectiveness is shown by computing mode energies as a function of integration time. Radial distribution functions are also calculated using constrained quasiclassical and standard classical molecular dynamics at low temperature and at 300 K and compared to rigorous quantum path integral calculations.

The Ribosome Shape Directs mRNA Translocation through Entrance and Exit Dynamics

USDA-ARS?s Scientific Manuscript database

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs (transfer ribonucleic acids) and mRNA (messenger ribonucleic acid); here the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal struc...

Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model

NASA Astrophysics Data System (ADS)

Fujisaki, Hiroshi; Yagi, Kiyoshi; Kikuchi, Hiroto; Takami, Toshiya; Stock, Gerhard

2017-01-01

Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure-dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations.

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

PubMed

Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

2012-07-01

The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

Finite element normal mode analysis of resistance welding jointed of dissimilar plate hat structure

NASA Astrophysics Data System (ADS)

Nazri, N. A.; Sani, M. S. M.

2017-10-01

Structural joints offer connection between structural element (beam, plate, solid etc.) in order to build a whole assembled structure. The complex behaviour of connecting elements plays a valuable role in characteristics of dynamic such as natural frequencies and mode shapes. In automotive structures, the trustworthiness arrangement of the structure extremely depends on joints. In this paper, top hat structure is modelled and designed with spot welding joint using dissimilar materials which is mild steel 1010 and stainless steel 304, using finite element software. Different types of connector elements such as rigid body element (RBE2), welding joint element (CWELD), and bar element (CBAR) are applied to represent real connection between two dissimilar plates. Normal mode analysis is simulated with different types of joining element in order to determine modal properties. Natural frequencies using RBE2, CBAR and CWELD are compared to equivalent rigid body method. Connection that gives the lowest percentage error among these three will be selected as the most reliable joining for resistance spot weld. From the analysis, it is shown that CWELD is better compared to others in term of weld joining among dissimilar plate materials. It is expected that joint modelling of finite element plays significant role in structural dynamics.

Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode.

PubMed

Bastida, Adolfo; Zúñiga, José; Requena, Alberto; Miguel, Beatriz; Candela, María Emilia; Soler, Miguel Angel

2016-01-21

Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.

Structural response calculations for a reverse ballistics test of an earth penetrator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alves, D.F.; Goudreau, G.L.

1976-08-01

A dynamic response calculation has been performed on a half-scale earth penetrator to be tested on a reverse ballistics test in Aug. 1976. In this test a 14 in. dia sandstone target is fired at the EP at 1800 ft/sec at normal impact. Basically two types of calculations were made. The first utilized an axisymmetric, finite element code DTVIS2 in the dynamic mode and with materials having linear elastic properties. CRT's radial and axial force histories were smoothed to eliminate grid encounter frequency and applied to the nodal points along the nose of the penetrator. Given these inputs DTVIS2 thenmore » calculated the internal dynamic response. Secondly, SAP4, a structural analysis code, is utilized to calculate axial frequencies and mode shapes of the structure. A special one dimensional display facilitates interpretation of the mode shape. DTVIS2 and SAP4 use a common mesh description. Special considerations in the calculation are the assessment of the effect of gaps and preload and the internal axial sliding of components.« less

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

PubMed

Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc

2017-03-14

Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effectsmore » in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.« less

Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations.

PubMed

Soler, Miguel A; Zúñiga, José; Requena, Alberto; Bastida, Adolfo

2017-02-01

Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.

Three-dimensional vesicles under shear flow: numerical study of dynamics and phase diagram.

PubMed

Biben, Thierry; Farutin, Alexander; Misbah, Chaouqi

2011-03-01

The study of vesicles under flow, a model system for red blood cells (RBCs), is an essential step in understanding various intricate dynamics exhibited by RBCs in vivo and in vitro. Quantitative three-dimensional analyses of vesicles under flow are presented. The regions of parameters to produce tumbling (TB), tank-treating, vacillating-breathing (VB), and even kayaking (or spinning) modes are determined. New qualitative features are found: (i) a significant widening of the VB mode region in parameter space upon increasing shear rate γ and (ii) a robustness of normalized period of TB and VB with γ. Analytical support is also provided. We make a comparison with existing experimental results. In particular, we find that the phase diagram of the various dynamics depends on three dimensionless control parameters, while a recent experimental work reported that only two are sufficient.

Macroscopic damping model for structural dynamics with random polycrystalline configurations

NASA Astrophysics Data System (ADS)

Yang, Yantao; Cui, Junzhi; Yu, Yifan; Xiang, Meizhen

2018-06-01

In this paper the macroscopic damping model for dynamical behavior of the structures with random polycrystalline configurations at micro-nano scales is established. First, the global motion equation of a crystal is decomposed into a set of motion equations with independent single degree of freedom (SDOF) along normal discrete modes, and then damping behavior is introduced into each SDOF motion. Through the interpolation of discrete modes, the continuous representation of damping effects for the crystal is obtained. Second, from energy conservation law the expression of the damping coefficient is derived, and the approximate formula of damping coefficient is given. Next, the continuous damping coefficient for polycrystalline cluster is expressed, the continuous dynamical equation with damping term is obtained, and then the concrete damping coefficients for a polycrystalline Cu sample are shown. Finally, by using statistical two-scale homogenization method, the macroscopic homogenized dynamical equation containing damping term for the structures with random polycrystalline configurations at micro-nano scales is set up.

CSM solutions of rotating blade dynamics using integrating matrices

NASA Technical Reports Server (NTRS)

Lakin, William D.

1992-01-01

The dynamic behavior of flexible rotating beams continues to receive considerable research attention as it constitutes a fundamental problem in applied mechanics. Further, beams comprise parts of many rotating structures of engineering significance. A topic of particular interest at the present time involves the development of techniques for obtaining the behavior in both space and time of a rotor acted upon by a simple airload loading. Most current work on problems of this type use solution techniques based on normal modes. It is certainly true that normal modes cannot be disregarded, as knowledge of natural blade frequencies is always important. However, the present work has considered a computational structural mechanics (CSM) approach to rotor blade dynamics problems in which the physical properties of the rotor blade provide input for a direct numerical solution of the relevant boundary-and-initial-value problem. Analysis of the dynamics of a given rotor system may require solution of the governing equations over a long time interval corresponding to many revolutions of the loaded flexible blade. For this reason, most of the common techniques in computational mechanics, which treat the space-time behavior concurrently, cannot be applied to the rotor dynamics problem without a large expenditure of computational resources. By contrast, the integrating matrix technique of computational mechanics has the ability to consistently incorporate boundary conditions and 'remove' dependence on a space variable. For problems involving both space and time, this feature of the integrating matrix approach thus can generate a 'splitting' which forms the basis of an efficient CSM method for numerical solution of rotor dynamics problems.

Combined inelastic neutron scattering and solid state DFT study of dynamics of hydrogen atoms in trioctahedral 1M phlogopite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smrčok, Ľubomír; Kolesnikov, Alexander I; Rieder, Milan

2012-01-01

Inelastic neutron scattering (INS) was used to study vibrational dynamics of the hydrogen atoms in natural trioctahedral phlogopite, K0.93Na0.03(Mg2.47Fe0.22Al0.16Fe0.04Tl0.06)[Si2.84Al1.16]O10OH1.71F0.28Cl0.01, within the 50-1000 cm-1 energy range. The INS spectra collected using direct geometry spectrometer SEQUOIA at ORNL were interpreted by means of the solid-state DFT calculations covering both normal mode analysis and molecular dynamics. To optimize the structure and to calculate the vibrational modes under harmonic approximation both a hybrid PBE0 and the AM05 functional were used, while the molecular dynamics calculations (60ps/1fs) were performed only with the computationally less-demanding AM05 functional. The main contributions to the dominant band within ~750-550more » cm-1 are symmetric and antisymmetric Mg-O-H bending modes, overlapping with the skeletal stretching and bending modes causing weaker secondary movements of H atoms of inner hydroxyl groups. Signatures of the Mg-O-H bending modes appear down to ~400 cm-1, where a region of octahedra deformation modes starts. These deformations cause just shallow movements of the hydrogen atoms and are mirrored by the modes with close vibrational energies. The region from ~330 cm-1 down to the low energy end of the spectrum portrays induced vibrations of the H atoms caused by deformation of individual polyhedra, translational vibrations of the parts of the 2:1 layer relative one to another, and librational and translational vibrations of the layer. The main difference between the INS spectrum of dioctahedral Al-muscovite and trioctahedral Mg-phlogopite is that the Mg-O-H modes are all assigned to in-plane vibrations of the respective hydrogen atoms.« less

Combined inelastic neutron scattering and solid-state DFT study of dynamics of hydrogen atoms in trioctahedral 1 M phlogopite

NASA Astrophysics Data System (ADS)

Smrčok, L'ubomír; Kolesnikov, Alexander I.; Rieder, Milan

2012-10-01

Inelastic neutron scattering (INS) was used to study the vibrational dynamics of the hydrogen atoms in natural trioctahedral phlogopite, K0.93Na0.03(Mg2.47Fe0.22Al0.16Fe0.04Tl0.06)[Si2.84Al1.16]O10OH1.71F0.28Cl0.01, within the 50-1,000 cm-1 energy range. The INS spectra collected using direct geometry spectrometer SEQUOIA (ORNL) were interpreted by means of the solid-state DFT calculations covering both normal mode analysis and molecular dynamics. To optimize the structure and to calculate the vibrational modes under harmonic approximation, both a hybrid PBE0 and the AM05 functional were used, while the molecular dynamics calculations (60 ps/1 fs) were performed only with the computationally less-demanding AM05 functional. The main contributions to the dominant band within ~750-550 cm-1 are symmetric and antisymmetric Mg-O-H bending modes, overlapping with the skeletal stretching and bending modes causing weaker secondary movements of H atoms of inner hydroxyl groups. Signatures of the Mg-O-H bending modes appear down to ~400 cm-1, where a region of octahedra deformation modes starts. These deformations cause just shallow movements of the hydrogen atoms and are mirrored by the modes with close vibrational energies. The region from ~330 cm-1 down to the low-energy end of the spectrum portrays induced vibrations of the H atoms caused by deformation of individual polyhedra, translational vibrations of the parts of the 2:1 layer relative one to another, and librational and translational vibrations of the layer. The main difference between the INS spectrum of dioctahedral Al-muscovite and trioctahedral Mg-phlogopite is that the Mg-O-H modes are all assigned to in-plane vibrations of the respective hydrogen atoms.

Spatio-temporal analysis of irregular vocal fold oscillations: Biphonation due to desynchronization of spatial modes

NASA Astrophysics Data System (ADS)

Neubauer, Jürgen; Mergell, Patrick; Eysholdt, Ulrich; Herzel, Hanspeter

2001-12-01

This report is on direct observation and modal analysis of irregular spatio-temporal vibration patterns of vocal fold pathologies in vivo. The observed oscillation patterns are described quantitatively with multiline kymograms, spectral analysis, and spatio-temporal plots. The complex spatio-temporal vibration patterns are decomposed by empirical orthogonal functions into independent vibratory modes. It is shown quantitatively that biphonation can be induced either by left-right asymmetry or by desynchronized anterior-posterior vibratory modes, and the term ``AP (anterior-posterior) biphonation'' is introduced. The presented phonation examples show that for normal phonation the first two modes sufficiently explain the glottal dynamics. The spatio-temporal oscillation pattern associated with biphonation due to left-right asymmetry can be explained by the first three modes. Higher-order modes are required to describe the pattern for biphonation induced by anterior-posterior vibrations. Spatial irregularity is quantified by an entropy measure, which is significantly higher for irregular phonation than for normal phonation. Two asymmetry measures are introduced: the left-right asymmetry and the anterior-posterior asymmetry, as the ratios of the fundamental frequencies of left and right vocal fold and of anterior-posterior modes, respectively. These quantities clearly differentiate between left-right biphonation and anterior-posterior biphonation. This paper proposes methods to analyze quantitatively irregular vocal fold contour patterns in vivo and complements previous findings of desynchronization of vibration modes in computer modes and in in vitro experiments.

The Dynamics of Violence and Homelessness among Young Families

ERIC Educational Resources Information Center

Swick, Kevin James

2008-01-01

Violence is one of the most prevalent elements in the lives of homeless families with young children. This violence may come in various forms: domestic violence, street violence, violence in one's childhood, witnessing violence, and other avenues and modes. Violence disrupts the normal bonding between parent and child. It isolates and degrades…

Dynamic testing and analysis of extension-twist-coupled composite tubular spars

NASA Astrophysics Data System (ADS)

Lake, Renee C.; Izapanah, Amir P.; Baucon, Robert M.

The results from a study aimed at improving the dynamic and aerodynamic characteristics of composite rotor blades through the use of extension-twist elastic coupling are presented. A set of extension-twist-coupled composite tubular spars, representative of the primary load carrying structure within a helicopter rotor blade, was manufactured using four plies of woven graphite/epoxy cloth 'prepreg.' These spars were non-circular in cross section design and were therefore subject to warping deformations. Three cross-sectional geometries were developed: square, D-shape, and flattened ellipse. Results from free-free vibration tests of the spars were compared with results from normal modes and frequency analyses of companion shell-finite-element models developed in MSC/NASTRAN. Five global or 'non-shell' modes were identified within the 0-2000 Hz range for each spar. The frequencies and associated mode shapes for the D-shape spar were correlated with analytical results, showing agreement within 13.8 percent. Frequencies corresponding to the five global mode shapes for the square spar agreed within 9.5 percent of the analytical results. Five global modes were similarly identified for the elliptical spar and agreed within 4.9 percent of the respective analytical results.

Dynamic testing and analysis of extension-twist-coupled composite tubular spars

NASA Technical Reports Server (NTRS)

Lake, Renee C.; Izapanah, Amir P.; Baucon, Robert M.

1992-01-01

The results from a study aimed at improving the dynamic and aerodynamic characteristics of composite rotor blades through the use of extension-twist elastic coupling are presented. A set of extension-twist-coupled composite tubular spars, representative of the primary load carrying structure within a helicopter rotor blade, was manufactured using four plies of woven graphite/epoxy cloth 'prepreg.' These spars were non-circular in cross section design and were therefore subject to warping deformations. Three cross-sectional geometries were developed: square, D-shape, and flattened ellipse. Results from free-free vibration tests of the spars were compared with results from normal modes and frequency analyses of companion shell-finite-element models developed in MSC/NASTRAN. Five global or 'non-shell' modes were identified within the 0-2000 Hz range for each spar. The frequencies and associated mode shapes for the D-shape spar were correlated with analytical results, showing agreement within 13.8 percent. Frequencies corresponding to the five global mode shapes for the square spar agreed within 9.5 percent of the analytical results. Five global modes were similarly identified for the elliptical spar and agreed within 4.9 percent of the respective analytical results.

Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family

PubMed Central

Maguid, Sandra; Fernandez-Alberti, Sebastian; Ferrelli, Leticia; Echave, Julian

2005-01-01

We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features. PMID:15749782

Structural dynamics and vibrations of damped, aircraft-type structures

NASA Technical Reports Server (NTRS)

Young, Maurice I.

1992-01-01

Engineering preliminary design methods for approximating and predicting the effects of viscous or equivalent viscous-type damping treatments on the free and forced vibration of lightly damped aircraft-type structures are developed. Similar developments are presented for dynamic hysteresis viscoelastic-type damping treatments. It is shown by both engineering analysis and numerical illustrations that the intermodal coupling of the undamped modes arising from the introduction of damping may be neglected in applying these preliminary design methods, except when dissimilar modes of these lightly damped, complex aircraft-type structures have identical or nearly identical natural frequencies. In such cases, it is shown that a relatively simple, additional interaction calculation between pairs of modes exhibiting this 'modal response' phenomenon suffices in the prediction of interacting modal damping fractions. The accuracy of the methods is shown to be very good to excellent, depending on the normal natural frequency separation of the system modes, thereby permitting a relatively simple preliminary design approach. This approach is shown to be a natural precursor to elaborate finite element, digital computer design computations in evaluating the type, quantity, and location of damping treatment.

oGNM: online computation of structural dynamics using the Gaussian Network Model

PubMed Central

Yang, Lee-Wei; Rader, A. J.; Liu, Xiong; Jursa, Cristopher Jon; Chen, Shann Ching; Karimi, Hassan A.; Bahar, Ivet

2006-01-01

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5–6 orders of magnitude faster than those using conventional normal mode analyses. Two cases studies illustrate the utility of oGNM. The first shows that the thermal fluctuations predicted for 1250 non-homologous proteins correlate well with X-ray crystallographic data over a broad range [7.3–15 Å] of inter-residue interaction cutoff distances and the correlations improve with increasing observation temperatures. The second study, focused on 64 oligonucleotides and oligonucleotide–protein complexes, shows that good agreement with experiments is achieved by representing each nucleotide by three GNM nodes (as opposed to one-node-per-residue in proteins) along with uniform interaction ranges for all components of the complexes. These results open the way to a rapid assessment of the dynamics of DNA/RNA-containing complexes. The server can be accessed at . PMID:16845002

Numerical computation of linear instability of detonations

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry; Kasimov, Aslan

2017-11-01

We propose a method to study linear stability of detonations by direct numerical computation. The linearized governing equations together with the shock-evolution equation are solved in the shock-attached frame using a high-resolution numerical algorithm. The computed results are processed by the Dynamic Mode Decomposition technique to generate dispersion relations. The method is applied to the reactive Euler equations with simple-depletion chemistry as well as more complex multistep chemistry. The results are compared with those known from normal-mode analysis. We acknowledge financial support from King Abdullah University of Science and Technology.

Development and Integration of Control System Models

NASA Technical Reports Server (NTRS)

Kim, Young K.

1998-01-01

The computer simulation tool, TREETOPS, has been upgraded and used at NASA/MSFC to model various complicated mechanical systems and to perform their dynamics and control analysis with pointing control systems. A TREETOPS model of Advanced X-ray Astrophysics Facility - Imaging (AXAF-1) dynamics and control system was developed to evaluate the AXAF-I pointing performance for Normal Pointing Mode. An optical model of Shooting Star Experiment (SSE) was also developed and its optical performance analysis was done using the MACOS software.

Some studies on the use of NASTRAN for nuclear power plant structural analysis and design

NASA Technical Reports Server (NTRS)

Setlur, A. V.; Valathur, M.

1973-01-01

Studies made on the use of NASTRAN for nuclear power plant analysis and design are presented. These studies indicate that NASTRAN could be effectively used for static, dynamic and special purpose problems encountered in the design of such plants. Normal mode capability of NASTRAN is extended through a post-processor program to handle seismic analysis. Static and dynamic substructuring is discussed. Extension of NASTRAN to include the needs in the civil engineering industry is discussed.

A new algorithm for construction of coarse-grained sites of large biomolecules.

PubMed

Li, Min; Zhang, John Z H; Xia, Fei

2016-04-05

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.

Molecular dynamics: deciphering the data.

PubMed

Dauber-Osguthorpe, P; Maunder, C M; Osguthorpe, D J

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerned motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

Molecular dynamics: Deciphering the data

NASA Astrophysics Data System (ADS)

Dauber-Osguthorpe, Pnina; Maunder, Colette M.; Osguthorpe, David J.

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerted motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

Rapid flattening of butterfly pitch angle distributions of radiation belt electrons by whistler-mode chorus

NASA Astrophysics Data System (ADS)

Yang, Chang; Su, Zhenpeng; Xiao, Fuliang; Zheng, Huinan; Wang, Yuming; Wang, Shui; Spence, H. E.; Reeves, G. D.; Baker, D. N.; Blake, J. B.; Funsten, H. O.

2016-08-01

Van Allen radiation belt electrons exhibit complex dynamics during geomagnetically active periods. Investigation of electron pitch angle distributions (PADs) can provide important information on the dominant physical mechanisms controlling radiation belt behaviors. Here we report a storm time radiation belt event where energetic electron PADs changed from butterfly distributions to normal or flattop distributions within several hours. Van Allen Probes observations showed that the flattening of butterfly PADs was closely related to the occurrence of whistler-mode chorus waves. Two-dimensional quasi-linear STEERB simulations demonstrate that the observed chorus can resonantly accelerate the near-equatorially trapped electrons and rapidly flatten the corresponding electron butterfly PADs. These results provide a new insight on how chorus waves affect the dynamic evolution of radiation belt electrons.

A variational approach to dynamics of flexible multibody systems

NASA Technical Reports Server (NTRS)

Wu, Shih-Chin; Haug, Edward J.; Kim, Sung-Soo

1989-01-01

This paper presents a variational formulation of constrained dynamics of flexible multibody systems, using a vector-variational calculus approach. Body reference frames are used to define global position and orientation of individual bodies in the system, located and oriented by position of its origin and Euler parameters, respectively. Small strain linear elastic deformation of individual components, relative to their body references frames, is defined by linear combinations of deformation modes that are induced by constraint reaction forces and normal modes of vibration. A library of kinematic couplings between flexible and/or rigid bodies is defined and analyzed. Variational equations of motion for multibody systems are obtained and reduced to mixed differential-algebraic equations of motion. A space structure that must deform during deployment is analyzed, to illustrate use of the methods developed.

Programmable controlled mode-locked fiber laser using a digital micromirror device.

PubMed

Liu, Wu; Fan, Jintao; Xie, Chen; Song, Youjian; Gu, Chenlin; Chai, Lu; Wang, Chingyue; Hu, Minglie

2017-05-15

A digital micromirror device (DMD)-based arbitrary spectrum amplitude shaper is incorporated into a large-mode-area photonic crystal fiber laser cavity. The shaper acts as an in-cavity programmable filter and provides large tunable dispersion from normal to anomalous. As a result, mode-locking is achieved in different dispersion regimes with watt-level high output power. By programming different filter profiles on the DMD, the laser generates femtosecond pulse with a tunable central wavelength and controllable bandwidth. Under conditions of suitable cavity dispersion and pump power, design-shaped spectra are directly obtained by varying the amplitude transfer function of the filter. The results show the versatility of the DMD-based in-cavity filter for flexible control of the pulse dynamics in a mode-locked fiber laser.

Mixing induced by a propagating normal mode in long term experiments

NASA Astrophysics Data System (ADS)

Dossmann, Yvan; Pollet, Florence; Odier, Philippe; Dauxois, Thierry

2017-04-01

The energy pathways from propagating internal waves to the scales of irreversible mixing in the ocean are numerous. The triadic resonant instability (TRI) is an intrinsic destabilization process that can lead to mixing away from topographies. It consists in the destabilization of a primary internal wave generation leading to the radiation of two secondary waves of lower frequencies and different wave vectors. In the process, internal wave energy is carried down to smaller scales. A previous study focused on the assessment of instantaneous turbulent fluxes fields associated with the TRI process in laboratory experiments [1]. The present study investigates the integrated impact of mixing processes induced by a propagative normal mode over long term experiments using a similar setup. Configurations for which the TRI process is either favored or inhibited are tackled. Optical measurements using the light attenuation technique allow to follow the internal waves dynamics and the evolution of the density profile between two runs of one hour typical duration. The horizontally averaged turbulent diffusivity Kt(z) and the mixing efficiency Γ are assessed. One finds values up to Kt = 10-6 m2/s and Γ = 11 %, with slightly larger values in the presence of TRI. The maximum value for Kt is measured at the position(s) of the maximum shear normal mode shear for both normal modes 1 and 2. The development of staircases in the density profile is observed after several hours of forcing. This mechanism can be explained by Phillips' argument by which sharp interfaces can form due to vertical variations of the buoyancy flux. The staircases are responsible for large variations in the vertical distribution of turbulent diffusivity. These results could help to refine parameterizations of the impact of low order normal modes in ocean mixing. Reference : [1] Dossmann et al. 2016, Mixing by internal waves quantified using combined PIV/PLIF technique, Experiments in Fluids, 57, 132.

Constrained maximum likelihood modal parameter identification applied to structural dynamics

NASA Astrophysics Data System (ADS)

El-Kafafy, Mahmoud; Peeters, Bart; Guillaume, Patrick; De Troyer, Tim

2016-05-01

A new modal parameter estimation method to directly establish modal models of structural dynamic systems satisfying two physically motivated constraints will be presented. The constraints imposed in the identified modal model are the reciprocity of the frequency response functions (FRFs) and the estimation of normal (real) modes. The motivation behind the first constraint (i.e. reciprocity) comes from the fact that modal analysis theory shows that the FRF matrix and therefore the residue matrices are symmetric for non-gyroscopic, non-circulatory, and passive mechanical systems. In other words, such types of systems are expected to obey Maxwell-Betti's reciprocity principle. The second constraint (i.e. real mode shapes) is motivated by the fact that analytical models of structures are assumed to either be undamped or proportional damped. Therefore, normal (real) modes are needed for comparison with these analytical models. The work done in this paper is a further development of a recently introduced modal parameter identification method called ML-MM that enables us to establish modal model that satisfies such motivated constraints. The proposed constrained ML-MM method is applied to two real experimental datasets measured on fully trimmed cars. This type of data is still considered as a significant challenge in modal analysis. The results clearly demonstrate the applicability of the method to real structures with significant non-proportional damping and high modal densities.

Time series analysis of collective motions in proteins

NASA Astrophysics Data System (ADS)

Alakent, Burak; Doruker, Pemra; ćamurdan, Mehmet C.

2004-01-01

The dynamics of α-amylase inhibitor tendamistat around its native state is investigated using time series analysis of the principal components of the Cα atomic displacements obtained from molecular dynamics trajectories. Collective motion along a principal component is modeled as a homogeneous nonstationary process, which is the result of the damped oscillations in local minima superimposed on a random walk. The motion in local minima is described by a stationary autoregressive moving average model, consisting of the frequency, damping factor, moving average parameters and random shock terms. Frequencies for the first 50 principal components are found to be in the 3-25 cm-1 range, which are well correlated with the principal component indices and also with atomistic normal mode analysis results. Damping factors, though their correlation is less pronounced, decrease as principal component indices increase, indicating that low frequency motions are less affected by friction. The existence of a positive moving average parameter indicates that the stochastic force term is likely to disturb the mode in opposite directions for two successive sampling times, showing the modes tendency to stay close to minimum. All these four parameters affect the mean square fluctuations of a principal mode within a single minimum. The inter-minima transitions are described by a random walk model, which is driven by a random shock term considerably smaller than that for the intra-minimum motion. The principal modes are classified into three subspaces based on their dynamics: essential, semiconstrained, and constrained, at least in partial consistency with previous studies. The Gaussian-type distributions of the intermediate modes, called "semiconstrained" modes, are explained by asserting that this random walk behavior is not completely free but between energy barriers.

Space Shuttle main engine powerhead structural modeling, stress and fatigue life analysis. Volume 2: Dynamics of blades and nozzles SSME HPFTP and HPOTP

NASA Technical Reports Server (NTRS)

Hammett, J. C.; Hayes, C. H.; Price, J. M.; Robinson, J. K.; Teal, G. A.; Thomson, J. M.; Tilley, D. M.; Welch, C. T.

1983-01-01

Normal modes of the blades and nozzles of the HPFTP and HPOTP are defined and potential driving forces for the blades are identified. The computer models used in blade analyses are described, with results. Similar information is given for the nozzles.

Effect of a Material Contrast on a Dynamic Rupture: 3-D

NASA Astrophysics Data System (ADS)

Harris, R. A.; Day, S. M.

2003-12-01

We use numerical simulations of spontaneously propagating ruptures to examine the effect of a material contrast on earthquake dynamics. We specifically study the case of a lateral contrast whereby the fault is the boundary between two different rock-types. This scenario was previously studied in two-dimensions by Harris and Day [BSSA, 1997], and Andrews and Ben-Zion [JGR, 1997], in addition to subsequent 2-D studies, but it has not been known if the two-dimensional results are applicable to the real three-dimensional world. The addition of the third dimension implies a transition from pure mode II (i.e., plane-strain) to mixed-mode crack dynamics, which is more complicated since in mode II the shear and normal stresses are coupled whereas in mode III (i.e., anti-plane strain) they are not coupled. We use a slip-weakening fracture criterion and examine the effect on an earthquake rupture of material contrasts of up to 50 percent across the fault zone. We find a surprisingly good agreement between our earlier 2-D results, and our 3-D results for along-strike propagation. We find that the analytical solution presented in Harris and Day [BSSA, 1997] does an excellent job at predicting the bilateral, along-strike rupture velocities for the three-dimensional situation. In contrast, the along-dip propagation behaves much as expected for a purely mode-III rupture, with the rupture velocities up-dip and down-dip showing the expected symmetries.

Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis

PubMed Central

Dorner, Mariah E; McMunn, Ryan D; Bartholow, Thomas G; Calhoon, Brecken E; Conlon, Michelle R; Dulli, Jessica M; Fehling, Samuel C; Fisher, Cody R; Hodgson, Shane W; Keenan, Shawn W; Kruger, Alyssa N; Mabin, Justin W; Mazula, Daniel L; Monte, Christopher A; Olthafer, Augustus; Sexton, Ashley E; Soderholm, Beatrice R; Strom, Alexander M; Hati, Sanchita

2015-01-01

Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide-range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of pro are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in Cα atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes. PMID:26130403

Nature of the octahedral tilting phase transitions in perovskites: A case study of CaMnO3

NASA Astrophysics Data System (ADS)

Klarbring, Johan; Simak, Sergei I.

2018-01-01

The temperature-induced antiferrodistortive (AFD) structural phase transitions in CaMnO3, a typical perovskite oxide, are studied using first-principles density functional theory calculations. These transitions are caused by tilting of the MnO6 octahedra that are related to unstable phonon modes in the high-symmetry cubic perovskite phase. Transitions due to octahedral tilting in perovskites normally are believed to fit into the standard soft-mode picture of displacive phase transitions. We calculate phonon-dispersion relations and potential-energy landscapes as functions of the unstable phonon modes and argue based on the results that the phase transitions are better described as being of order-disorder type. This means that the cubic phase emerges as a dynamical average when the system hops between local minima on the potential-energy surface. We then perform ab initio molecular dynamics simulations and find explicit evidence of the order-disorder dynamics in the system. Our conclusions are expected to be valid for other perovskite oxides, and we finally suggest how to predict the nature (displacive or order-disorder) of the AFD phase transitions in any perovskite system.

Earth's Outer Core Properties Estimated Using Bayesian Inversion of Normal Mode Eigenfrequencies

NASA Astrophysics Data System (ADS)

Irving, J. C. E.; Cottaar, S.; Lekic, V.

2016-12-01

The outer core is arguably Earth's most dynamic region, and consists of an iron-nickel liquid with an unknown combination of lighter alloying elements. Frequencies of Earth's normal modes provide the strongest constraints on the radial profiles of compressional wavespeed, VΦ, and density, ρ, in the outer core. Recent great earthquakes have yielded new normal mode measurements; however, mineral physics experiments and calculations are often compared to the Preliminary reference Earth model (PREM), which is 35 years old and does not provide uncertainties. Here we investigate the thermo-elastic properties of the outer core using Earth's free oscillations and a Bayesian framework. To estimate radial structure of the outer core and its uncertainties, we choose to exploit recent datasets of normal mode centre frequencies. Under the self-coupling approximation, centre frequencies are unaffected by lateral heterogeneities in the Earth, for example in the mantle. Normal modes are sensitive to both VΦ and ρ in the outer core, with each mode's specific sensitivity depending on its eigenfunctions. We include a priori bounds on outer core models that ensure compatibility with measurements of mass and moment of inertia. We use Bayesian Monte Carlo Markov Chain techniques to explore different choices in parameterizing the outer core, each of which represents different a priori constraints. We test how results vary (1) assuming a smooth polynomial parametrization, (2) allowing for structure close to the outer core's boundaries, (3) assuming an Equation-of-State and adiabaticity and inverting directly for thermo-elastic parameters. In the second approach we recognize that the outer core may have distinct regions close to the core-mantle and inner core boundaries and investigate models which parameterize the well mixed outer core separately from these two layers. In the last approach we seek to map the uncertainties directly into thermo-elastic parameters including the bulk modulus, its pressure derivative, and molar mass and volume, with particular attention paid to the (inherent) trade-offs between the different coefficients. We discuss our results in terms of added uncertainty to the light element composition of the outer core and the potential existence of anomalous structure near the outer core's boundaries.

Representing and selecting vibrational angular momentum states for quasiclassical trajectory chemical dynamics simulations.

PubMed

Lourderaj, Upakarasamy; Martínez-Núñez, Emilio; Hase, William L

2007-10-18

Linear molecules with degenerate bending modes have states, which may be represented by the quantum numbers N and L. The former gives the total energy for these modes and the latter identifies their vibrational angular momentum jz. In this work, the classical mechanical analog of the N,L-quantum states is reviewed, and an algorithm is presented for selecting initial conditions for these states in quasiclassical trajectory chemical dynamics simulations. The algorithm is illustrated by choosing initial conditions for the N = 3 and L = 3 and 1 states of CO2. Applications of this algorithm are considered for initial conditions without and with zero-point energy (zpe) included in the vibrational angular momentum states and the C-O stretching modes. The O-atom motions in the x,y-plane are determined for these states from classical trajectories in Cartesian coordinates and are compared with the motion predicted by the normal-mode model. They are only in agreement for the N = L = 3 state without vibrational angular momentum zpe. For the remaining states, the Cartesian O-atom motions are considerably different from the elliptical motion predicted by the normal-mode model. This arises from bend-stretch coupling, including centrifugal distortion, in the Cartesian trajectories, which results in tubular instead of elliptical motion. Including zpe in the C-O stretch modes introduces considerable complexity into the O-atom motions for the vibrational angular momentum states. The short-time O-atom motions for these trajectories are highly irregular and do not appear to have any identifiable characteristics. However, the O-atom motions for trajectories integrated for substantially longer period of times acquire unique properties. With C-O stretch zpe included, the long-time O-atom motion becomes tubular for trajectories integrated to approximately 14 ps for the L = 3 states and to approximately 44 ps for the L = 1 states.

Vibrational dynamics of vocal folds using nonlinear normal modes.

PubMed

Pinheiro, Alan P; Kerschen, Gaëtan

2013-08-01

Many previous works involving physical models, excised and in vivo larynges have pointed out nonlinear vibration in vocal folds during voice production. Moreover, theoretical studies involving mechanical modeling of these folds have tried to gain a profound understanding of the observed nonlinear phenomena. In this context, the present work uses the nonlinear normal mode theory to investigate the nonlinear modal behavior of 16 subjects using a two-mass mechanical modeling of the vocal folds. The free response of the conservative system at different energy levels is considered to assess the impact of the structural nonlinearity of the vocal fold tissues. The results show very interesting and complex nonlinear phenomena including frequency-energy dependence, subharmonic regimes and, in some cases, modal interactions, entrainment and bifurcations. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

Stiffnesses of a solid-rocket motor from an ambient vibration survey

NASA Technical Reports Server (NTRS)

Rubin, S.; Searle, G. A.; Wagner, R. G.

1988-01-01

Experience with many spacecraft configurations boosted by a variety of launch vehicles indicates that the maximum loads experienced throughout most of the structure are inertial in origin. These loads arise from the dynamic elastic response of the flight vehicle to the transient disturbances of launch and flight, and are highly dependent on the dynamic characteristics of both the spacecraft and the launch vehicle. It has proved to be most advantageous, in the analysis of this critical dependency of loads upon vehicle dynamic properties, to establish a mathematical model in terms of normal mode characteristics. In this way, the vibration behavior of an elastomechanical structure (or substructure) can be described by means of the so-called modal or natural degrees of freedom. The conduct of a mode survey test and the use of a suitably test-verified model in loads analyses is essential to the flight worthiness certification process of space systems. The desirability of such tests is confirmed by the fact that, almost invariably, significant deficiencies in the analytical models are revealed by the results. Therefore, this experimental program was undertaken to determine those properties of a solid-propellant rocket motor (SRM) which are required to characterize a dynamic model. Random ambient-excited accelerations were measured at a series of stations along the motor for the purpose of identifying the motor beam-like stiffnesses in bending, shear, and torsion. From a system identification point of view, it is significant that stiffness properties of a subsystem (the motor) are determined from modes of the full system (motor/stand configuration) using mode shape data of the subsystem only. This contrasts with traditional system identification approaches which rely upon complete system mode shapes.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

[Basic research on vocal fold dynamics: three-dimensional vibration analysis of human and canine larynges].

PubMed

Döllinger, M; Rosanowski, F; Eysholdt, U; Lohscheller, J

2008-12-01

The understanding of normal and pathological vocal fold dynamics is the basis for a pathophysiological motivated voice therapy. Crucial vocal fold dynamics concerning voice production occur at the medial part of the vocal fold which is seen as the most critical region of mucosal wave propagation. Due to the limited size of the larynx the possibilities of laryngeal imaging by endoscopic techniques are limited. This work describes an experimental set-up that enables quantification of the entire medial and superior vocal fold surface using excised human and in vivo canine larynges. The data obtained enable analysis of vocal fold deflections, velocities, and mucosal wave propagation. The reciprocal dependencies can be examined and different areas of vocal fold dynamics located. The vertical components obscured in clinical endoscopy can be visualized. This is not negligible. In particular it is shown that the vertical deflection, which cannot be observed by clinical examination, plays an important part in the dynamics and therefore cannot be omitted for therapeutic procedures. The theoretically assumed entrainment and influence of the two main vibration modes enabling normal phonation is confirmed.

Conformational dynamics and ligand binding in the multi-domain protein PDC109.

PubMed

Kim, Hyun Jin; Choi, Moo Young; Kim, Hyung J; Llinás, Miguel

2010-02-18

PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2) repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs), a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD) simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

Intermittent many-body dynamics at equilibrium

NASA Astrophysics Data System (ADS)

Danieli, C.; Campbell, D. K.; Flach, S.

2017-06-01

The equilibrium value of an observable defines a manifold in the phase space of an ergodic and equipartitioned many-body system. A typical trajectory pierces that manifold infinitely often as time goes to infinity. We use these piercings to measure both the relaxation time of the lowest frequency eigenmode of the Fermi-Pasta-Ulam chain, as well as the fluctuations of the subsequent dynamics in equilibrium. The dynamics in equilibrium is characterized by a power-law distribution of excursion times far off equilibrium, with diverging variance. Long excursions arise from sticky dynamics close to q -breathers localized in normal mode space. Measuring the exponent allows one to predict the transition into nonergodic dynamics. We generalize our method to Klein-Gordon lattices where the sticky dynamics is due to discrete breathers localized in real space.

Nonextensive GES instability with nonlinear pressure effects

NASA Astrophysics Data System (ADS)

Gohain, Munmi; Karmakar, Pralay Kumar

2018-03-01

We herein analyze the instability dynamics associated with the nonextensive nonthermal gravito-electrostatic sheath (GES) model for the perturbed solar plasma portraiture. The usual neutral gas approximation is herewith judiciously relaxed and the laboratory plasma-wall interaction physics is procedurally incorporated amid barotropic nonlinearity. The main motivation here stems from the true nature of the solar plasma system as a set of concentric nonlocal nonthermal sub-layers as evidenced from different multi-space satellite probes and missions. The formalism couples the solar interior plasma (SIP, bounded) and solar wind plasma (SWP, unbounded) via the diffused solar surface boundary (SSB) formed due to an exact long-range gravito-electrostatic force-equilibration. A linear normal mode ansatz reveals both dispersive and non-dispersive features of the modified GES collective wave excitations. It is seen that the thermostatistical GES stability depends solely on the electron-to-ion temperature ratio. The damping behavior on both the scales is more pronounced in the acoustic domain, K → ∞ , than the gravitational domain, K → 0 ; where, K is the Jeans-normalized angular wave number. It offers a unique quasi-linear coupling of the gravitational and acoustic fluctuations amid the GES force action. The results may be useful to see the excitation dynamics of natural normal modes in bounded nonextensive astero-environs from a new viewpoint of the plasma-wall coupling mechanism.

Tearing mode dynamics and locking in the presence of external magnetic perturbations

NASA Astrophysics Data System (ADS)

Fridström, R.; Munaretto, S.; Frassinetti, L.; Chapman, B. E.; Brunsell, P. R.; Sarff, J. S.

2016-06-01

In normal operation, Madison Symmetric Torus (MST) [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)] reversed-field pinch plasmas exhibit several rotating tearing modes (TMs). Application of a resonant magnetic perturbation (RMP) results in braking of mode rotation and, if the perturbation amplitude is sufficiently high, in a wall-locked state. The coils that produce the magnetic perturbation in MST give rise to RMPs with several toroidal harmonics. As a result, simultaneous deceleration of all modes is observed. The measured TM dynamics is shown to be in qualitative agreement with a magnetohydrodynamical model of the RMP interaction with the TM [R. Fitzpatrick, Nucl. Fusion 33, 1049 (1993)] adapted to MST. To correctly model the TM dynamics, the electromagnetic torque acting on several TMs is included. Quantitative agreement of the TM slowing-down time was obtained for a kinematic viscosity in the order of νki n≈10 -20 m2/s. Analysis of discharges with different plasma densities shows an increase of the locking threshold with increasing density. Modeling results show good agreement with the experimental trend, assuming a density-independent kinematic viscosity. Comparison of the viscosity estimates in this paper to those made previously with other techniques in MST plasmas suggests the possibility that the RMP technique may allow for estimates of the viscosity over a broad range of plasmas in MST and other devices.

Respirator triggering of electron-beam computed tomography (EBCT): differences in dynamic changes between augmented ventilation and controlled mechanical ventilation

NASA Astrophysics Data System (ADS)

Recheis, Wolfgang A.; Kleinsasser, Axel; Schuster, Antonius H.; Loeckinger, Alexander; Frede, Thomas; Springer, Peter; Hoermann, Christoph; zur Nedden, Dieter

2000-04-01

The purpose was to evaluate differences in dynamic changes of the lung aeration (air-tissue ratio) between augmented modes of ventilation (AMV) and controlled mechanical ventilation (CMV) in normal subjects. 4 volunteers, ventilated with the different respirator protocols via face mask, were scanned using the EBCT in the 50 ms mode. A software analyzed the respirator's digitized pressure and volume signals of two subsequent ventilation phases. Using these values it was possible to calculate the onset of inspiration or expiration of the next respiratory phase. The calculated starting point was then used to trigger the EBCT. The dynamic changes of air- tissue ratios were evaluated in three separate regions: a ventral, an intermediate and a dorsal area. AMV results in increase of air-tissue ratio in the dorsal lung area due to the active contraction of the diaphragm, whereas CMV results in a more pronounced increase in air-tissue ratio of the ventral lung area. This study gives further insight into the dynamic changes of the lung's biomechanics by comparing augmented ventilation and controlled mechanical ventilation in the healthy proband.

Thermal transport in bismuth telluride quintuple layer: mode-resolved phonon properties and substrate effects

PubMed Central

Shao, Cheng; Bao, Hua

2016-01-01

The successful exfoliation of atomically-thin bismuth telluride (Bi2Te3) quintuple layer (QL) attracts tremendous research interest in this strongly anharmonic quasi-two-dimensional material. The thermal transport properties of this material are not well understood, especially the mode-wise properties and when it is coupled with a substrate. In this work, we have performed molecular dynamics simulations and normal mode analysis to study the mode-resolved thermal transport in freestanding and supported Bi2Te3 QL. The detailed mode-wise phonon properties are calculated and the accumulated thermal conductivities with respect to phonon mean free path (MFP) are constructed. It is shown that 60% of the thermal transport is contributed by phonons with MFP longer than 20 nm. Coupling with a-SiO2 substrate leads to about 60% reduction of thermal conductivity. Through varying the interfacial coupling strength and the atomic mass of substrate, we also find that phonon in Bi2Te3 QL is more strongly scattered by interfacial potential and its transport process is less affected by the dynamics of substrate. Our study provides an in-depth understanding of heat transport in Bi2Te3 QL and is helpful in further tailoring its thermal property through nanostructuring. PMID:27263656

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Preliminary experiments on pharmacokinetic diffuse fluorescence tomography of CT-scanning mode

NASA Astrophysics Data System (ADS)

Zhang, Yanqi; Wang, Xin; Yin, Guoyan; Li, Jiao; Zhou, Zhongxing; Zhao, Huijuan; Gao, Feng; Zhang, Limin

2016-10-01

In vivo tomographic imaging of the fluorescence pharmacokinetic parameters in tissues can provide additional specific and quantitative physiological and pathological information to that of fluorescence concentration. This modality normally requires a highly-sensitive diffuse fluorescence tomography (DFT) working in dynamic way to finally extract the pharmacokinetic parameters from the measured pharmacokinetics-associated temporally-varying boundary intensity. This paper is devoted to preliminary experimental validation of our proposed direct reconstruction scheme of instantaneous sampling based pharmacokinetic-DFT: A highly-sensitive DFT system of CT-scanning mode working with parallel four photomultiplier-tube photon-counting channels is developed to generate an instantaneous sampling dataset; A direct reconstruction scheme then extracts images of the pharmacokinetic parameters using the adaptive-EKF strategy. We design a dynamic phantom that can simulate the agent metabolism in living tissue. The results of the dynamic phantom experiments verify the validity of the experiment system and reconstruction algorithms, and demonstrate that system provides good resolution, high sensitivity and quantitativeness at different pump speed.

Exciton dynamics in a site-controlled quantum dot coupled to a photonic crystal cavity

NASA Astrophysics Data System (ADS)

Jarlov, C.; Lyasota, A.; Ferrier, L.; Gallo, P.; Dwir, B.; Rudra, A.; Kapon, E.

2015-11-01

Exciton and cavity mode (CM) dynamics in site-controlled pyramidal quantum dots (QDs), integrated with linear photonic crystal membrane cavities, are investigated for a range of temperatures and photo-excitation power levels. The absence of spurious multi-excitonic effects, normally observed in similar structures based on self-assembled QDs, permits the observation of effects intrinsic to two-level systems embedded in a solid state matrix and interacting with optical cavity modes. The coupled exciton and CM dynamics follow the same trend, indicating that the CM is fed only by the exciton transition. The Purcell reduction of the QD and CM decay times is reproduced well by a theoretical model that includes exciton linewidth broadening and temperature dependent non-radiative processes, from which we extract a Purcell factor of 17 ± 5. For excitation powers above QD saturation, we show the influence of quantum wire barrier states at short delay time, and demonstrate the absence of multiexcitonic background emission.

Low-Energy Excitation Spectra in the Excitonic Phase of Cobalt Oxides

NASA Astrophysics Data System (ADS)

Yamaguchi, Tomoki; Sugimoto, Koudai; Ohta, Yukinori

2017-04-01

We study the excitonic phase and low-energy excitation spectra of perovskite cobalt oxides. Constructing the five-orbital Hubbard model defined on the three-dimensional cubic lattice for the 3d bands of Pr0.5Ca0.5CoO3, we calculate the excitonic susceptibility in the normal state in the random-phase approximation (RPA) to show the presence of the instability toward excitonic condensation. On the basis of the excitonic ground state with a magnetic multipole obtained in the mean-field approximation, we calculate the dynamical susceptibility of the excitonic phase in the RPA and find that there appear a gapless collective excitation in the spin-transverse mode (Goldstone mode) and a gapful collective excitation in the spin-longitudinal mode (Higgs mode). The experimental relevance of our results is discussed.

Nonlinear damping of oblique whistler mode waves through Landau resonance

NASA Astrophysics Data System (ADS)

Hsieh, Y.; Omura, Y.

2017-12-01

Nonlinear trapping of electrons through Landau resonance is a characteristic dynamics in oblique whistler-mode wave particle interactions. The resonance velocity of the Landau resonance at quasi-parallel propagation becomes very close to the parallel group velocity of whistler-mode wave at frequency around 0.5 Ωe, causing a long distance of resonant interaction and strong acceleration of resonant electrons [1]. We demonstrate these effective accelerations for electrons with high equatorial pitch angle ( > 60°) by test particle simulations with parameters for the Earth's inner magnetosphere at L=5. In the simulations, we focus on slightly oblique whistler mode waves with wave normal angle < 20°. Analyzing the wave electric field E and the resonant current J, which is composed of electrons undergoing the Landau resonance, we find that the J·E is mainly positive, which denotes the damping of the wave. Furthermore, we confirm that this positive J•E is dominated by transverse component Jperp·Eperp rather than by longitudinal component Jpara·Eperp. The simulation results reveal that the Landau resonance contributes to the nonlinear damping at 0.5 Ωe for whistler mode waves. Reference [1] Hsieh, Y.-K., and Y. Omura (2017), Nonlinear dynamics of electrons interacting with oblique whistler mode chorus in the magnetosphere, J. Geophys. Res. Space Physics, 122, doi:10.1002/2016JA023255.

Quantum dynamical simulation of photoinduced electron transfer processes in dye-semiconductor systems: theory and application to coumarin 343 at TiO₂.

PubMed

Li, Jingrui; Kondov, Ivan; Wang, Haobin; Thoss, Michael

2015-04-10

A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.

Rapid flattening of butterfly pitch angle distributions of radiation belt electrons by whistler-mode chorus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Chang; Su, Zhenpeng; Xiao, Fuliang

Van Allen radiation belt electrons exhibit complex dynamics during geomagnetically active periods. Investigation of electron pitch angle distributions (PADs) can provide important information on the dominant physical mechanisms controlling radiation belt behaviors. In this paper, we report a storm time radiation belt event where energetic electron PADs changed from butterfly distributions to normal or flattop distributions within several hours. Van Allen Probes observations showed that the flattening of butterfly PADs was closely related to the occurrence of whistler-mode chorus waves. Two-dimensional quasi-linear STEERB simulations demonstrate that the observed chorus can resonantly accelerate the near-equatorially trapped electrons and rapidly flatten themore » corresponding electron butterfly PADs. Finally, these results provide a new insight on how chorus waves affect the dynamic evolution of radiation belt electrons.« less

Rapid flattening of butterfly pitch angle distributions of radiation belt electrons by whistler-mode chorus

DOE PAGES

Yang, Chang; Su, Zhenpeng; Xiao, Fuliang; ...

2016-08-16

Van Allen radiation belt electrons exhibit complex dynamics during geomagnetically active periods. Investigation of electron pitch angle distributions (PADs) can provide important information on the dominant physical mechanisms controlling radiation belt behaviors. In this paper, we report a storm time radiation belt event where energetic electron PADs changed from butterfly distributions to normal or flattop distributions within several hours. Van Allen Probes observations showed that the flattening of butterfly PADs was closely related to the occurrence of whistler-mode chorus waves. Two-dimensional quasi-linear STEERB simulations demonstrate that the observed chorus can resonantly accelerate the near-equatorially trapped electrons and rapidly flatten themore » corresponding electron butterfly PADs. Finally, these results provide a new insight on how chorus waves affect the dynamic evolution of radiation belt electrons.« less

Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.

PubMed

Wang, Wei Bu; Liang, Yu; Zhang, Jing; Wu, Yi Dong; Du, Jian Jun; Li, Qi Ming; Zhu, Jian Zhuo; Su, Ji Guo

2018-06-22

Intra-molecular energy transport between distant functional sites plays important roles in allosterically regulating the biochemical activity of proteins. How to identify the specific intra-molecular signaling pathway from protein tertiary structure remains a challenging problem. In the present work, a non-equilibrium dynamics method based on the elastic network model (ENM) was proposed to simulate the energy propagation process and identify the specific signaling pathways within proteins. In this method, a given residue was perturbed and the propagation of energy was simulated by non-equilibrium dynamics in the normal modes space of ENM. After that, the simulation results were transformed from the normal modes space to the Cartesian coordinate space to identify the intra-protein energy transduction pathways. The proposed method was applied to myosin and the third PDZ domain (PDZ3) of PSD-95 as case studies. For myosin, two signaling pathways were identified, which mediate the energy transductions form the nucleotide binding site to the 50 kDa cleft and the converter subdomain, respectively. For PDZ3, one specific signaling pathway was identified, through which the intra-protein energy was transduced from ligand binding site to the distant opposite side of the protein. It is also found that comparing with the commonly used cross-correlation analysis method, the proposed method can identify the anisotropic energy transduction pathways more effectively.

Effect of arm swing strategy on local dynamic stability of human gait.

PubMed

Punt, Michiel; Bruijn, Sjoerd M; Wittink, Harriet; van Dieën, Jaap H

2015-02-01

Falling causes long term disability and can even lead to death. Most falls occur during gait. Therefore improving gait stability might be beneficial for people at risk of falling. Recently arm swing has been shown to influence gait stability. However at present it remains unknown which mode of arm swing creates the most stable gait. To examine how different modes of arm swing affect gait stability. Ten healthy young male subjects volunteered for this study. All subjects walked with four different arm swing instructions at seven different gait speeds. The Xsens motion capture suit was used to capture gait kinematics. Basic gait parameters, variability and stability measures were calculated. We found an increased stability in the medio-lateral direction with excessive arm swing in comparison to normal arm swing at all gait speeds. Moreover, excessive arm swing increased stability in the anterior-posterior and vertical direction at low gait speeds. Ipsilateral and inphase arm swing did not differ compared to a normal arm swing. Excessive arm swing is a promising gait manipulation to improve local dynamic stability. For excessive arm swing in the ML direction there appears to be converging evidence. The effect of excessive arm swing on more clinically relevant groups like the more fall prone elderly or stroke survivors is worth further investigating. Excessive arm swing significantly increases local dynamic stability of human gait. Copyright © 2014 Elsevier B.V. All rights reserved.

Veering and nonlinear interactions of a clamped beam in bending and torsion

NASA Astrophysics Data System (ADS)

Ehrhardt, David A.; Hill, Thomas L.; Neild, Simon A.; Cooper, Jonathan E.

2018-03-01

Understanding the linear and nonlinear dynamic behaviour of beams is critical for the design of many engineering structures such as spacecraft antennae, aircraft wings, and turbine blades. When the eigenvalues of such structures are closely-spaced, nonlinearity may lead to interactions between the underlying linear normal modes (LNMs). This work considers a clamped-clamped beam which exhibits nonlinear behaviour due to axial tension from large amplitudes of deformation. An additional cross-beam, mounted transversely and with a movable mass at each tip, allows tuning of the primary torsion LNM such that it is close to the primary bending LNM. Perturbing the location of one mass relative to that of the other leads to veering between the eigenvalues of the bending and torsion LNMs. For a number of selected geometries in the region of veering, a nonlinear reduced order model (NLROM) is created and the nonlinear normal modes (NNMs) are used to describe the underlying nonlinear behaviour of the structure. The relationship between the 'closeness' of the eigenvalues and the nonlinear dynamic behaviour is demonstrated in the NNM backbone curves, and veering-like behaviour is observed. Finally, the forced and damped dynamics of the structure are predicted using several analytical and numerical tools and are compared to experimental measurements. As well as showing a good agreement between the predicted and measured responses, phenomena such as a 1:1 internal resonance and quasi-periodic behaviour are identified.

Observation of Wood's anomalies on surface gravity waves propagating on a channel.

PubMed

Schmessane, Andrea

2016-09-01

I report on experiments demonstrating the appearance of Wood's anomalies in surface gravity waves propagating along a channel with a submerged obstacle. Space-time measurements of surface gravity waves allow one to compute the stationary complex field of the wave and the amplitude growth of localized and propagative modes over all the entire channel, including the scattering region. This allows one to access the near and far field dynamics, which constitute a new and complementary way of observation of mode resonances of the incoming wave displaying Wood's anomalies. Transmission coefficient, dispersion relations and normalized wave energy of the incoming wave and the excited mode are measured and found to be in good agreement with theoretical predictions.

Breathing Mode in Complex Plasmas

NASA Astrophysics Data System (ADS)

Fujioka, K.; Henning, C.; Ludwig, P.; Bonitz, M.; Melzer, A.; Vitkalov, S.

2007-11-01

The breathing mode is a fundamental normal mode present in Coulomb systems, and may have utility in identifying particle charge and the Debye length of certain systems. The question remains whether this mode can be extended to strongly coupled Yukawa balls [1]. These systems are characterized by particles confined within a parabolic potential well and interacting through a shielded Coulomb potential [2,3]. The breathing modes for a variety of systems in 1, 2, and 3 dimensions are computed by solving the eigenvalue problem given by the dynamical (Hesse) matrix. These results are compared to theoretical investigations that assume a strict definition for a breathing mode within the system, and an analysis is made of the most fitting model to utilize in the study of particular systems of complex plasmas [1,4]. References [1] T.E. Sheridan, Phys. of Plasmas. 13, 022106 (2006)[2] C. Henning et al., Phys. Rev. E 74, 056403 (2006)[3] M. Bonitz et al., Phys. Rev. Lett. 96, 075001 (2006)[4] C. Henning et al., submitted for publication

A static acoustic signature system for the analysis of dynamic flight information

NASA Technical Reports Server (NTRS)

Ramer, D. J.

1978-01-01

The Army family of helicopters was analyzed to measure the polar octave band acoustic signature in various modes of flight. A static array of calibrated microphones was used to simultaneously acquire the signature and differential times required to mathematically position the aircraft in space. The signature was then reconstructed, mathematically normalized to a fixed radius around the aircraft.

Study of thermal scattering for organic tissues through molecular dynamics

NASA Astrophysics Data System (ADS)

Ramos, Ricardo; Cantargi, Florencia; Marquez Damian, Jose Ignacio; Gonçalves-Carralves, Manuel Sztejnberg

2017-09-01

Boron Neutron Capture Therapy (BNCT) is an experimental therapy for tumors which is based on the nuclear reaction that occurs when 10B is irradiated with thermal neutrons. Calculations for BNCT with Monte Carlo N-Particle (MCNP) take into account the thermal scattering treatment for hydrogen bound in bulk water for any organic tissue. However, in these tissues, hydrogen is also present in macromolecules (protein, lipids, etc.) and in confined water. Thermal scattering cross section for hydrogen in an organic tissue can be determined by calculating the scattering law S(α,β). This function can be obtained with the nuclear data processing system NJOY from the vibrational frequency spectrum of an atom in a molecular system. We performed calculations of the frequency spectrum from molecular dynamics simulations using the program GROMACS. Systems composed of a peptide in a water box were considered, with different proportions of water molecules. All-atom potentials for modeling this molecules were used in order to represent the internal vibrational normal modes for the atoms of hydrogen. The results showed several internal normal modes that in the case of hydrogen bound in bulk water do not appear.

Stochastic mixed-mode oscillations in a three-species predator-prey model

NASA Astrophysics Data System (ADS)

Sadhu, Susmita; Kuehn, Christian

2018-03-01

The effect of demographic stochasticity, in the form of Gaussian white noise, in a predator-prey model with one fast and two slow variables is studied. We derive the stochastic differential equations (SDEs) from a discrete model. For suitable parameter values, the deterministic drift part of the model admits a folded node singularity and exhibits a singular Hopf bifurcation. We focus on the parameter regime near the Hopf bifurcation, where small amplitude oscillations exist as stable dynamics in the absence of noise. In this regime, the stochastic model admits noise-driven mixed-mode oscillations (MMOs), which capture the intermediate dynamics between two cycles of population outbreaks. We perform numerical simulations to calculate the distribution of the random number of small oscillations between successive spikes for varying noise intensities and distance to the Hopf bifurcation. We also study the effect of noise on a suitable Poincaré map. Finally, we prove that the stochastic model can be transformed into a normal form near the folded node, which can be linked to recent results on the interplay between deterministic and stochastic small amplitude oscillations. The normal form can also be used to study the parameter influence on the noise level near folded singularities.

Principal dynamic mode analysis of neural mass model for the identification of epileptic states

NASA Astrophysics Data System (ADS)

Cao, Yuzhen; Jin, Liu; Su, Fei; Wang, Jiang; Deng, Bin

2016-11-01

The detection of epileptic seizures in Electroencephalography (EEG) signals is significant for the diagnosis and treatment of epilepsy. In this paper, in order to obtain characteristics of various epileptiform EEGs that may differentiate different states of epilepsy, the concept of Principal Dynamic Modes (PDMs) was incorporated to an autoregressive model framework. First, the neural mass model was used to simulate the required intracerebral EEG signals of various epileptiform activities. Then, the PDMs estimated from the nonlinear autoregressive Volterra models, as well as the corresponding Associated Nonlinear Functions (ANFs), were used for the modeling of epileptic EEGs. The efficient PDM modeling approach provided physiological interpretation of the system. Results revealed that the ANFs of the 1st and 2nd PDMs for the auto-regressive input exhibited evident differences among different states of epilepsy, where the ANFs of the sustained spikes' activity encountered at seizure onset or during a seizure were the most differentiable from that of the normal state. Therefore, the ANFs may be characteristics for the classification of normal and seizure states in the clinical detection of seizures and thus provide assistance for the diagnosis of epilepsy.

Multimode Jahn-Teller effect in bulk systems: A case of the N V 0 center in diamond

DOE PAGES

Zhang, Jianhua; Wang, Cai -Zhuang; Zhu, Zizhong; ...

2018-04-15

Here, the multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (NV 0) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the NV 0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the NV 0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, andmore » it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the NV 0 center.« less

Multimode Jahn-Teller effect in bulk systems: A case of the N V0 center in diamond

NASA Astrophysics Data System (ADS)

Zhang, Jianhua; Wang, Cai-Zhuang; Zhu, Zizhong; Liu, Qing Huo; Ho, Kai-Ming

2018-04-01

The multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (N V0 ) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the N V0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the N V0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, and it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the N V0 center.

Multimode Jahn-Teller effect in bulk systems: A case of the N V 0 center in diamond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jianhua; Wang, Cai -Zhuang; Zhu, Zizhong

Here, the multimode Jahn-Teller (JT) effect in a bulk system of a neutral nitrogen-vacancy (NV 0) center in diamond is investigated via first-principles density-functional-theory calculations and the intrinsic distortion path (IDP) method. The adiabatic potential energy surface of the electronic ground state of the NV 0 center is calculated based on the local spin-density approximation. Our calculations confirm the presence of the dynamic Jahn-Teller effect in the ground 2E state of the NV 0 center. Within the harmonic approximation, the IDP method provides the reactive path of JT distortion from unstable high-symmetry geometry to stable low-symmetry energy minimum geometry, andmore » it describes the active normal modes participating in the distortion. We find that there is more than one vibrational mode contributing to the distortion, and their contributions change along the IDP. Several vibrational modes with large contributions to JT distortion, especially those modes close to 44 meV, are clearly observed as the phonon sideband in photoluminescence spectra in a series of experiments, indicating that the dynamic Jahn-Teller effect plays an important role in the optical transition of the NV 0 center.« less

Relating normal vibrational modes to local vibrational modes with the help of an adiabatic connection scheme

NASA Astrophysics Data System (ADS)

Zou, Wenli; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

2012-08-01

Information on the electronic structure of a molecule and its chemical bonds is encoded in the molecular normal vibrational modes. However, normal vibrational modes result from a coupling of local vibrational modes, which means that only the latter can provide detailed insight into bonding and other structural features. In this work, it is proven that the adiabatic internal coordinate vibrational modes of Konkoli and Cremer [Int. J. Quantum Chem. 67, 29 (1998)], 10.1002/(SICI)1097-461X(1998)67:1<29::AID-QUA3>3.0.CO;2-0 represent a unique set of local modes that is directly related to the normal vibrational modes. The missing link between these two sets of modes are the compliance constants of Decius, which turn out to be the reciprocals of the local mode force constants of Konkoli and Cremer. Using the compliance constants matrix, the local mode frequencies of any molecule can be converted into its normal mode frequencies with the help of an adiabatic connection scheme that defines the coupling of the local modes in terms of coupling frequencies and reveals how avoided crossings between the local modes lead to changes in the character of the normal modes.

Normal modes of the shallow water system on the cubed sphere

NASA Astrophysics Data System (ADS)

Kang, H. G.; Cheong, H. B.; Lee, C. H.

2017-12-01

Spherical harmonics expressed as the Rossby-Haurwitz waves are the normal modes of non-divergent barotropic model. Among the normal modes in the numerical models, the most unstable mode will contaminate the numerical results, and therefore the investigation of normal mode for a given grid system and a discretiztaion method is important. The cubed-sphere grid which consists of six identical faces has been widely adopted in many atmospheric models. This grid system is non-orthogonal grid so that calculation of the normal mode is quiet challenge problem. In the present study, the normal modes of the shallow water system on the cubed sphere discretized by the spectral element method employing the Gauss-Lobatto Lagrange interpolating polynomials as orthogonal basis functions is investigated. The algebraic equations for the shallow water equation on the cubed sphere are derived, and the huge global matrix is constructed. The linear system representing the eigenvalue-eigenvector relations is solved by numerical libraries. The normal mode calculated for the several horizontal resolution and lamb parameters will be discussed and compared to the normal mode from the spherical harmonics spectral method.

iMODS: internal coordinates normal mode analysis server.

PubMed

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

2014-07-01

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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

PubMed

Araujo, Gabriela C; Silva, Ricardo H T; Scott, Luis P B; Araujo, Alexandre S; Souza, Fatima P; de Oliveira, Ronaldo Junio

2016-12-01

The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

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

PubMed Central

Cowsik, R.

2007-01-01

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

Dielectric and vibrational properties of amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2004-09-01

We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.

The use of normal forms for analysing nonlinear mechanical vibrations

PubMed Central

Neild, Simon A.; Champneys, Alan R.; Wagg, David J.; Hill, Thomas L.; Cammarano, Andrea

2015-01-01

A historical introduction is given of the theory of normal forms for simplifying nonlinear dynamical systems close to resonances or bifurcation points. The specific focus is on mechanical vibration problems, described by finite degree-of-freedom second-order-in-time differential equations. A recent variant of the normal form method, that respects the specific structure of such models, is recalled. It is shown how this method can be placed within the context of the general theory of normal forms provided the damping and forcing terms are treated as unfolding parameters. The approach is contrasted to the alternative theory of nonlinear normal modes (NNMs) which is argued to be problematic in the presence of damping. The efficacy of the normal form method is illustrated on a model of the vibration of a taut cable, which is geometrically nonlinear. It is shown how the method is able to accurately predict NNM shapes and their bifurcations. PMID:26303917

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

PubMed Central

Yu, Xiaozhen; Sigler, Sara C.; Hossain, Delwar; Wierdl, Monika; Gwaltney, Steven R.; Potter, Philip M.; Wadkins, Randy M.

2013-01-01

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member. PMID:22127613

An Aeroelastic Analysis of a Thin Flexible Membrane

NASA Technical Reports Server (NTRS)

Scott, Robert C.; Bartels, Robert E.; Kandil, Osama A.

2007-01-01

Studies have shown that significant vehicle mass and cost savings are possible with the use of ballutes for aero-capture. Through NASA's In-Space Propulsion program, a preliminary examination of ballute sensitivity to geometry and Reynolds number was conducted, and a single-pass coupling between an aero code and a finite element solver was used to assess the static aeroelastic effects. There remain, however, a variety of open questions regarding the dynamic aeroelastic stability of membrane structures for aero-capture, with the primary challenge being the prediction of the membrane flutter onset. The purpose of this paper is to describe and begin addressing these issues. The paper includes a review of the literature associated with the structural analysis of membranes and membrane utter. Flow/structure analysis coupling and hypersonic flow solver options are also discussed. An approach is proposed for tackling this problem that starts with a relatively simple geometry and develops and evaluates analysis methods and procedures. This preliminary study considers a computationally manageable 2-dimensional problem. The membrane structural models used in the paper include a nonlinear finite-difference model for static and dynamic analysis and a NASTRAN finite element membrane model for nonlinear static and linear normal modes analysis. Both structural models are coupled with a structured compressible flow solver for static aeroelastic analysis. For dynamic aeroelastic analyses, the NASTRAN normal modes are used in the structured compressible flow solver and 3rd order piston theories were used with the finite difference membrane model to simulate utter onset. Results from the various static and dynamic aeroelastic analyses are compared.

Normal mode study of the earth's rigid body motions

NASA Technical Reports Server (NTRS)

Chao, B. F.

1983-01-01

In this paper it is shown that the earth's rigid body (rb) motions can be represented by an analytical set of eigensolutions to the equation of motion for elastic-gravitational free oscillations. Thus each degree of freedom in the rb motion is associated with a rb normal mode. Cases of both nonrotating and rotating earth models are studied, and it is shown that the rb modes do incorporate neatly into the earth's system of normal modes of free oscillation. The excitation formula for the rb modes are also obtained, based on normal mode theory. Physical implications of the results are summarized and the fundamental differences between rb modes and seismic modes are emphasized. In particular, it is ascertained that the Chandler wobble, being one of the rb modes belonging to the rotating earth, can be studied using the established theory of normal modes.

Defense Logistics Standard Systems Functional Requirements.

DTIC Science & Technology

1987-03-01

Artificial Intelligence - the development of a machine capability to perform functions normally concerned with human intelligence, such as learning , adapting...Basic Data Base Machine Configurations .... ......... D- 18 xx ~ ?f~~~vX PART I: MODELS - DEFENSE LOGISTICS STANDARD SYSTEMS FUNCTIONAL REQUIREMENTS...On-line, Interactive Access. Integrating user input and machine output in a dynamic, real-time, give-and- take process is considered the optimum mode

Nonlinear Reduced-Order Simulation Using An Experimentally Guided Modal Basis

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Przekop, Adam

2012-01-01

A procedure is developed for using nonlinear experimental response data to guide the modal basis selection in a nonlinear reduced-order simulation. The procedure entails using nonlinear acceleration response data to first identify proper orthogonal modes. Special consideration is given to cases in which some of the desired response data is unavailable. Bases consisting of linear normal modes are then selected to best represent the experimentally determined transverse proper orthogonal modes and either experimentally determined inplane proper orthogonal modes or the special case of numerically computed in-plane companions. The bases are subsequently used in nonlinear modal reduction and dynamic response simulations. The experimental data used in this work is simulated to allow some practical considerations, such as the availability of in-plane response data and non-idealized test conditions, to be explored. Comparisons of the nonlinear reduced-order simulations are made with the surrogate experimental data to demonstrate the effectiveness of the approach.

Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding.

PubMed

Habibi, Mona; Plotkin, Steven S; Rottler, Jörg

2018-02-06

We investigate the correlation between soft vibrational modes and unfolding events in simulated force spectroscopy of proteins. Unfolding trajectories are obtained from molecular dynamics simulations of a Gō model of a monomer of a mutant of superoxide dismutase 1 protein containing all heavy atoms in the protein, and a normal mode analysis is performed based on the anisotropic network model. We show that a softness map constructed from the superposition of the amplitudes of localized soft modes correlates with unfolding events at different stages of the unfolding process. Soft residues are up to eight times more likely to undergo disruption of native structure than the average amino acid. The memory of the softness map is retained for extensions of up to several nanometers, but decorrelates more rapidly during force drops. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Bearing Fault Diagnosis by a Robust Higher-Order Super-Twisting Sliding Mode Observer

PubMed Central

Kim, Jong-Myon

2018-01-01

An effective bearing fault detection and diagnosis (FDD) model is important for ensuring the normal and safe operation of machines. This paper presents a reliable model-reference observer technique for FDD based on modeling of a bearing’s vibration data by analyzing the dynamic properties of the bearing and a higher-order super-twisting sliding mode observation (HOSTSMO) technique for making diagnostic decisions using these data models. The HOSTSMO technique can adaptively improve the performance of estimating nonlinear failures in rolling element bearings (REBs) over a linear approach by modeling 5 degrees of freedom under normal and faulty conditions. The effectiveness of the proposed technique is evaluated using a vibration dataset provided by Case Western Reserve University, which consists of vibration acceleration signals recorded for REBs with inner, outer, ball, and no faults, i.e., normal. Experimental results indicate that the proposed technique outperforms the ARX-Laguerre proportional integral observation (ALPIO) technique, yielding 18.82%, 16.825%, and 17.44% performance improvements for three levels of crack severity of 0.007, 0.014, and 0.021 inches, respectively. PMID:29642459

Bearing Fault Diagnosis by a Robust Higher-Order Super-Twisting Sliding Mode Observer.

PubMed

Piltan, Farzin; Kim, Jong-Myon

2018-04-07

An effective bearing fault detection and diagnosis (FDD) model is important for ensuring the normal and safe operation of machines. This paper presents a reliable model-reference observer technique for FDD based on modeling of a bearing's vibration data by analyzing the dynamic properties of the bearing and a higher-order super-twisting sliding mode observation (HOSTSMO) technique for making diagnostic decisions using these data models. The HOSTSMO technique can adaptively improve the performance of estimating nonlinear failures in rolling element bearings (REBs) over a linear approach by modeling 5 degrees of freedom under normal and faulty conditions. The effectiveness of the proposed technique is evaluated using a vibration dataset provided by Case Western Reserve University, which consists of vibration acceleration signals recorded for REBs with inner, outer, ball, and no faults, i.e., normal. Experimental results indicate that the proposed technique outperforms the ARX-Laguerre proportional integral observation (ALPIO) technique, yielding 18.82%, 16.825%, and 17.44% performance improvements for three levels of crack severity of 0.007, 0.014, and 0.021 inches, respectively.

Nonlinear Pressurization and Modal Analysis Procedure for Dynamic Modeling of Inflatable Structures

NASA Technical Reports Server (NTRS)

Smalley, Kurt B.; Tinker, Michael L.; Saxon, Jeff (Technical Monitor)

2002-01-01

An introduction and set of guidelines for finite element dynamic modeling of nonrigidized inflatable structures is provided. A two-step approach is presented, involving 1) nonlinear static pressurization of the structure and updating of the stiffness matrix and 2) hear normal modes analysis using the updated stiffness. Advantages of this approach are that it provides physical realism in modeling of pressure stiffening, and it maintains the analytical convenience of a standard bear eigensolution once the stiffness has been modified. Demonstration of the approach is accomplished through the creation and test verification of an inflated cylinder model using a large commercial finite element code. Good frequency and mode shape comparisons are obtained with test data and previous modeling efforts, verifying the accuracy of the technique. Problems encountered in the application of the approach, as well as their solutions, are discussed in detail.

Acoustic multipath arrivals in the horizontal plane due to approaching nonlinear internal waves.

PubMed

Badiey, Mohsen; Katsnelson, Boris G; Lin, Ying-Tsong; Lynch, James F

2011-04-01

Simultaneous measurements of acoustic wave transmissions and a nonlinear internal wave packet approaching an along-shelf acoustic path during the Shallow Water 2006 experiment are reported. The incoming internal wave packet acts as a moving frontal layer reflecting (or refracting) sound in the horizontal plane. Received acoustic signals are filtered into acoustic normal mode arrivals. It is shown that a horizontal multipath interference is produced. This has previously been called a horizontal Lloyd's mirror. The interference between the direct path and the refracted path depends on the mode number and frequency of the acoustic signal. A mechanism for the multipath interference is shown. Preliminary modeling results of this dynamic interaction using vertical modes and horizontal parabolic equation models are in good agreement with the observed data.

Response of a store with tunable natural frequencies in compressible cavity flow

DOE PAGES

Wagner, Justin L.; Casper, Katya M.; Beresh, Steven J.; ...

2016-05-20

Fluid–structure interactions that occur during aircraft internal store carriage were experimentally explored at Mach 0.58–1.47 using a generic, aerodynamic store installed in a rectangular cavity having a length-to-depth ratio of seven. The store vibrated in response to the cavity flow at its natural structural frequencies, and it exhibited a directionally dependent response to cavity resonance frequencies. Cavity tones excited the store in the streamwise and wall-normal directions consistently, whereas the spanwise response to cavity tones was much more limited. Increased surface area associated with tail fins raised vibration levels. The store had interchangeable components to vary its natural frequencies bymore » about 10–300 Hz. By tuning natural frequencies, mode-matched cases were explored where a prominent cavity tone frequency matched a structural natural frequency of the store. Mode matching in the streamwise and wall-normal directions produced substantial increases in peak store vibrations, though the response of the store remained linear with dynamic pressure. Near mode-matched frequencies, changes in cavity tone frequencies of only 1% altered store peak vibrations by as much as a factor of two. In conclusion, mode matching in the spanwise direction did little to increase vibrations.« less

The dynamic simulation of the Progetto Energia combined cycle power plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giglio, R.; Cerabolini, M.; Pisacane, F.

1996-12-31

Over the next four years, the Progetto Energia project is building several cogeneration plants to satisfy the increasing demands of Italy`s industrial complex and the country`s demand for electrical power. Located at six different sites within Italy`s borders these Combined Cycle Cogeneration Plants will supply a total of 500 MW of electricity and 100 tons/hr of process steam to Italian industries and residences. To ensure project success, a dynamic model of the 50 MW base unit was developed. The goal established for the model was to predict the dynamic behavior of the complex thermodynamic system in order to assess equipmentmore » performance and control system effectiveness for normal operation and, more importantly, abrupt load changes. In addition to fulfilling its goals, the dynamic study guided modifications to controller logic that significantly improved steam drum pressure control and bypassed steam de-superheating performance. Simulations of normal and abrupt transient events allowed engineers to define optimum controller gain coefficients. The paper discusses the Combined Cycle plant configuration, its operating modes and control system, the dynamic model representation, the simulation results and project benefits.« less

Transverse discrete breathers in unstrained graphene

NASA Astrophysics Data System (ADS)

Barani, Elham; Lobzenko, Ivan P.; Korznikova, Elena A.; Soboleva, Elvira G.; Dmitriev, Sergey V.; Zhou, Kun; Marjaneh, Aliakbar Moradi

2017-02-01

Discrete breathers (DB) are spatially localized vibrational modes of large amplitude in defect-free nonlinear lattices. The search for DBs in graphene is of high importance, taking into account that this one atom thick layer of carbon is promising for a number of applications. There exist several reports on successful excitation of DBs in graphene, based on molecular dynamics and ab initio simulations. In a recent work by Hizhnyakov with co-authors the possibility to excite a DB with atoms oscillating normal to the graphene sheet has been reported. In the present study we use a systematic approach for finding initial conditions to excite transverse DBs in graphene. The approach is based on the analysis of the frequency-amplitude dependence for a delocalized, short-wavelength vibrational mode. This mode is a symmetry-dictated exact solution to the dynamic equations of the atomic motion, regardless the mode amplitude and regardless the type of interatomic potentials used in the simulations. It is demonstrated that if the AIREBO potential is used, the mode frequency increases with the amplitude bifurcating from the upper edge of the phonon spectrum for out-of-plane phonons. Then a bell-shaped function is superimposed on this delocalized mode to obtain a spatially localized vibrational mode, i.e., a DB. Placing the center of the bell-shaped function at different positions with respect to the lattice sites, three different DBs are found. Typically, the degree of spatial localization of DBs increases with the DB amplitude, but the transverse DBs in graphene reported here demonstrate the opposite trend. The results are compared to those obtained with the use of the Savin interatomic potential and no transverse DBs are found in this case. The results of this study contribute to a better understanding of the nonlinear dynamics of graphene and they call for the ab initio simulations to verify which of the two potentials used in this study is more precise.

Internal polarization dynamics of vector dissipative-soliton-resonance pulses in normal dispersion fiber lasers.

PubMed

Li, Daojing; Shen, Deyuan; Li, Lei; Tang, Dingyuan; Su, Lei; Zhao, Luming

2018-03-15

Internal polarization dynamics of vector dissipative-soliton-resonance (DSR) pulses in a mode-locked fiber laser are investigated. By utilizing a wave plate analyzer configuration to analyze the special structure of a DSR pulse, we find that polarization state is not uniform across a resonant dissipative soliton. Specifically, although the central plane wave of the resonant dissipative soliton acquires nearly a single fixed polarization, the dissipative fronts feature polarization states that are different and spatially varying. This distinct polarization distribution is maintained while the whole soliton extends with increasing gain. Numerical simulation further confirms the experimental observations.

Dark solitons in laser radiation build-up dynamics.

PubMed

Woodward, R I; Kelleher, E J R

2016-03-01

We reveal the existence of slowly decaying dark solitons in the radiation build-up dynamics of bright pulses in all-normal dispersion mode-locked fiber lasers, numerically modeled in the framework of a generalized nonlinear Schrödinger equation. The evolution of noise perturbations to quasistationary dark solitons is examined, and the significance of background shape and soliton-soliton collisions on the eventual soliton decay is established. We demonstrate the role of a restoring force in extending soliton interactions in conservative systems to include the effects of dissipation, as encountered in laser cavities, and generalize our observations to other nonlinear systems.

Normal mode analysis and applications in biological physics.

PubMed

Dykeman, Eric C; Sankey, Otto F

2010-10-27

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.

Local vibrational modes of the water dimer - Comparison of theory and experiment

NASA Astrophysics Data System (ADS)

Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D.

2012-12-01

Local and normal vibrational modes of the water dimer are calculated at the CCSD(T)/CBS level of theory. The local H-bond stretching frequency is 528 cm-1 compared to a normal mode stretching frequency of just 143 cm-1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to mass coupling, a change in the anharmonicity, and coupling with the local HOH bending modes. The local mode stretching force constant is related to the strength of the H-bond whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the H-bond strength.

Phenomenology of break-up modes in contact free externally heated nanoparticle laden fuel droplets

NASA Astrophysics Data System (ADS)

Pathak, Binita; Basu, Saptarshi

2016-12-01

We study thermally induced atomization modes in contact free (acoustically levitated) nanoparticle laden fuel droplets. The initial droplet size, external heat supplied, and suspended particle concentration (wt. %) in droplets govern the stability criterion which ultimately determines the dominant mode of atomization. Pure fuel droplets exhibit two dominant modes of breakup namely primary and secondary. Primary modes are rather sporadic and normally do not involve shape oscillations. Secondary atomization however leads to severe shape deformations and catastrophic intense breakup of the droplets. The dominance of these modes has been quantified based on the external heat flux, dynamic variation of surface tension, acoustic pressure, and droplet size. Addition of particles alters the regimes of the primary and secondary atomization and introduces bubble induced boiling and bursting. We analyze this new mode of atomization and estimate the time scale of bubble growth up to the point of bursting using energy balance to determine the criterion suitable for parent droplet rupture. All the three different modes of breakup have been well identified in a regime map determined in terms of Weber number and the heat utilization rate which is defined as the energy utilized for transient heating, vaporization, and boiling in droplets.

Dissipative vector soliton in a dispersion-managed fiber laser with normal dispersion.

PubMed

Wang, Siming; Fan, Xuliang; Zhao, Luming; Wang, Yong; Tang, Dingyuan; Shen, Deyuan

2014-12-10

We numerically study the vector dynamics of dissipative solitons (DSs) in a 2 μm dispersion-managed fiber laser mode locked by a semiconductor saturable absorber mirror and operated in the normal dispersion regime. It is shown that the effective gain bandwidth is crucial for the DS generation. The steep spectral edges of DSs are the consequence of the interaction among the normal dispersion, fiber nonlinearity, gain and loss, and gain dispersion effect, etc. We numerically duplicate the experimental results and further explore the vector features of the generated DSs. Two DSs formed along the two orthogonal polarization directions which, incoherently coupled with each other, could propagate in the birefringent cavity with the same group velocity.

Analysis of an unswept propfan blade with a semiempirical dynamic stall model

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Kaza, K. R. V.

1989-01-01

The time history response of a propfan wind tunnel model with dynamic stall is studied analytically. The response obtained from the analysis is compared with available experimental data. The governing equations of motion are formulated in terms of blade normal modes which are calculated using the COSMIC-NASTRAN computer code. The response analysis considered the blade plunging and pitching motions. The lift, drag and moment coefficients for angles of attack below the static stall angle are obtained from a quasi-steady theory. For angles above static stall angles, a semiempirical dynamic stall model based on a correction to angle of attack is used to obtain lift, drag and moment coefficients. Using these coefficients, the aerodynamic forces are calculated at a selected number of strips, and integrated to obtain the total generalized forces. The combined momentum-blade element theory is used to calculate the induced velocity. The semiempirical stall model predicted a limit cycle oscillation near the setting angle at which large vibratory stresses were observed in an experiment. The predicted mode and frequency of oscillation also agreed with those measured in the experiment near the setting angle.

Control logic for exhaust gas driven turbocharger

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adeff, G.A.

1991-12-31

This patent describes a method of controlling an exhaust gas driven turbocharger supplying charge air for an internal combustion engine powering vehicle, the turbocharger being adjustable from a normal mode to a power mode in which the charge air available to the engine during vehicle acceleration is increased over that available when the turbocharger is in the normal mode, the vehicle including engine power control means switchable by the vehicle operator from a normal mode to a power mode so that the vehicle operator may selectively elect either the normal mode or the power mode, comprising the steps of measuringmore » the speed of the vehicle, permitting the vehicle operator to elect either the power mode or the normal mode for a subsequent vehicle acceleration, and then adjusting the turbocharger to the power mode when the speed of the vehicle is less than a predetermined reference speed and the vehicle operator has elected to power mode to increase the charge air available to the engine and thereby increasing engine power on a subsequent acceleration of the vehicle.« less

A minimization principle for the description of modes associated with finite-time instabilities

PubMed Central

Babaee, H.

2016-01-01

We introduce a minimization formulation for the determination of a finite-dimensional, time-dependent, orthonormal basis that captures directions of the phase space associated with transient instabilities. While these instabilities have finite lifetime, they can play a crucial role either by altering the system dynamics through the activation of other instabilities or by creating sudden nonlinear energy transfers that lead to extreme responses. However, their essentially transient character makes their description a particularly challenging task. We develop a minimization framework that focuses on the optimal approximation of the system dynamics in the neighbourhood of the system state. This minimization formulation results in differential equations that evolve a time-dependent basis so that it optimally approximates the most unstable directions. We demonstrate the capability of the method for two families of problems: (i) linear systems, including the advection–diffusion operator in a strongly non-normal regime as well as the Orr–Sommerfeld/Squire operator, and (ii) nonlinear problems, including a low-dimensional system with transient instabilities and the vertical jet in cross-flow. We demonstrate that the time-dependent subspace captures the strongly transient non-normal energy growth (in the short-time regime), while for longer times the modes capture the expected asymptotic behaviour. PMID:27118900

Rheology of Foam Near the Order-Disorder Transition

NASA Technical Reports Server (NTRS)

Holt, R. Glynn; McDaniel, J. Gregory

2001-01-01

The first part of our research results are summarized in the recent journal publication: J. Gregory McDaniel and R. Glynn Holt, 'Measurement of aqueous foam rheology by acoustic levitation', Phys. Rev. E 61, 2204 (2000). This aspect of the work was a combination of experiment and analysis. We built a levitation system capable of acoustically levitating small samples of aqueous foam of arbitrary gas and liquid volume fractions. We then modulated the acoustic field to induce normal mode oscillations of the foam samples. The observables from the experiment were frequency and mode number. For dry (roughly > 70% gas by volume) foams and small deformations, we developed an effective medium, normal-modes analysis which took the frequency and mode number from experiment, and gave us the shear elastic modulus of the foam as a function of Poisson's ratio. The second part of our results may be found in a soon-to-be submitted manuscript 'Dynamics of aqueous foam drops', I.Sh. Akhatov, J.G. McDaniel and R.G. Holt, describing our modeling in the wet foam limit by considering the acoustic problem. This aspect of the research is purely theoretical. Beginning from a mass-conserving mixture law, the fully nonlinear equations of motion for a wet (roughly < 10% gas by volume) foam drop of initially spherical shape were derived. The frequencies for normal mode oscillations were derived in the linear inviscid limit. The nonlinear equations were numerically solved to elicit the motion of a foam drop under acoustic excitation. The role of the time-varying void fraction in breathing-mode oscillations is of particular interest. As of the end of the current (NAG#3-2121) grant, this work was not yet concluded. We continue to work on this aspect in order to extend the analysis to cover the transition regime of gas volume fractions, as well as to compare to experiments in the wet regime.

Normal-mode selectivity in ultrafast Raman excitations in C60

NASA Astrophysics Data System (ADS)

Zhang, G. P.; George, Thomas F.

2006-01-01

Ultrafast Raman spectra are a powerful tool to probe vibrational excitations, but inherently they are not normal-mode specific. For a system as complicated as C60 , there is no general rule to target a specific mode. A detailed study presented here aims to investigate normal-mode selectivity in C60 by an ultrafast laser. To accurately measure mode excitation, we formally introduce the kinetic-energy-based normal-mode analysis which overcomes the difficulty with the strong lattice anharmonicity and relaxation. We first investigate the resonant excitation and find that mode selectivity is normally difficult to achieve. However, for off-resonant excitations, it is possible to selectively excite a few modes in C60 by properly choosing an optimal laser pulse duration, which agrees with previous experimental and theoretical findings. Going beyond the phenomenological explanation, our study shines new light on the origin of the optimal duration: The phase matching between the laser field and mode vibration determines which mode is strongly excited or suppressed. This finding is very robust and should be a useful guide for future experimental and theoretical studies in more complicated systems.

Normal mode selectivity in ultrafast Raman excitations in C60

NASA Astrophysics Data System (ADS)

Zhang, Guoping; George, Thomas F.

2006-05-01

Ultrafast Raman spectra are a powerful tool to probe vibrational excitations, but inherently they are not normal-mode specific. For a system as complicated as C60, there is no general rule to target a specific mode. A detailed study presented here aims to investigate normal mode selectivity in C60 by an ultrafast laser. To accurately measure mode excitation, we formally introduce the kinetic energy-based normal mode analysis which overcomes the difficulty with the strong lattice anharmonicity and relaxation. We first investigate the resonant excitation and find that mode selectivity is normally difficult to achieve. However, for off-resonant excitations, it is possible to selectively excite a few modes in C60 by properly choosing an optimal laser pulse duration, which agrees with previous experimental and theoretical findings. Going beyond the phenomenological explanation, our study shines new light on the origin of the optimal duration: The phase matching between laser field and mode vibration determines which mode is strongly excited or suppressed. This finding is very robust and may be a useful guide for future experimental and theoretical studies in more complicated systems.

Phenomenology in minimal theory of massive gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Felice, Antonio De; Mukohyama, Shinji; Kavli Institute for the Physics and Mathematics of the Universe

2016-04-15

We investigate the minimal theory of massive gravity (MTMG) recently introduced. After reviewing the original construction based on its Hamiltonian in the vielbein formalism, we reformulate it in terms of its Lagrangian in both the vielbein and the metric formalisms. It then becomes obvious that, unlike previous attempts in the literature of Lorentz-violating massive gravity, not only the potential but also the kinetic structure of the action is modified from the de Rham-Gabadadze-Tolley (dRGT) massive gravity theory. We confirm that the number of physical degrees of freedom in MTMG is two at fully nonlinear level. This proves the absence ofmore » various possible pathologies such as superluminality, acausality and strong coupling. Afterwards, we discuss the phenomenology of MTMG in the presence of a dust fluid. We find that on a flat homogeneous and isotropic background we have two branches. One of them (self-accelerating branch) naturally leads to acceleration without the genuine cosmological constant or dark energy. For this branch both the scalar and the vector modes behave exactly as in general relativity (GR). The phenomenology of this branch differs from GR in the tensor modes sector, as the tensor modes acquire a non-zero mass. Hence, MTMG serves as a stable nonlinear completion of the self-accelerating cosmological solution found originally in dRGT theory. The other branch (normal branch) has a dynamics which depends on the time-dependent fiducial metric. For the normal branch, the scalar mode sector, even though as in GR only one scalar mode is present (due to the dust fluid), differs from the one in GR, and, in general, structure formation will follow a different phenomenology. The tensor modes will be massive, whereas the vector modes, for both branches, will have the same phenomenology as in GR.« less

Design of a linear projector for use with the normal modes of the GLAS 4th order GCM

NASA Technical Reports Server (NTRS)

Bloom, S. C.

1984-01-01

The design of a linear projector for use with the normal modes of a model of atmospheric circulation is discussed. A central element in any normal mode initialization scheme is the process by which a set of data fields - winds, temperatures or geopotentials, and surface pressures - are expressed ("projected') in terms of the coefficients of a model's normal modes. This process is completely analogous to the Fourier decomposition of a single field (indeed a FFT applied in the zonal direction is a part of the process). Complete separability in all three spatial dimensions is assumed. The basis functions for the modal expansion are given. An important feature of the normal modes is their coupling of the structures of different fields, thus a coefficient in a normal mode expansion would contain both mass and momentum information.

Antiferromagnetic resonance excited by oscillating electric currents

NASA Astrophysics Data System (ADS)

Sluka, Volker

2017-12-01

In antiferromagnetic materials the order parameter exhibits resonant modes at frequencies that can be in the terahertz range, making them interesting components for spintronic devices. Here, it is shown that antiferromagnetic resonance can be excited using the inverse spin-Hall effect in a system consisting of an antiferromagnetic insulator coupled to a normal-metal waveguide. The time-dependent interplay between spin torque, ac spin accumulation, and magnetic degrees of freedom is studied. It is found that the dynamics of the antiferromagnet affects the frequency-dependent conductivity of the normal metal. Further, a comparison is made between spin-current-induced and Oersted-field-induced excitation under the condition of constant power injection.

Microtubule dynamics in cell division: exploring living cells with polarized light microscopy.

PubMed

Inoué, Shinya

2008-01-01

This Perspective is an account of my early experience while I studied the dynamic organization and behavior of the mitotic spindle and its submicroscopic filaments using polarized light microscopy. The birefringence of spindle filaments in normally dividing plant and animal cells, and those treated by various agents, revealed (a) the reality of spindle fibers and fibrils in healthy living cells; (b) the labile, dynamic nature of the molecular filaments making up the spindle fibers; (c) the mode of fibrogenesis and action of orienting centers; and (d) force-generating properties based on the disassembly and assembly of the fibrils. These studies, which were carried out directly on living cells using improved polarizing microscopes, in fact predicted the reversible assembly properties of microtubules.

Dynamics of a movable micromirror in a nonlinear optical cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Tarun; ManMohan; Bhattacherjee, Aranya B.

We consider the dynamics of a movable mirror (cantilever) of a nonlinear optical cavity. We show that a chi{sup (3)} medium with a strong Kerr nonlinearity placed inside a cavity inhibits the normal mode splitting (NMS) due to the photon blockade mechanism. This study demonstrates that the displacement spectrum of the micromirror could be used as a tool to detect the photon blockade effect. Moreover the ability to control the photon number fluctuation by tuning the Kerr nonlinearity emerges as a new handle to coherently control the dynamics of the micromirror, which further could be useful in the realization ofmore » tuneable quantum-mechanical devices. We also found that the temperature of the micromechanical mirror increases with increasing Kerr nonlinearity.« less

Identification of a novel dynamic red blindness in human by event-related brain potentials.

PubMed

Zhang, Jiahua; Kong, Weijia; Yang, Zhongle

2010-12-01

Dynamic color is an important carrier that takes information in some special occupations. However, up to the present, there are no available and objective tests to evaluate dynamic color processing. To investigate the characteristics of dynamic color processing, we adopted two patterns of visual stimulus called "onset-offset" which reflected static color stimuli and "sustained moving" without abrupt mode which reflected dynamic color stimuli to evoke event-related brain potentials (ERPs) in primary color amblyopia patients (abnormal group) and subjects with normal color recognition ability (normal group). ERPs were recorded by Neuroscan system. The results showed that in the normal group, ERPs in response to the dynamic red stimulus showed frontal positive amplitudes with a latency of about 180 ms, a negative peak at about 240 ms and a peak latency of the late positive potential (LPP) in a time window between 290 and 580 ms. In the abnormal group, ERPs in response to the dynamic red stimulus were fully lost and characterized by vanished amplitudes between 0 and 800 ms. No significant difference was noted in ERPs in response to the dynamic green and blue stimulus between the two groups (P>0.05). ERPs of the two groups in response to the static red, green and blue stimulus were not much different, showing a transient negative peak at about 170 ms and a peak latency of LPP in a time window between 350 and 650 ms. Our results first revealed that some subjects who were not identified as color blindness under static color recognition could not completely apperceive a sort of dynamic red stimulus by ERPs, which was called "dynamic red blindness". Furthermore, these results also indicated that low-frequency ERPs induced by "sustained moving" may be a good and new method to test dynamic color perception competence.

Infrared spectra of the ammonium ion in ammonium hexavanadate (NH 4) 2V 6O 16

NASA Astrophysics Data System (ADS)

de Waal, D.; Heyns, A. M.; Range, K.-J.; Eglmeier, C.

The infrared bands of the NH +4 and ND +4 groups in (NH 4) 2V 6O 16 and its deuterated analogue can be assigned with a fair amount of certainty at 90 K under the space group P2 1/ m( C22 h). The ND stretching modes of isotopically dilute NH 3D + ions in the crystal are in agreement with the predicted splitting into Cs, Cs and C1(2) components. The frequencies, shapes and temperature dependence of these modes suggest that both normal and bifurcated hydrogen bonds are formed. The latter closely resembles corresponding bonds in NH 4VO 3, but the normal hydrogen bonds are not as strong as the similar bonds in NH 4VO 3. This can be expected as NH +4 ions are dynamic in character in (NH 4) 2V 6O 16 and remain so down to temperatures of 90 K.

Dynamical criterion for a marginally unstable, quasi-linear behavior in a two-layer model

NASA Technical Reports Server (NTRS)

Ebisuzaki, W.

1988-01-01

A two-layer quasi-geostrophic flow forced by meridional variations in heating can be in regimes ranging from radiative equilibrium to forced geostrophic turbulence. Between these extremes is a regime where the time-mean (zonal) flow is marginally unstable. Using scaling arguments, it is concluded that such a marginally unstable state should occur when a certain parameter, measuring the strength of wave-wave interactions relative to the beta effect and advection by the thermal wind, is small. Numerical simulations support this proposal. A transition from the marginally unstable regime to a more nonlinear regime is then examined through numerical simulations with different radiative forcings. It is found that transition is not caused by secondary instability of waves in the marginally unstable regime. Instead, the time-mean flow can support a number of marginally unstable normal modes. These normal modes interact with each other, and if they are of sufficient amplitude, the flow enters a more nonlinear regime.

Dynamic detailed model of a molten salt tower receiver, with ThermoSysPro library: Impacts of several failures or operational transients on the receiver dynamic behavior

NASA Astrophysics Data System (ADS)

Hefni, Baligh El; Bourdil, Charles

2017-06-01

Molten salt technology represents nowadays the most cost-effective technology for electricity generation for solar power plant. The molten salt tower receiver is based on a field of individually sun-tracking mirrors (heliostats) that reflect the incident sunshine to a receiver at the top of a centrally located tower. The objective of this study is to assess the impact of several transients issued from different scenarios (failure or normal operation mode) on the receiver dynamic behavior. A dynamic detailed model of Solar Two molten salt central receiver has been developed. The component model is meant to be used for receiver modeling with the ThermoSysPro library, developed by EDF. The paper also gives the results of the dynamic simulation for the selected scenarios on Solar Two receiver.

The Shock and Vibration Digest. Volume 16, Number 7

DTIC Science & Technology

1984-07-01

Brayton -Moser :,. existence of classical normal modes in various classes equations has been presented (32, 33]. Two methods of problems, the concept of...and Re- "Connections between the Generalized Hamil- strained Dynamical Systems," J. Appl. Mech., ton-Lagrange and Brayton -Moser Equations," Trans...committees within the division. Short Ccourses are also offered as a part of this conference, Walter Taylor described how he used a microcom- and the

The Shock and Vibration Digest, Volume 16, Number 10

DTIC Science & Technology

1984-10-01

shaped, arid a general polygonal-shaped membrane Fourier expansion -collocation method and the finite without symmetry They also derived, with the help...geometry is not applicable; therefore, a Fourier sine series expansion technique. The meth- not much work on the dynamic behavior of skew- od was applied...particular m.-de are obtained. This normal mode expansion form of deflection surface. The stability of motion approach has recently been used in a series of

Dissociative Recombination Chemistry and Plasma Dynamics

DTIC Science & Technology

2008-06-16

the fractional square of product momentum with product momentum vectors . Qx and Qy denote the degenerate bend two-body dissociation limits...with product momentum vectors . Qx and Qy denote the degenerate bend normal modes for C2v symmetry H2D and HD2 isomers of H3. symmetry for the Qx...heavy (D atom) products in general receive a greater partitioning of energy than the light product. This may have important implications for

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.

Collective excitations and ultrafast dipolar solvation dynamics in water-ethanol binary mixture

NASA Astrophysics Data System (ADS)

Hazra, Milan K.; Bagchi, Biman

2018-03-01

In order to understand the intermolecular vibrational spectrum and the collective excitations of water-ethanol binary mixture, we investigate the density of states and the power spectrum using computer simulations aided by theory. We investigate in particular the spectra at intermediate to low frequencies (a few hundreds to few tens of cm-1) by calculating (i) the density of states from quenched normal modes, (ii) the power spectrum from velocity time correlation function, and (iii) the far infrared and dielectric spectra (that is, the Cole-Cole plot) from the total dipole moment time correlation function. The different spectra are in broad agreement with each other and at the same time reveal unique characteristics of the water-ethanol mixture. Inverse participation ratio reveals several interesting features. Libration of pure ethanol is more localized than that of pure water. With increasing ethanol content, we observe localization of the collective libration mode as well as of the hindered translational and rotational mode. An interesting mixing between the libration of water and ethanol is observed. Solvation dynamics of tryptophan measured by equilibrium energy fluctuation time correlation function show surprisingly strong non-linear dependence on composition that can be tested against experiments.

Collective excitations and ultrafast dipolar solvation dynamics in water-ethanol binary mixture.

PubMed

Hazra, Milan K; Bagchi, Biman

2018-03-21

In order to understand the intermolecular vibrational spectrum and the collective excitations of water-ethanol binary mixture, we investigate the density of states and the power spectrum using computer simulations aided by theory. We investigate in particular the spectra at intermediate to low frequencies (a few hundreds to few tens of cm -1 ) by calculating (i) the density of states from quenched normal modes, (ii) the power spectrum from velocity time correlation function, and (iii) the far infrared and dielectric spectra (that is, the Cole-Cole plot) from the total dipole moment time correlation function. The different spectra are in broad agreement with each other and at the same time reveal unique characteristics of the water-ethanol mixture. Inverse participation ratio reveals several interesting features. Libration of pure ethanol is more localized than that of pure water. With increasing ethanol content, we observe localization of the collective libration mode as well as of the hindered translational and rotational mode. An interesting mixing between the libration of water and ethanol is observed. Solvation dynamics of tryptophan measured by equilibrium energy fluctuation time correlation function show surprisingly strong non-linear dependence on composition that can be tested against experiments.

Evolutionary pulsational mode dynamics in nonthermal turbulent viscous astrofluids

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Dutta, Pranamika

2017-11-01

The pulsational mode of gravitational collapse in a partially ionized self-gravitating inhomogeneous viscous nonthermal nonextensive astrofluid in the presence of turbulence pressure is illustratively analyzed. The constitutive thermal species, lighter electrons and ions, are thermostatistically treated with the nonthermal κ-distribution laws. The inertial species, such as identical heavier neutral and charged dust microspheres, are modelled in the turbulent fluid framework. All the possible linear processes responsible for dust-dust collisions are accounted. The Larson logatropic equations of state relating the dust thermal (linear) and turbulence (nonlinear) pressures with dust densities are included. A regular linear normal perturbation analysis (local) over the complex astrocloud ensues in a generalized quartic dispersion relation with unique nature of plasma-dependent multi-parametric coefficients. A numerical standpoint is provided to showcase the basic mode features in a judicious astronomical paradigm. It is shown that both the kinematic viscosity of the dust fluids and nonthermality parameter (kappa, the power-law tail index) of the thermal species act as stabilizing (damping) agent against the gravity; and so forth. The underlying evolutionary microphysics is explored. The significance of redistributing astrofluid material via waveinduced accretion in dynamic nonhomologic structureless cloud collapse leading to hierarchical astrostructure formation is actualized.

Physical modeling of Tibetan bowls

NASA Astrophysics Data System (ADS)

Antunes, Jose; Inacio, Octavio

2004-05-01

Tibetan bowls produce rich penetrating sounds, used in musical contexts and to induce a state of relaxation for meditation or therapy purposes. To understand the dynamics of these instruments under impact and rubbing excitation, we developed a simulation method based on the modal approach, following our previous papers on physical modeling of plucked/bowed strings and impacted/bowed bars. This technique is based on a compact representation of the system dynamics, in terms of the unconstrained bowl modes. Nonlinear contact/friction interaction forces, between the exciter (puja) and the bowl, are computed at each time step and projected on the bowl modal basis, followed by step integration of the modal equations. We explore the behavior of two different-sized bowls, for extensive ranges of excitation conditions (contact/friction parameters, normal force, and tangential puja velocity). Numerical results and experiments show that various self-excited motions may arise depending on the playing conditions and, mainly, on the contact/friction interaction parameters. Indeed, triggering of a given bowl modal frequency mainly depends on the puja material. Computed animations and experiments demonstrate that self-excited modes spin, following the puja motion. Accordingly, the sensed pressure field pulsates, with frequency controlled by the puja spinning velocity and the spatial pattern of the singing mode.

Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities.

PubMed Central

Loppnow, G R; Mathies, R A

1988-01-01

Resonance Raman excitation profiles have been measured for the bovine visual pigment rhodopsin using excitation wavelengths ranging from 457.9 to 647.1 nm. A complete Franck-Condon analysis of the absorption spectrum and resonance Raman excitation profiles has been performed using an excited-state, time-dependent wavepacket propagation technique. This has enabled us to determine the change in geometry upon electronic excitation of rhodopsin's 11-cis-retinal protonated Schiff base chromophore along 25 normal coordinates. Intense low-frequency Raman lines are observed at 98, 135, 249, 336, and 461 cm-1 whose intensities provide quantitative, mode-specific information about the excited-state torsional deformations that lead to isomerization. The dominant contribution to the width of the absorption band in rhodopsin results from Franck-Condon progressions in the 1,549 cm-1 ethylenic normal mode. The lack of vibronic structure in the absorption spectrum is shown to be caused by extensive progressions in low-frequency torsional modes and a large homogeneous linewidth (170 cm-1 half-width) together with thermal population of low-frequency modes and inhomogeneous site distribution effects. The resonance Raman cross-sections of rhodopsin are unusually weak because the excited-state wavepacket moves rapidly (approximately 35 fs) and permanently away from the Franck-Condon geometry along skeletal stretching and torsional coordinates. PMID:3416032

Elementary dispersion analysis of some mimetic discretizations on triangular C-grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korn, P., E-mail: peter.korn@mpimet.mpg.de; Danilov, S.; A.M. Obukhov Institute of Atmospheric Physics, Moscow

2017-02-01

Spurious modes supported by triangular C-grids limit their application for modeling large-scale atmospheric and oceanic flows. Their behavior can be modified within a mimetic approach that generalizes the scalar product underlying the triangular C-grid discretization. The mimetic approach provides a discrete continuity equation which operates on an averaged combination of normal edge velocities instead of normal edge velocities proper. An elementary analysis of the wave dispersion of the new discretization for Poincaré, Rossby and Kelvin waves shows that, although spurious Poincaré modes are preserved, their frequency tends to zero in the limit of small wavenumbers, which removes the divergence noisemore » in this limit. However, the frequencies of spurious and physical modes become close on shorter scales indicating that spurious modes can be excited unless high-frequency short-scale motions are effectively filtered in numerical codes. We argue that filtering by viscous dissipation is more efficient in the mimetic approach than in the standard C-grid discretization. Lumping of mass matrices appearing with the velocity time derivative in the mimetic discretization only slightly reduces the accuracy of the wave dispersion and can be used in practice. Thus, the mimetic approach cures some difficulties of the traditional triangular C-grid discretization but may still need appropriately tuned viscosity to filter small scales and high frequencies in solutions of full primitive equations when these are excited by nonlinear dynamics.« less

Correlation of finite element free vibration predictions using random vibration test data. M.S. Thesis - Cleveland State Univ.

NASA Technical Reports Server (NTRS)

Chambers, Jeffrey A.

1994-01-01

Finite element analysis is regularly used during the engineering cycle of mechanical systems to predict the response to static, thermal, and dynamic loads. The finite element model (FEM) used to represent the system is often correlated with physical test results to determine the validity of analytical results provided. Results from dynamic testing provide one means for performing this correlation. One of the most common methods of measuring accuracy is by classical modal testing, whereby vibratory mode shapes are compared to mode shapes provided by finite element analysis. The degree of correlation between the test and analytical mode shapes can be shown mathematically using the cross orthogonality check. A great deal of time and effort can be exhausted in generating the set of test acquired mode shapes needed for the cross orthogonality check. In most situations response data from vibration tests are digitally processed to generate the mode shapes from a combination of modal parameters, forcing functions, and recorded response data. An alternate method is proposed in which the same correlation of analytical and test acquired mode shapes can be achieved without conducting the modal survey. Instead a procedure is detailed in which a minimum of test information, specifically the acceleration response data from a random vibration test, is used to generate a set of equivalent local accelerations to be applied to the reduced analytical model at discrete points corresponding to the test measurement locations. The static solution of the analytical model then produces a set of deformations that once normalized can be used to represent the test acquired mode shapes in the cross orthogonality relation. The method proposed has been shown to provide accurate results for both a simple analytical model as well as a complex space flight structure.

IR spectral assignments for the hydrated excess proton in liquid water.

PubMed

Biswas, Rajib; Carpenter, William; Fournier, Joseph A; Voth, Gregory A; Tokmakoff, Andrei

2017-04-21

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm -1 for every local proton configuration, with the region 2000-2600 cm -1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H + ⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H 5 O2+moiety.

IR spectral assignments for the hydrated excess proton in liquid water

NASA Astrophysics Data System (ADS)

Biswas, Rajib; Carpenter, William; Fournier, Joseph A.; Voth, Gregory A.; Tokmakoff, Andrei

2017-04-01

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5+O2 moiety.

Respirator triggering of electron beam computed tomography (EBCT): evaluation of dynamic changes during mechanical expiration in the traumatized patient

NASA Astrophysics Data System (ADS)

Recheis, Wolfgang A.; Kleinsasser, Axel; Hatschenberger, Robert; Knapp, Rudolf; zur Nedden, Dieter; Hoermann, Christoph

1999-05-01

The purpose of this project is to evaluate the dynamic changes during expiration at different levels of positive end- expiratory pressure (PEEP) in the ventilated patient. We wanted to discriminate between normal lung function and acute respiratory distress syndrome (ARDS). After approval by the local Ethic Committee we studied two ventilated patients: (1) with normal lung function; (2) ARDS). We used the 50 ms scan mode of the EBCT. The beam was positioned 1 cm above the diaphragm. The table position remained unchanged. An electronic trigger was developed, that utilizes the respirators synchronizing signal to start the EBCT at the onset of expiration. During controlled mechanical expiration at two levels of PEEP (0 and 15 cm H2O), pulmonary aeration was rated as: well-aerated (-900HU/-500HU), poorly- aerated (-500HU/-100HU) and non-aerated (-100HU/+100HU). Pathological and normal lung function showed different dynamic changes (FIG.4-12). The different PEEP levels resulted in a significant change of pulmonary aeration in the same patient. Although we studied only a very limited number of patients, respirator triggered EBCT may be accurate in discriminating pathological changes due to the abnormal lung function in the mechanically ventilated patient.

Inhomogeneity of epidemic spreading with entropy-based infected clusters.

PubMed

Wen-Jie, Zhou; Xing-Yuan, Wang

2013-12-01

Considering the difference in the sizes of the infected clusters in the dynamic complex networks, the normalized entropy based on infected clusters (δ*) is proposed to characterize the inhomogeneity of epidemic spreading. δ* gives information on the variability of the infected clusters in the system. We investigate the variation in the inhomogeneity of the distribution of the epidemic with the absolute velocity v of moving agent, the infection density ρ, and the interaction radius r. By comparing δ* in the dynamic networks with δH* in homogeneous mode, the simulation experiments show that the inhomogeneity of epidemic spreading becomes smaller with the increase of v, ρ, r.

NERVA dynamic analysis methodology, SPRVIB

NASA Technical Reports Server (NTRS)

Vronay, D. F.

1972-01-01

The general dynamic computer code called SPRVIB (Spring Vib) developed in support of the NERVA (nuclear engine for rocket vehicle application) program is described. Using normal mode techniques, the program computes kinematical responses of a structure caused by various combinations of harmonic and elliptic forcing functions or base excitations. Provision is made for a graphical type of force or base excitation input to the structure. A description of the required input format and a listing of the program are presented, along with several examples illustrating the use of the program. SPRVIB is written in FORTRAN 4 computer language for use on the CDC 6600 or the IBM 360/75 computers.

High-Frequency Normal Mode Propagation in Aluminum Cylinders

USGS Publications Warehouse

Lee, Myung W.; Waite, William F.

2009-01-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sibaev, M.; Crittenden, D. L., E-mail: deborah.crittenden@canterbury.ac.nz

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{sup −1} in fundamental frequencies, on average, across a sizable testmore » 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/.« less

Mode division multiplexing technology for single-fiber optical trapping axial-position adjustment.

PubMed

Liu, Zhihai; Wang, Lei; Liang, Peibo; Zhang, Yu; Yang, Jun; Yuan, Libo

2013-07-15

We demonstrate trapped yeast cell axial-position adjustment without moving the optical fiber in a single-fiber optical trapping system. The dynamic axial-position adjustment is realized by controlling the power ratio of the fundamental mode beam (LP01) and the low-order mode beam (LP11) generated in a normal single-core fiber. In order to separate the trapping positions produced by the two mode beams, we fabricate a special fiber tapered tip with a selective two-step method. A yeast cell of 6 μm diameter is moved along the optical axis direction for a distance of ~3 μm. To the best of our knowledge, this is the first demonstration of the trapping position adjustment without moving the fiber for single-fiber optical tweezers. The excitation and utilization of multimode beams in a single fiber constitutes a new development for single-fiber optical trapping and makes possible more practical applications in biomedical research fields.

Hierarchical nonlinear dynamics of human attention.

PubMed

Rabinovich, Mikhail I; Tristan, Irma; Varona, Pablo

2015-08-01

Attention is the process of focusing mental resources on a specific cognitive/behavioral task. Such brain dynamics involves different partially overlapping brain functional networks whose interconnections change in time according to the performance stage, and can be stimulus-driven or induced by an intrinsically generated goal. The corresponding activity can be described by different families of spatiotemporal discrete patterns or sequential dynamic modes. Since mental resources are finite, attention modalities compete with each other at all levels of the hierarchy, from perception to decision making and behavior. Cognitive activity is a dynamical process and attention possesses some universal dynamical characteristics. Thus, it is time to apply nonlinear dynamical theory for the description and prediction of hierarchical attentional tasks. Such theory has to include the analyses of attentional control stability, the time cost of attention switching, the finite capacity of informational resources in the brain, and the normal and pathological bifurcations of attention sequential dynamics. In this paper we have integrated today's knowledge, models and results in these directions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Guided-mode interactions in thin films with surface corrugation

NASA Astrophysics Data System (ADS)

Seshadri, S. R.

1994-12-01

The guided modes in a thin-film planar dielectric waveguide sandwiched between a cover and a substrate (two different dielectrics) are considered. The interface between the cover and the film has a smooth corrugation in the longitudinal direction. For weak corrugations, the guided-mode interactions are investigated using the expansion in terms of ideal normal modes. A corresponding treament is given for the not-so-weak corrugations using the expansion in terms of local normal modes. The coupling coefficients are evaluated and reduced to simple forms. The theories are specialized for the treatment of contradirectional coupling between two guided modes taking place selectively in the neighborhood of the Bragg frequency. The coupled-mode equations governing the contradirectional interaction obtained from the local normal mode expansion procedure, in the limit of weak periodic corrugations, are identical to those deduced directly using the ideal normal mode expansion technique. The treatments for both the transverse electric and the transvers magnetic modes are included.

Normal Mode Derived Models of the Physical Properties of Earth's Outer Core

NASA Astrophysics Data System (ADS)

Irving, J. C. E.; Cottaar, S.; Lekic, V.; Wu, W.

2017-12-01

Earth's outer core, the largest reservoir of metal in our planet, is comprised of an iron alloy of an uncertain composition. Its dynamical behaviour is responsible for the generation of Earth's magnetic field, with convection driven both by thermal and chemical buoyancy fluxes. Existing models of the seismic velocity and density of the outer core exhibit some variation, and there are only a small number of models which aim to represent the outer core's density.It is therefore important that we develop a better understanding of the physical properties of the outer core. Though most of the outer core is likely to be well mixed, it is possible that the uppermost outer core is stably stratified: it may be enriched in light elements released during the growth of the solid, iron enriched, inner core; by elements dissolved from the mantle into the outer core; or by exsolution of compounds previously dissolved in the liquid metal which will eventually be swept into the mantle. The stratified layer may host MAC or Rossby waves and it could impede communication between the chemically differentiated mantle and outer core, including screening out some of the geodynamo's signal. We use normal mode center frequencies to estimate the physical properties of the outer core in a Bayesian framework. We estimate the mineral physical parameters needed to best produce velocity and density models of the outer core which are consistent with the normal mode observations. We require that our models satisfy realistic physical constraints. We create models of the outer core with and without a distinct uppermost layer and assess the importance of this region.Our normal mode-derived models are compared with observations of body waves which travel through the outer core. In particular, we consider SmKS waves which are especially sensitive to the uppermost outer core and are therefore an important way to understand the robustness of our models.

A Coupled Aeroelastic Model for Launch Vehicle Stability Analysis

NASA Technical Reports Server (NTRS)

Orr, Jeb S.

2010-01-01

A technique for incorporating distributed aerodynamic normal forces and aeroelastic coupling effects into a stability analysis model of a launch vehicle is presented. The formulation augments the linear state-space launch vehicle plant dynamics that are compactly derived as a system of coupled linear differential equations representing small angular and translational perturbations of the rigid body, nozzle, and sloshing propellant coupled with normal vibration of a set of orthogonal modes. The interaction of generalized forces due to aeroelastic coupling and thrust can be expressed as a set of augmenting non-diagonal stiffness and damping matrices in modal coordinates with no penalty on system order. While the eigenvalues of the structural response in the presence of thrust and aeroelastic forcing can be predicted at a given flight condition independent of the remaining degrees of freedom, the coupled model provides confidence in closed-loop stability in the presence of rigid-body, slosh, and actuator dynamics. Simulation results are presented that characterize the coupled dynamic response of the Ares I launch vehicle and the impact of aeroelasticity on control system stability margins.

Reynolds-number-dependent dynamical transitions on hydrodynamic synchronization modes of externally driven colloids

NASA Astrophysics Data System (ADS)

Oyama, Norihiro; Teshigawara, Kosuke; Molina, John Jairo; Yamamoto, Ryoichi; Taniguchi, Takashi

2018-03-01

The collective dynamics of externally driven Np-colloidal systems (1 ≤Np≤4 ) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number as determined by the strength of the external driving force and the confining wall distance. For a system with Np=3 , we found that at a critical Reynolds number a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally. The dynamical mode transition was analyzed in detail from the following two viewpoints: (1) spectrum analysis of the time evolution of a tagged particle velocity and (2) the relative acceleration of the doublet cluster with respect to the singlet particle. For a system with Np=4 , we found similar dynamical mode transitions from the doublet-singlet-singlet mode to the triplet-singlet mode and further to the quartet mode.

Reynolds-number-dependent dynamical transitions on hydrodynamic synchronization modes of externally driven colloids.

PubMed

Oyama, Norihiro; Teshigawara, Kosuke; Molina, John Jairo; Yamamoto, Ryoichi; Taniguchi, Takashi

2018-03-01

The collective dynamics of externally driven N_{p}-colloidal systems (1≤N_{p}≤4) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number as determined by the strength of the external driving force and the confining wall distance. For a system with N_{p}=3, we found that at a critical Reynolds number a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally. The dynamical mode transition was analyzed in detail from the following two viewpoints: (1) spectrum analysis of the time evolution of a tagged particle velocity and (2) the relative acceleration of the doublet cluster with respect to the singlet particle. For a system with N_{p}=4, we found similar dynamical mode transitions from the doublet-singlet-singlet mode to the triplet-singlet mode and further to the quartet mode.

State-to-state mode selectivity in the HD + OH reaction: Perspectives from two product channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Bin; Guo, Hua, E-mail: hguo@unm.edu; Sun, Zhigang

The state-to-state quantum dynamics (J{sub tot} = 0) of the HD + OH(υ{sub 2} = 0, 1) reaction is studied using a reactant coordinate based method, which allows the analysis of both the H + DOH and D + HOH channels with a single propagation. The stretching vibration of the newly formed bond, namely, the OD bond in DOH and one OH bond in HOH, is excited, thanks to its strong coupling with the reaction coordinate at the transition state. On the other hand, the vibrational energy deposited into the OH reactant (υ{sub 2} = 1) is sequestered during themore » reaction in the spectator OH mode. The combined effect leads to the excitation of both the OD and OH stretching modes in the DOH product, and the dominance of the (002) normal-mode state population in the HOH product, which in the local-mode picture corresponds to the excitation of both OH bonds with one quantum each. The energy flow in this prototypical tetratomic reaction can be understood in terms of the sudden vector projection model.« less

First principles study of vibrational dynamics of ceria-titania hybrid clusters

NASA Astrophysics Data System (ADS)

Majid, Abdul; Bibi, Maryam

2017-04-01

Density functional theory based calculations were performed to study vibrational properties of ceria, titania, and ceria-titania hybrid clusters. The findings revealed the dominance of vibrations related to oxygen when compared to those of metallic atoms in the clusters. In case of hybrid cluster, the softening of normal modes related to exterior oxygen atoms in ceria and softening/hardening of high/low frequency modes related to titania dimmers are observed. The results calculated for monomers conform to symmetry predictions according to which three IR and three Raman active modes were detected for TiO2, whereas two IR active and one Raman active modes were observed for CeO2. The comparative analysis indicates that the hybrid cluster CeTiO4 contains simultaneous vibrational fingerprints of the component dimmers. The symmetry, nature of vibrations, IR and Raman activity, intensities, and atomic involvement in different modes of the clusters are described in detail. The study points to engineering of CeTiO4 to tailor its properties for technological visible region applications in photocatalytic and electrochemical devices.

Free energy and entropy of a dipolar liquid by computer simulations

NASA Astrophysics Data System (ADS)

Palomar, Ricardo; Sesé, Gemma

2018-02-01

Thermodynamic properties for a system composed of dipolar molecules are computed. Free energy is evaluated by means of the thermodynamic integration technique, and it is also estimated by using a perturbation theory approach, in which every molecule is modeled as a hard sphere within a square well, with an electric dipole at its center. The hard sphere diameter, the range and depth of the well, and the dipole moment have been calculated from properties easily obtained in molecular dynamics simulations. Connection between entropy and dynamical properties is explored in the liquid and supercooled states by using instantaneous normal mode calculations. A model is proposed in order to analyze translation and rotation contributions to entropy separately. Both contributions decrease upon cooling, and a logarithmic correlation between excess entropy associated with translation and the corresponding proportion of imaginary frequency modes is encountered. Rosenfeld scaling law between reduced diffusion and excess entropy is tested, and the origin of its failure at low temperatures is investigated.

On using the Hilbert transform for blind identification of complex modes: A practical approach

NASA Astrophysics Data System (ADS)

Antunes, Jose; Debut, Vincent; Piteau, Pilippe; Delaune, Xavier; Borsoi, Laurent

2018-01-01

The modal identification of dynamical systems under operational conditions, when subjected to wide-band unmeasured excitations, is today a viable alternative to more traditional modal identification approaches based on processing sets of measured FRFs or impulse responses. Among current techniques for performing operational modal identification, the so-called blind identification methods are the subject of considerable investigation. In particular, the SOBI (Second-Order Blind Identification) method was found to be quite efficient. SOBI was originally developed for systems with normal modes. To address systems with complex modes, various extension approaches have been proposed, in particular: (a) Using a first-order state-space formulation for the system dynamics; (b) Building complex analytic signals from the measured responses using the Hilbert transform. In this paper we further explore the latter option, which is conceptually interesting while preserving the model order and size. Focus is on applicability of the SOBI technique for extracting the modal responses from analytic signals built from a set of vibratory responses. The novelty of this work is to propose a straightforward computational procedure for obtaining the complex cross-correlation response matrix to be used for the modal identification procedure. After clarifying subtle aspects of the general theoretical framework, we demonstrate that the correlation matrix of the analytic responses can be computed through a Hilbert transform of the real correlation matrix, so that the actual time-domain responses are no longer required for modal identification purposes. The numerical validation of the proposed technique is presented based on time-domain simulations of a conceptual physical multi-modal system, designed to display modes ranging from normal to highly complex, while keeping modal damping low and nearly independent of the modal complexity, and which can prove very interesting in test bench applications. Numerical results for complex modal identifications are presented, and the quality of the identified modal matrix and modal responses, extracted using the complex SOBI technique and implementing the proposed formulation, is assessed.

Normalized modes at selected points without normalization

NASA Astrophysics Data System (ADS)

Kausel, Eduardo

2018-04-01

As every textbook on linear algebra demonstrates, the eigenvectors for the general eigenvalue problem | K - λM | = 0 involving two real, symmetric, positive definite matrices K , M satisfy some well-defined orthogonality conditions. Equally well-known is the fact that those eigenvectors can be normalized so that their modal mass μ =ϕT Mϕ is unity: it suffices to divide each unscaled mode by the square root of the modal mass. Thus, the normalization is the result of an explicit calculation applied to the modes after they were obtained by some means. However, we show herein that the normalized modes are not merely convenient forms of scaling, but that they are actually intrinsic properties of the pair of matrices K , M, that is, the matrices already "know" about normalization even before the modes have been obtained. This means that we can obtain individual components of the normalized modes directly from the eigenvalue problem, and without needing to obtain either all of the modes or for that matter, any one complete mode. These results are achieved by means of the residue theorem of operational calculus, a finding that is rather remarkable inasmuch as the residues themselves do not make use of any orthogonality conditions or normalization in the first place. It appears that this obscure property connecting the general eigenvalue problem of modal analysis with the residue theorem of operational calculus may have been overlooked up until now, but which has in turn interesting theoretical implications.Á

Application and Evaluation of Control Modes for Risk-Based Engine Performance Enhancements

NASA Technical Reports Server (NTRS)

Liu, Yuan; Litt, Jonathan S.; Sowers, T. Shane; Owen, A. Karl (Compiler); Guo, Ten-Huei

2014-01-01

The engine control system for civil transport aircraft imposes operational limits on the propulsion system to ensure compliance with safety standards. However, during certain emergency situations, aircraft survivability may benefit from engine performance beyond its normal limits despite the increased risk of failure. Accordingly, control modes were developed to improve the maximum thrust output and responsiveness of a generic high-bypass turbofan engine. The algorithms were designed such that the enhanced performance would always constitute an elevation in failure risk to a consistent predefined likelihood. This paper presents an application of these risk-based control modes to a combined engine/aircraft model. Through computer and piloted simulation tests, the aim is to present a notional implementation of these modes, evaluate their effects on a generic airframe, and demonstrate their usefulness during emergency flight situations. Results show that minimal control effort is required to compensate for the changes in flight dynamics due to control mode activation. The benefits gained from enhanced engine performance for various runway incursion scenarios are investigated. Finally, the control modes are shown to protect against potential instabilities during propulsion-only flight where all aircraft control surfaces are inoperable.

Application and Evaluation of Control Modes for Risk-Based Engine Performance Enhancements

NASA Technical Reports Server (NTRS)

Liu, Yuan; Litt, Jonathan S.; Sowers, T. Shane; Owen, A. Karl; Guo, Ten-Huei

2015-01-01

The engine control system for civil transport aircraft imposes operational limits on the propulsion system to ensure compliance with safety standards. However, during certain emergency situations, aircraft survivability may benefit from engine performance beyond its normal limits despite the increased risk of failure. Accordingly, control modes were developed to improve the maximum thrust output and responsiveness of a generic high-bypass turbofan engine. The algorithms were designed such that the enhanced performance would always constitute an elevation in failure risk to a consistent predefined likelihood. This paper presents an application of these risk-based control modes to a combined engine/aircraft model. Through computer and piloted simulation tests, the aim is to present a notional implementation of these modes, evaluate their effects on a generic airframe, and demonstrate their usefulness during emergency flight situations. Results show that minimal control effort is required to compensate for the changes in flight dynamics due to control mode activation. The benefits gained from enhanced engine performance for various runway incursion scenarios are investigated. Finally, the control modes are shown to protect against potential instabilities during propulsion-only flight where all aircraft control surfaces are inoperable.

Mode-Locking Behavior of Izhikevich Neuron Under Periodic External Forcing

NASA Astrophysics Data System (ADS)

Farokhniaee, Amirali; Large, Edward

2015-03-01

In this study we obtained the regions of existence of various mode-locked states on the periodic-strength plane, which are called Arnold Tongues, for Izhikevich neurons. The study is based on the new model for neurons by Izhikevich (2003) which is the normal form of Hodgkin-Huxley neuron. This model is much simpler in terms of the dimension of the coupled non-linear differential equations compared to other existing models, but excellent for generating the complex spiking patterns observed in real neurons. Many neurons in the auditory system of the brain must encode amplitude variations of a periodic signal. These neurons under periodic stimulation display rich dynamical states including mode-locking and chaotic responses. Periodic stimuli such as sinusoidal waves and amplitude modulated (AM) sounds can lead to various forms of n : m mode-locked states, similar to mode-locking phenomenon in a LASER resonance cavity. Obtaining Arnold tongues provides useful insight into the organization of mode-locking behavior of neurons under periodic forcing. Hence we can describe the construction of harmonic and sub-harmonic responses in the early processing stages of the auditory system, such as the auditory nerve and cochlear nucleus.

Using Entanglement to Measure Temperatures and Frequencies of Individual Normal Modes in a Strongly Coupled 2D Plasma of Be+

NASA Astrophysics Data System (ADS)

Sawyer, Brian; Britton, Joseph; Keith, Adam; Wang, C.-C. Joseph; Freericks, James; Bollinger, John

2013-10-01

Confined non-neutral plasmas of ions in the regime of strong coupling serve as a platform for studying a diverse range of phenomena including: dense astrophysical matter, quantum computation/simulation, dynamical decoupling, and precision measurements. We describe a method of simultaneously detecting and measuring the temperature of transverse plasma modes in two-dimensional crystals of cold 9Be+ confined within a Penning trap. We employ a spin-dependent optical dipole force (ODF) generated from off-resonant laser beams to directly excite plasma modes transverse to the crystal plane of ~ 100 ions. Extremely small mode excitations (~ 1 nm) may be detected through spin-motion entanglement induced by an ODF as small as 10 yN , and even the shortest-wavelength (~ 20 μm) modes are excited and detected through the spin dependence of the force. This mode-specific thermometry has facilitated characterization and mitigation of ion heating sources in this system. Future work may include sub-yN force detection, spectroscopy/thermometry of the more complex in-plane oscillations, and implementation/confirmation of sub-Doppler cooling. The authors acknowledge support from the DARPA-OLE program.

Exact mode volume and Purcell factor of open optical systems

NASA Astrophysics Data System (ADS)

Muljarov, E. A.; Langbein, W.

2016-12-01

The Purcell factor quantifies the change of the radiative decay of a dipole in an electromagnetic environment relative to free space. Designing this factor is at the heart of photonics technology, striving to develop ever smaller or less lossy optical resonators. The Purcell factor can be expressed using the electromagnetic eigenmodes of the resonators, introducing the notion of a mode volume for each mode. This approach allows an analytic treatment, reducing the Purcell factor and other observables to sums over eigenmode resonances. Calculating the mode volumes requires a correct normalization of the modes. We introduce an exact normalization of modes, not relying on perfectly matched layers. We present an analytic theory of the Purcell effect based on this exact mode normalization and the resulting effective mode volume. We use a homogeneous dielectric sphere in vacuum, which is analytically solvable, to exemplify these findings. We furthermore verify the applicability of the normalization to numerically determined modes of a finite dielectric cylinder.

3D dust clouds (Yukawa Balls) in strongly coupled dusty plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melzer, A.; Passvogel, M.; Miksch, T.

2010-06-16

Three-dimensional finite systems of charged dust particles confined to concentric spherical shells in a dusty plasma, so-called 'Yukawa balls', have been studied with respect to their static and dynamic properties. Here, we review the charging of particles in a dusty plasma discharge by computer simulations and the respective particle arrangements. The normal mode spectrum of Yukawa balls is measured from the 3D thermal Brownian motion of the dust particles around their equilibrium positions.

Washout of ⁸²Rb as a marker of impaired tissue integrity, obtained by list-mode cardiac PET/CT: relationship with perfusion/metabolism patterns of myocardial viability.

PubMed

Chien, David T; Bravo, Paco; Higuchi, Takahiro; Merrill, Jennifer; Bengel, Frank M

2011-08-01

Myocardial washout of the potassium analogue (82)Rb may indicate tissue impairment. Few studies have evaluated its usefulness for viability assessment, and controversial results were reported. We revisited this topic using list-mode positron emission tomography (PET)/CT. A total of 22 patients with chronic ischemic cardiomyopathy (ICM) and 11 control subjects with normal CT coronary angiogram were studied. Rest (82)Rb PET/CT studies were acquired in list mode and resampled to static, gated, and dynamic images. Using a 17-segment model, (82)Rb washout was determined by monoexponential fitting of myocardial time-activity curves. In ICM patients, (18)F-fluorodeoxyglucose (FDG) studies were obtained in the same session and segments were classified as normally perfused, mismatch, or matched defect. (82)Rb washout was minimal and homogeneous in control subjects. Normally perfused segments of ICM did not differ (p = 0.33). ICM patients had a left ventricular ejection fraction (LVEF) of 25 ± 12%, 25/353 mismatched, and 46/353 matched defect segments. (82)Rb washout was higher in hypoperfused vs normal segments (p < 0.05), but not different between mismatch and matched defect (p = 0.18). Intraindividual analysis in nine patients showing both FDG mismatch and matched defect confirmed absence of differences. Overall, segmental (82)Rb washout correlated inversely with (82)Rb uptake (r = -0.70; p < 0.05) and less well with FDG uptake (r = -0.31; p < 0.05). Using state-of-the-art PET/CT technology for myocardial viability assessment, (82)Rb washout does not distinguish between perfusion/metabolism patterns of hibernating myocardium and scar. Tissue integrity may be at least partially impaired in hibernation.

Off-equilibrium infrared structure of self-interacting scalar fields: Universal scaling, vortex-antivortex superfluid dynamics, and Bose-Einstein condensation

NASA Astrophysics Data System (ADS)

Deng, Jian; Schlichting, Soeren; Venugopalan, Raju; Wang, Qun

2018-05-01

We map the infrared dynamics of a relativistic single-component (N =1 ) interacting scalar field theory to that of nonrelativistic complex scalar fields. The Gross-Pitaevskii (GP) equation, describing the real-time dynamics of single-component ultracold Bose gases, is obtained at first nontrivial order in an expansion proportional to the powers of λ ϕ2/m2 where λ , ϕ , and m are the coupling constant, the scalar field, and the particle mass respectively. Our analytical studies are corroborated by numerical simulations of the spatial and momentum structure of overoccupied scalar fields in (2+1)-dimensions. Universal scaling of infrared modes, vortex-antivortex superfluid dynamics, and the off-equilibrium formation of a Bose-Einstein condensate are observed. Our results for the universal scaling exponents are in agreement with those extracted in the numerical simulations of the GP equation. As in these simulations, we observe coarsening phase kinetics in the Bose superfluid with strongly anomalous scaling exponents relative to that of vertex resummed kinetic theory. Our relativistic field theory framework further allows one to study more closely the coupling between superfluid and normal fluid modes, specifically the turbulent momentum and spatial structure of the coupling between a quasiparticle cascade to the infrared and an energy cascade to the ultraviolet. We outline possible applications of the formalism to the dynamics of vortex-antivortex formation and to the off-equilibrium dynamics of the strongly interacting matter formed in heavy-ion collisions.

Causal analysis of self-sustaining processes in the logarithmic layer of wall-bounded turbulence

NASA Astrophysics Data System (ADS)

Bae, H. J.; Encinar, M. P.; Lozano-Durán, A.

2018-04-01

Despite the large amount of information provided by direct numerical simulations of turbulent flows, their underlying dynamics remain elusive even in the most simple and canonical configurations. Most common approaches to investigate the turbulence phenomena do not provide a clear causal inference between events, which is essential to determine the dynamics of self-sustaining processes. In the present work, we examine the causal interactions between streaks, rolls and mean shear in the logarithmic layer of a minimal turbulent channel flow. Causality between structures is assessed in a non-intrusive manner by transfer entropy, i.e., how much the uncertainty of one structure is reduced by knowing the past states of the others. We choose to represent streaks by the first Fourier modes of the streamwise velocity, while rolls are defined by the wall-normal and spanwise velocity modes. The results show that the process is mainly unidirectional rather than cyclic, and that the log-layer motions are sustained by extracting energy from the mean shear which controls the dynamics and time-scales. The well-known lift-up effect is also identified, but shown to be of secondary importance in the causal network between shear, streaks and rolls.

Metal isotope and density functional study of the tetracarboxylatodicopper(II) core vibrations

NASA Astrophysics Data System (ADS)

Drożdżewski, Piotr; Brożyna, Anna

2005-11-01

Vibrational spectra of tetrakis(acetato)diaquadicopper(II) complex have been deeply examined in order to provide a detailed description of dynamics of [Cu 2O 8C 4] core being a typical structural unit of most copper(II) carboxylates. Low frequency bands related to significant motions of metal atoms were detected by metal isotope substitution. Observed spectra and isotope shifts were reproduced in DFT calculations. For clear presentation of computed normal vibrations, a D 4h symmetry approximation was successfully applied. Basing on observed isotope shifts and calculation results, all skeletal vibrations have been analyzed including normal mode with the largest Cu ⋯Cu stretching amplitude assigned to Raman band at 178 cm -1.

Demixing-stimulated lane formation in binary complex plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, C.-R.; Jiang, K.; Suetterlin, K. R.

2011-11-29

Recently lane formation and phase separation have been reported for experiments with binary complex plasmas in the PK3-Plus laboratory onboard the International Space Station (ISS). Positive non-additivity of particle interactions is known to stimulate phase separation (demixing), but its effect on lane formation is unknown. In this work, we used Langevin dynamics (LD) simulation to probe the role of non-additivity interactions on lane formation. The competition between laning and demixing leads to thicker lanes. Analysis based on anisotropic scaling indices reveals a crossover from normal laning mode to a demixing-stimulated laning mode. Extensive numerical simulations enabled us to identify amore » critical value of the non-additivity parameter {Delta} for the crossover.« less

A new method to real-normalize measured complex modes

NASA Technical Reports Server (NTRS)

Wei, Max L.; Allemang, Randall J.; Zhang, Qiang; Brown, David L.

1987-01-01

A time domain subspace iteration technique is presented to compute a set of normal modes from the measured complex modes. By using the proposed method, a large number of physical coordinates are reduced to a smaller number of model or principal coordinates. Subspace free decay time responses are computed using properly scaled complex modal vectors. Companion matrix for the general case of nonproportional damping is then derived in the selected vector subspace. Subspace normal modes are obtained through eigenvalue solution of the (M sub N) sup -1 (K sub N) matrix and transformed back to the physical coordinates to get a set of normal modes. A numerical example is presented to demonstrate the outlined theory.

Investigation of the piezoelectric thimble tactile device operating modes.

PubMed

Bansevicius, Ramutis; Dragasius, Egidijus; Grigas, Vytautas; Jurenas, Vytautas; Mazeika, Darius; Zvironas, Arunas

2014-01-01

A multifunctional device to transfer graphical or text information for blind or visually impaired is presented. The prototype using tactile perception has been designed where information displayed on the screen of electronic device (mobile phone, PC) is transferred by oscillating needle, touching the fingertip. Having the aim to define optimal parameters of the fingertip excitation by needle, the computational analysis of different excitation modes has been carried out. A 3D solid computational finite element model of the skin segment, comprising four main fingertip skin layers (stratum corneum, epidermis, dermis and hypodermis) was built by using ANSYS Workbench FEA software. Harmonic analysis of its stress-strain state under excitation with different frequency (up to 10000 Hz) and harmonic force (0.01 N), acting outer stratum corneum layer in normal direction at one, two or three points has been performed. The influence of the mode of dynamic loading of skin was evaluated (in terms of the tactile signal level) on the basis of the normal and shear elastic strain in dermis, where mechanoreceptors are placed. It is shown that the tactile perception of information, delivered by three vibrating pins, may be influenced by configuration of excitation points (their number and phase of loading) and the frequency of excitation.

Dielectric properties of proteins from simulations: tools and techniques

NASA Astrophysics Data System (ADS)

Simonson, Thomas; Perahia, David

1995-09-01

Tools and techniques to analyze the dielectric properties of proteins are described. Microscopic dielectric properties are determined by a susceptibility tensor of order 3 n, where n is the number of protein atoms. For perturbing charges not too close to the protein, the dielectric relaxation free energy is directly related to the dipole-dipole correlation matrix of the unperturbed protein, or equivalently to the covariance matrix of its atomic displacements. These are straightforward to obtain from existing molecular dynamics packages such as CHARMM or X- PLOR. Macroscopic dielectric properties can be derived from the dipolar fluctuations of the protein, by idealizing the protein as one or more spherical media. The dipolar fluctuations are again directly related to the covariance matrix of the atomic displacements. An interesting consequence is that the quasiharmonic approximation, which by definition exactly reproduces this covariance matrix, gives the protein dielectric constant exactly. Finally a technique is reviewed to obtain normal or quasinormal modes of vibration of symmetric protein assemblies. Using elementary group theory, and eliminating the high-frequency modes of vibration of each monomer, the limiting step in terms of memory and computation is finding the normal modes of a single monomer, with the other monomers held fixed. This technique was used to study the dielectric properties of the Tobacco Mosaic Virus protein disk.

Information processing of visually presented picture and word stimuli by young hearing-impaired and normal-hearing children.

PubMed

Kelly, R R; Tomlison-Keasey, C

1976-12-01

Eleven hearing-impaired children and 11 normal-hearing children (mean = four years 11 months) were visually presented familiar items in either picture or word form. Subjects were asked to recognize the stimuli they had seen from cue cards consisting of pictures or words. They were then asked to recall the sequence of stimuli by arranging the cue cards selected. The hearing-impaired group and normal-hearing subjects performed differently with the picture/picture (P/P) and word/word (W/W) modes in the recognition phase. The hearing impaired performed equally well with both modes (P/P and W/W), while the normal hearing did significantly better on the P/P mode. Furthermore, the normal-hearing group showed no difference in processing like modes (P/P and W/W) when compared to unlike modes (W/P and P/W). In contrast, the hearing-impaired subjects did better on like modes. The results were interpreted, in part, as supporting the position that young normal-hearing children dual code their visual information better than hearing-impaired children.

Flexible Modes Control Using Sliding Mode Observers: Application to Ares I

NASA Technical Reports Server (NTRS)

Shtessel, Yuri B.; Hall, Charles E.; Baev, Simon; Orr, Jeb S.

2010-01-01

The launch vehicle dynamics affected by bending and sloshing modes are considered. Attitude measurement data that are corrupted by flexible modes could yield instability of the vehicle dynamics. Flexible body and sloshing modes are reconstructed by sliding mode observers. The resultant estimates are used to remove the undesirable dynamics from the measurements, and the direct effects of sloshing and bending modes on the launch vehicle are compensated by means of a controller that is designed without taking the bending and sloshing modes into account. A linearized mathematical model of Ares I launch vehicle was derived based on FRACTAL, a linear model developed by NASA/MSFC. The compensated vehicle dynamics with a simple PID controller were studied for the launch vehicle model that included two bending modes, two slosh modes and actuator dynamics. A simulation study demonstrated stable and accurate performance of the flight control system with the augmented simple PID controller without the use of traditional linear bending filters.

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, respectively. The former is used to find the analytical solution of the normal modes (Borcia 2012). Plugging two independent solutions into the latter we investigate the generation mechanism of INMMF. We found R1^1=overbar{partial_z(u_r1 u_z^1)}, R2^1=overbar{partial_r(u_r1 u_r^1)} as source terms responsible for the generation of INMMF. The helical structure of the inertial waves causes the nonlinear terms R1 and R2 to be nonzero, contributing to the generation of INMMF. We used u_ra and u_za obtained from the analytical solution (Borcia 2012) and computed the source terms R1a and R2a and found a structural correspondence with the corresponding field computed from the DNS solution for the three normal modes investigated. The sum of R11 and R21 exhibits a good structural correspondence with INMMF. Interestingly, INMMF magnitude depends on the inertial wave beams and normal modes. For instance we found that INMMF is generated more efficiently for the libration frequency ω=1.58, although the resonant frequency is predicted by the analytical solution to be at ω=1.576 (normal mode (2,1)). Separating the inertial wave beams from the flow field obtained by DNS, using the analytical normal mode solution, we explored the phase lag between inertial wave beams and normal mode. We inferred that the normal mode amplitude is high only if the phase lag between the inertial wave beam and the normal mode is predominantly positive. In this case a high amplitude INMMF amplitude can be found. This supports the hypothesis that the normal modes are generated by the inertial wave beam in analogy to resonant forcing in classical mechanics. Interestingly, the 'optimum' phase lag found is much smaller than π/2. {Acknowledgement:} This work is a part of the project "Mischung und Grundstromanregung durch propagierende Trgheitswellen: Theorie, Experiment und Simulation" supported by the German Science Foundation (DFG). We would like to thank M. Klein, U. Harlander, I. Borcia and E. Schaller for helpful discussions and invaluable contributions. {References:} Borcia, I. D. & Harlander, U. 2012 Inertial waves in a rotating annulus with inclined inner cylinder: comparing the spectrum of wave attractor frequency bands and the eigenspectrum in the limit of zero inclination. Theor. Comput. Fluid Dyn. 27, 397-413.

Mitral annulus motion as determined by M-mode echocardiography in normal dogs and dogs with cardiac disease.

PubMed

Schober, K E; Fuentes, V L

2001-01-01

M-mode echocardiography was used to assess apical mitral annulus motion (MAM) in 103 normal dogs and 101 dogs with cardiac disease, to obtain information on systolic left ventricular long axis function. In normal dogs, a close relationship was found between MAM and body weight (r = 0.80, P < 0.001). There was a weak correlation between MAM and heart rate (r = -0.25, P < 0.05), but no correlation between MAM and age or left ventricular shortening fraction (P > 0.05). Mean MAM (95% confidence intervals) were established for normal dogs of differing body weight, and were 0.70 cm (0.65 to 0.75) in dogs < 15 kg, 1.08 cm (1.03 to 1.13) in dogs weighing 15 to 40 kg, and 1.51 cm (1.21 to 1.81) in dogs > 40 kg. "Cut-off" values to define decreased MAM for normal dogs of differing body weight were 0.45 cm (dogs < 15 kg), 0.80 cm (dogs 15-40 kg), and 1.20 cm (dogs > 40 kg). In dogs with cardiac disease, median MAM was normal in mitral valve endocardiosis or aortic stenosis, but significantly decreased (P < 0.05) in dilated cardiomyopathy. All dogs with mitral valve endocardiosis (n = 54) or aortic stenosis (n = 26) had MAM above the above-mentioned "cut-off" values, suggesting normal or increased left ventricular longitudinal systolic shortening, whereas 81% (17/21) of dogs with dilated cardiomyopathy had MAM below the "cut-off" value, indicating decreased long axis systolic function. It is concluded that MAM may be used to evaluate systolic left ventricular long axis performance in dogs and may add useful information on global left ventricular contraction dynamics.

An assessment of mode-coupling and falling-friction mechanisms in railway curve squeal through a simplified approach

NASA Astrophysics Data System (ADS)

Ding, Bo; Squicciarini, Giacomo; Thompson, David; Corradi, Roberto

2018-06-01

Curve squeal is one of the most annoying types of noise caused by the railway system. It usually occurs when a train or tram is running around tight curves. Although this phenomenon has been studied for many years, the generation mechanism is still the subject of controversy and not fully understood. A negative slope in the friction curve under full sliding has been considered to be the main cause of curve squeal for a long time but more recently mode coupling has been demonstrated to be another possible explanation. Mode coupling relies on the inclusion of both the lateral and vertical dynamics at the contact and an exchange of energy occurs between the normal and the axial directions. The purpose of this paper is to assess the role of the mode-coupling and falling-friction mechanisms in curve squeal through the use of a simple approach based on practical parameter values representative of an actual situation. A tramway wheel is adopted to study the effect of the adhesion coefficient, the lateral contact position, the contact angle and the damping ratio. Cases corresponding to both inner and outer wheels in the curve are considered and it is shown that there are situations in which both wheels can squeal due to mode coupling. Additionally, a negative slope is introduced in the friction curve while keeping active the vertical dynamics in order to analyse both mechanisms together. It is shown that, in the presence of mode coupling, the squealing frequency can differ from the natural frequency of either of the coupled wheel modes. Moreover, a phase difference between wheel vibration in the vertical and lateral directions is observed as a characteristic of mode coupling. For both these features a qualitative comparison is shown with field measurements which show the same behaviour.

Vibrational spectra of water solutions of azoles from QM/MM calculations: effects of solvation.

PubMed

Tanzi, Luana; Ramondo, Fabio; Guidoni, Leonardo

2012-10-18

Using microsolvation models and mixed quantum/classical ab initio molecular dynamics simulations, we investigate the vibrational properties of two azoles in water solution: pyrazole and oxazole. The effects of the water-azole hydrogen bonding are rationalized by an extensive comparison between structural parameters and harmonic frequencies obtained by microsolvation models. Following the effective normal-mode analysis introduced by Martinez et al. [Martinez et al., J. Chem. Phys. 2006, 125, 144106], we identify the vibrational frequencies of the solutes using the decomposition of the vibrational density of states of the gas phase and solution dynamics. The calculated shifts from gas phase to solution are fairly in agreement with the available experimental data.

High speed, wide velocity dynamic range Doppler optical coherence tomography (Part III): in vivo endoscopic imaging of blood flow in the rat and human gastrointestinal tracts

NASA Astrophysics Data System (ADS)

Yang, Victor X. D.; Gordon, Maggie L.; Tang, Shou-Jiang; Marcon, Norman E.; Gardiner, Geoffrey; Qi, Bing; Bisland, Stuart; Seng-Yue, Emily; Lo, Stewart; Pekar, Julius; Wilson, Brian C.; Vitkin, I. Alex

2003-09-01

We previously described a fiber based Doppler optical coherence tomography system [1] capable of imaging embryo cardiac blood flow at 4~16 frames per second with wide velocity dynamic range [2]. Coupling this system to a linear scanning fiber optical catheter design that minimizes friction and vibrations, we report here the initial results of in vivo endoscopic Doppler optical coherence tomography (EDOCT) imaging in normal rat and human esophagus. Microvascular flow in blood vessels less than 100 µm diameter was detected using a combination of color-Doppler and velocity variance imaging modes, during clinical endoscopy using a mobile EDOCT system.

Redistribution of carbonyl stretch mode energy in isolated and solvated N-methylacetamide: kinetic energy spectral density analyses.

PubMed

Jeon, Jonggu; Cho, Minhaeng

2011-12-07

The vibrational energy transfer from the excited carbonyl stretch mode in N-deuterated N-methylacetamide (NMA-d), both in isolation and in a heavy water cluster, is studied with nonequilibrium molecular dynamics (NEMD) simulations, employing a quantum mechanical/molecular mechanical (QM∕MM) force field at the semiempirical PM3 level. The nonequilibrium ensemble of vibrationally excited NMA-d is prepared by perturbing the positions and velocities of the carbonyl C and O atoms and its NEMD trajectories are obtained with a leap-frog algorithm properly modified for the initial perturbation. In addition to the time-domain analysis of the kinetic and potential energies, a novel method for the spectral analysis of the atomic kinetic energies is developed, in terms of the spectral density of kinetic energy, which provides the time-dependent changes of the frequency-resolved kinetic energies without the complications of normal mode analysis at every MD time step. Due to the QM description of the solute electronic structure, the couplings among the normal modes are captured more realistically than with classical force fields. The energy transfer in the isolated NMA-d is found to proceed first from the carbonyl bond to other modes with time scales of 3 ps or less, and then among the other modes over 3-21 ps. In the solvated NMA-d, most of the excess energy is first transferred to other intramolecular modes within 5 ps, which is subsequently dissipated to solvent with 7-19 ps time scales. The contribution of the direct energy transfer from the carbonyl bond to solvent was only 5% with ~7 ps time scale. Solvent reorganization that leads to destabilization of the electrostatic interactions is found to be crucial in the long time relaxation of the excess energy, while the water intramolecular modes do not contribute significantly. Detailed mode-specific energy transfer pathways are deduced for the isolated and solvated NMA-d and they show that the energy transfer in NMA-d is a highly cooperative process among the intramolecular modes and there is no single dominant pathway with more than 30% of transient contribution. © 2011 American Institute of Physics

Helicon normal modes in Proto-MPEX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piotrowicz, Pawel A.; Caneses, Juan F.; Green, David L.

Here, the Proto-MPEX helicon source has been operating in a high electron density 'helicon-mode'. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the 'helicon-mode'. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besidesmore » directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region.« less

Helicon normal modes in Proto-MPEX

DOE PAGES

Piotrowicz, Pawel A.; Caneses, Juan F.; Green, David L.; ...

2018-05-22

Here, the Proto-MPEX helicon source has been operating in a high electron density 'helicon-mode'. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the 'helicon-mode'. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besidesmore » directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region.« less

Excitation power quantities in phase resonance testing of nonlinear systems with phase-locked-loop excitation

NASA Astrophysics Data System (ADS)

Peter, Simon; Leine, Remco I.

2017-11-01

Phase resonance testing is one method for the experimental extraction of nonlinear normal modes. This paper proposes a novel method for nonlinear phase resonance testing. Firstly, the issue of appropriate excitation is approached on the basis of excitation power considerations. Therefore, power quantities known from nonlinear systems theory in electrical engineering are transferred to nonlinear structural dynamics applications. A new power-based nonlinear mode indicator function is derived, which is generally applicable, reliable and easy to implement in experiments. Secondly, the tuning of the excitation phase is automated by the use of a Phase-Locked-Loop controller. This method provides a very user-friendly and fast way for obtaining the backbone curve. Furthermore, the method allows to exploit specific advantages of phase control such as the robustness for lightly damped systems and the stabilization of unstable branches of the frequency response. The reduced tuning time for the excitation makes the commonly used free-decay measurements for the extraction of backbone curves unnecessary. Instead, steady-state measurements for every point of the curve are obtained. In conjunction with the new mode indicator function, the correlation of every measured point with the associated nonlinear normal mode of the underlying conservative system can be evaluated. Moreover, it is shown that the analysis of the excitation power helps to locate sources of inaccuracies in the force appropriation process. The method is illustrated by a numerical example and its functionality in experiments is demonstrated on a benchmark beam structure.

Rigid-flexible coupling dynamic modeling and investigation of a redundantly actuated parallel manipulator with multiple actuation modes

NASA Astrophysics Data System (ADS)

Liang, Dong; Song, Yimin; Sun, Tao; Jin, Xueying

2017-09-01

A systematic dynamic modeling methodology is presented to develop the rigid-flexible coupling dynamic model (RFDM) of an emerging flexible parallel manipulator with multiple actuation modes. By virtue of assumed mode method, the general dynamic model of an arbitrary flexible body with any number of lumped parameters is derived in an explicit closed form, which possesses the modular characteristic. Then the completely dynamic model of system is formulated based on the flexible multi-body dynamics (FMD) theory and the augmented Lagrangian multipliers method. An approach of combining the Udwadia-Kalaba formulation with the hybrid TR-BDF2 numerical algorithm is proposed to address the nonlinear RFDM. Two simulation cases are performed to investigate the dynamic performance of the manipulator with different actuation modes. The results indicate that the redundant actuation modes can effectively attenuate vibration and guarantee higher dynamic performance compared to the traditional non-redundant actuation modes. Finally, a virtual prototype model is developed to demonstrate the validity of the presented RFDM. The systematic methodology proposed in this study can be conveniently extended for the dynamic modeling and controller design of other planar flexible parallel manipulators, especially the emerging ones with multiple actuation modes.

Using chaotic artificial neural networks to model memory in the brain

NASA Astrophysics Data System (ADS)

Aram, Zainab; Jafari, Sajad; Ma, Jun; Sprott, Julien C.; Zendehrouh, Sareh; Pham, Viet-Thanh

2017-03-01

In the current study, a novel model for human memory is proposed based on the chaotic dynamics of artificial neural networks. This new model explains a biological fact about memory which is not yet explained by any other model: There are theories that the brain normally works in a chaotic mode, while during attention it shows ordered behavior. This model uses the periodic windows observed in a previously proposed model for the brain to store and then recollect the information.

The stability of the three transmembrane and the four transmembrane human vitamin K epoxide reductase models

NASA Astrophysics Data System (ADS)

Wu, Sangwook

2016-04-01

The three transmembrane and the four transmembrane helix models are suggested for human vitamin K epoxide reductase (VKOR). In this study, we investigate the stability of the human three transmembrane/four transmembrane VKOR models by employing a coarse-grained normal mode analysis and molecular dynamics simulation. Based on the analysis of the mobility of each transmembrane domain, we suggest that the three transmembrane human VKOR model is more stable than the four transmembrane human VKOR model.

Control of thermal therapies with moving power deposition field.

PubMed

Arora, Dhiraj; Minor, Mark A; Skliar, Mikhail; Roemer, Robert B

2006-03-07

A thermal therapy feedback control approach to control thermal dose using a moving power deposition field is developed and evaluated using simulations. A normal tissue safety objective is incorporated in the controller design by imposing constraints on temperature elevations at selected normal tissue locations. The proposed control technique consists of two stages. The first stage uses a model-based sliding mode controller that dynamically generates an 'ideal' power deposition profile which is generally unrealizable with available heating modalities. Subsequently, in order to approximately realize this spatially distributed idealized power deposition, a constrained quadratic optimizer is implemented to compute intensities and dwell times for a set of pre-selected power deposition fields created by a scanned focused transducer. The dwell times for various power deposition profiles are dynamically generated online as opposed to the commonly employed a priori-decided heating strategies. Dynamic intensity and trajectory generation safeguards the treatment outcome against modelling uncertainties and unknown disturbances. The controller is designed to enforce simultaneous activation of multiple normal tissue temperature constraints by rapidly switching between various power deposition profiles. The hypothesis behind the controller design is that the simultaneous activation of multiple constraints substantially reduces treatment time without compromising normal tissue safety. The controller performance and robustness with respect to parameter uncertainties is evaluated using simulations. The results demonstrate that the proposed controller can successfully deliver the desired thermal dose to the target while maintaining the temperatures at the user-specified normal tissue locations at or below the maximum allowable values. Although demonstrated for the case of a scanned focused ultrasound transducer, the developed approach can be extended to other heating modalities with moving deposition fields, such as external and interstitial ultrasound phased arrays, multiple radiofrequency needle applicators and microwave antennae.

Electromagnetically induced transparency in the case of elliptic polarization of interacting fields

NASA Astrophysics Data System (ADS)

Parshkov, Oleg M.

2018-04-01

The theoretical investigation results of disintegration effect of elliptic polarized shot probe pulses of electromagnetically induced transparency in the counterintuitive superposed elliptic polarized control field and in weak probe field approximation are presented. It is shown that this disintegration occurs because the probe field in the medium is the sum of two normal modes, which correspond to elliptic polarized pulses with different speeds of propagation. The polarization ellipses of normal modes have equal eccentricities and mutually perpendicular major axes. Major axis of polarization ellipse of one normal mode is parallel to polarization ellipse major axis of control field, and electric vector of this mode rotates in the opposite direction, than electric vector of the control field. The electric vector other normal mode rotates in the same direction that the control field electric vector. The normal mode speed of the first type aforementioned is less than that of the second type. The polarization characteristics of the normal mode depend uniquely on the polarization characteristics of elliptic polarized control field and remain changeless in the propagation process. The theoretical investigation is performed for Λ-scheme of degenerated quantum transitions between 3P0, 3P10 and 3P2 energy levels of 208Pb isotope.

Local thermal energy as a structural indicator in glasses.

PubMed

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-11

Identifying heterogeneous structures in glasses-such as localized soft spots-and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses-an intrinsic signature of glassy frustration-anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal [Formula: see text] density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field-a "softness field"-is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

Experimental and analytical investigation of dynamic characteristics of extension-twist-coupled composite tubular spars

NASA Astrophysics Data System (ADS)

Lake, Renee C.; Izadpanah, Amir P.; Baucom, Robert M.

1993-02-01

The results from a study aimed at improving the dynamic and aerodynamic characteristics of composite rotor blades through the use of extension-twist coupling are presented. A set of extension-twist-coupled composite spars was manufactured with four plies of graphite-epoxy cloth prepreg. These spars were noncircular in cross-section design and were therefore subject to warping deformations. Three different cross-sectional geometries were developed: D-shape, square, and flattened ellipse. Three spars of each type were fabricated to assess the degree of repeatability in the manufacturing process of extension-twist-coupled structures. Results from free-free vibration tests of the spars were compared with results from normal modes and frequency analyses of companion shell-finite-element models. Five global modes were identified within the frequency range from 0 to 2000 Hz for each spar. The experimental results for only one D-shape spar could be determined, however, and agreed within 13.8 percent of the analytical results. Frequencies corresponding to the five global modes for the three square spars agreed within 9.5, 11.6, and 8.5 percent of the respective analytical results and for the three elliptical spars agreed within 4.9, 7.7, and 9.6 percent of the respective analytical results.

Experimental and analytical investigation of dynamic characteristics of extension-twist-coupled composite tubular spars

NASA Technical Reports Server (NTRS)

Lake, Renee C.; Izadpanah, Amir P.; Baucom, Robert M.

1993-01-01

The results from a study aimed at improving the dynamic and aerodynamic characteristics of composite rotor blades through the use of extension-twist coupling are presented. A set of extension-twist-coupled composite spars was manufactured with four plies of graphite-epoxy cloth prepreg. These spars were noncircular in cross-section design and were therefore subject to warping deformations. Three different cross-sectional geometries were developed: D-shape, square, and flattened ellipse. Three spars of each type were fabricated to assess the degree of repeatability in the manufacturing process of extension-twist-coupled structures. Results from free-free vibration tests of the spars were compared with results from normal modes and frequency analyses of companion shell-finite-element models. Five global modes were identified within the frequency range from 0 to 2000 Hz for each spar. The experimental results for only one D-shape spar could be determined, however, and agreed within 13.8 percent of the analytical results. Frequencies corresponding to the five global modes for the three square spars agreed within 9.5, 11.6, and 8.5 percent of the respective analytical results and for the three elliptical spars agreed within 4.9, 7.7, and 9.6 percent of the respective analytical results.

A numerical investigation of head waves and leaky modes in fluid- filled boreholes.

USGS Publications Warehouse

Paillet, Frederick L.; Cheng, C.H.

1986-01-01

Although synthetic borehole seismograms can be computed for a wide range of borehole conditions, the physical nature of shear and compressional head waves in fluid-filled boreholes is poorly understood. Presents a series of numerical experiments designed to explain the physical mechanisms controlling head-wave propagation in boreholes. These calculations demonstrate the existence of compressional normal modes equivalent to shear normal modes, or pseudo-Rayleigh waves, with sequential cutoff frequencies spaced between the cutoff frequencies for the shear normal modes.-from Authors

Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.

PubMed

Kurkal-Siebert, Vandana; Smith, Jeremy C

2006-02-22

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Realistic Features in Analysing the Effect of the Seismic Motion upon Localized Structures Considering Base Isolation Influence on Their Dynamic Behaviour

NASA Astrophysics Data System (ADS)

Apostol, Bogdan Felix; Florin Balan, Stefan; Ionescu, Constantin

2017-12-01

The effects of the earthquakes on buildings and the concept of seismic base isolation are investigated by using the model of the vibrating bar embedded at one end. The normal modes and the eigenfrequencies of the bar are highlighted and the amplification of the response due to the excitation of the normal modes (eigenmodes) is computed. The effect is much enhanced at resonance, for oscillating shocks which contain eigenfrequencies of the bar. Also, the response of two linearly joined bars with one end embedded is calculated. It is shown that for very different elastic properties the eigenfrequencies are due mainly to the “softer” bar. The effect of the base isolation in seismic structural engineering is assessed by formulating the model of coupled harmonic oscillators, as a simplified model for the structure building-foundation viewed as two coupled vibrating bars. The coupling decreases the lower eigenfrequencies of the structure and increases the higher ones. Similar amplification factors are derived for coupled oscillators at resonance with an oscillating shock.

Turbulence and mixing from optimal perturbations to a stratified shear layer

NASA Astrophysics Data System (ADS)

Kaminski, Alexis; Caulfield, C. P.; Taylor, John

2014-11-01

The stability and mixing of stratified shear layers is a canonical problem in fluid dynamics with relevance to flows in the ocean and atmosphere. The Miles-Howard theorem states that a necessary condition for normal-mode instability in parallel, inviscid, steady stratified shear flows is that the gradient Richardson number, Rig is less than 1/4 somewhere in the flow. However, substantial transient growth of non-normal modes may be possible at finite times even when Rig > 1 / 4 everywhere in the flow. We have calculated the ``optimal perturbations'' associated with maximum perturbation energy gain for a stably-stratified shear layer. These optimal perturbations are then used to initialize direct numerical simulations. For small but finite perturbation amplitudes, the optimal perturbations grow at the predicted linear rate initially, but then experience sufficient transient growth to become nonlinear and susceptible to secondary instabilities, which then break down into turbulence. Remarkably, this occurs even in flows for which Rig > 1 / 4 everywhere. We will describe the nonlinear evolution of the optimal perturbations and characterize the resulting turbulence and mixing.

Domain motions of Argonaute, the catalytic engine of RNA interference

PubMed Central

Ming, Dengming; Wall, Michael E; Sanbonmatsu, Kevin Y

2007-01-01

Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. Results The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes – an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Conclusion Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference. PMID:18053142

An analytical study and wind tunnel tests of an aeromechanical gust-alleviation system for a light airplane

NASA Technical Reports Server (NTRS)

Stewart, E. C.

1976-01-01

The results of an analytical study of a system using stability derivatives determined in static wind tunnel tests of a 1/6 scale model of a popular, high wing, light airplane equipped with the gust alleviation system are reported. The longitudinal short period mode dynamics of the system are analyzed, and include the following: (1) root loci, (2) airplane frequency responses to vertical gusts, (3) power spectra of the airplane responses in a gust spectrum, (4) time history responses to vertical gusts, and (5) handling characteristics. The system reduces the airplane's normal acceleration response to vertical gusts while simultaneously increasing the pitching response and reducing the damping of the longitudinal short period mode. The normal acceleration response can be minimized by using the proper amount of static alleviation and a fast response system with a moderate amount of damping. The addition of a flap elevator interconnect or a pitch damper system further increases the alleviation while moderating the simultaneous increase in pitching response. The system provides direct lift control and may reduce the stick fixed longitudinal static stability.

Domain motions of Argonaute, the catalytic engine of RNA interference.

PubMed

Ming, Dengming; Wall, Michael E; Sanbonmatsu, Kevin Y

2007-11-30

The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

PubMed

Ahmed, Aqeel; Rippmann, Friedrich; Barnickel, Gerhard; Gohlke, Holger

2011-07-25

A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 Å) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity.

PubMed

Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

2018-03-05

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Megow, Jörg; Niehaus, Thomas; Kühn, Oliver

2017-02-01

Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

Delocalization and stretch-bend mixing of the HOH bend in liquid water

NASA Astrophysics Data System (ADS)

Carpenter, William B.; Fournier, Joseph A.; Biswas, Rajib; Voth, Gregory A.; Tokmakoff, Andrei

2017-08-01

Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H2O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H2O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm-1 to beyond 1900 cm-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δHOH on 2-7 water molecules.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

PubMed Central

Frappier, Vincent; Najmanovich, Rafael J.

2014-01-01

Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569

Normal modes of a small gamelan gong.

PubMed

Perrin, Robert; Elford, Daniel P; Chalmers, Luke; Swallowe, Gerry M; Moore, Thomas R; Hamdan, Sinin; Halkon, Benjamin J

2014-10-01

Studies have been made of the normal modes of a 20.7 cm diameter steel gamelan gong. A finite-element model has been constructed and its predictions for normal modes compared with experimental results obtained using electronic speckle pattern interferometry. Agreement was reasonable in view of the lack of precision in the manufacture of the instrument. The results agree with expectations for an axially symmetric system subject to small symmetry breaking. The extent to which the results obey Chladni's law is discussed. Comparison with vibrational and acoustical spectra enabled the identification of the small number of modes responsible for the sound output when played normally. Evidence of non-linear behavior was found, mainly in the form of subharmonics of true modes. Experiments using scanning laser Doppler vibrometry gave satisfactory agreement with the other methods.

Toothguide Trainer tests with color vision deficiency simulation monitor.

PubMed

Borbély, Judit; Varsányi, Balázs; Fejérdy, Pál; Hermann, Péter; Jakstat, Holger A

2010-01-01

The aim of this study was to evaluate whether simulated severe red and green color vision deficiency (CVD) influenced color matching results and to investigate whether training with Toothguide Trainer (TT) computer program enabled better color matching results. A total of 31 color normal dental students participated in the study. Every participant had to pass the Ishihara Test. Participants with a red/green color vision deficiency were excluded. A lecture on tooth color matching was given, and individual training with TT was performed. To measure the individual tooth color matching results in normal and color deficient display modes, the TT final exam was displayed on a calibrated monitor that served as a hardware-based method of simulating protanopy and deuteranopy. Data from the TT final exams were collected in normal and in severe red and green CVD-simulating monitor display modes. Color difference values for each participant in each display mode were computed (∑ΔE(ab)(*)), and the respective means and standard deviations were calculated. The Student's t-test was used in statistical evaluation. Participants made larger ΔE(ab)(*) errors in severe color vision deficient display modes than in the normal monitor mode. TT tests showed significant (p<0.05) difference in the tooth color matching results of severe green color vision deficiency simulation mode compared to normal vision mode. Students' shade matching results were significantly better after training (p=0.009). Computer-simulated severe color vision deficiency mode resulted in significantly worse color matching quality compared to normal color vision mode. Toothguide Trainer computer program improved color matching results. Copyright © 2010 Elsevier Ltd. All rights reserved.

The Effect of Background Plasma Temperature on Growth and Damping of Whistler Mode Wave Power in the Earth's Magnetosphere

NASA Astrophysics Data System (ADS)

Maxworth, A. S.; Golkowski, M.; Malaspina, D.; Jaynes, A. N.

2017-12-01

Whistler mode waves play a dominant role in the energy dynamics of the Earth's magnetosphere. Trajectory of whistler mode waves can be predicted by raytracing. Raytracing is a numerical method which solves the Haselgrove's equations at each time step taking the background plasma parameters in to account. The majority of previous raytracing work was conducted assuming a cold (0 K) background magnetospheric plasma. Here we perform raytracing in a finite temperature plasma with background electron and ion temperatures of a few eV. When encountered with a high energy (>10 keV) electron distribution, whistler mode waves can undergo a power attenuation and/or growth, depending on resonance conditions which are a function of wave frequency, wave normal angle and particle energy. In this work we present the wave power attenuation and growth analysis of whistler mode waves, during the interaction with a high energy electron distribution. We have numerically modelled the high energy electron distribution as an isotropic velocity distribution, as well as an anisotropic bi-Maxwellian distribution. Both cases were analyzed with and without the temperature effects for the background magnetospheric plasma. Finally we compare our results with the whistler mode energy distribution obtained by the EMFISIS instrument hosted at the Van Allen Probe spacecraft.

Variable optical attenuator and dynamic mode group equalizer for few mode fibers.

PubMed

Blau, Miri; Weiss, Israel; Gerufi, Jonathan; Sinefeld, David; Bin-Nun, Moran; Lingle, Robert; Grüner-Nielsen, Lars; Marom, Dan M

2014-12-15

Variable optical attenuation (VOA) for three-mode fiber is experimentally presented, utilizing an amplitude spatial light modulator (SLM), achieving up to -28dB uniform attenuation for all modes. Using the ability to spatially vary the attenuation distribution with the SLM, we also achieve up to 10dB differential attenuation between the fiber's two supported mode group (LP₀₁ and LP₁₁). The spatially selective attenuation serves as the basis of a dynamic mode-group equalizer (DME), potentially gain-balancing mode dependent optical amplification. We extend the experimental three mode DME functionality with a performance analysis of a fiber supporting 6 spatial modes in four mode groups. The spatial modes' distribution and overlap limit the available dynamic range and performance of the DME in the higher mode count case.

Dynamic analysis of rotor flex-structure based on nonlinear anisotropic shell models

NASA Astrophysics Data System (ADS)

Bauchau, Olivier A.; Chiang, Wuying

1991-05-01

In this paper an anisotropic shallow shell model is developed that accommodates transverse shearing deformations and arbitrarily large displacements and rotations, but strains are assumed to remain small. Two kinematic models are developed, the first using two DOF to locate the direction of the normal to the shell's midplane, the second using three. The latter model allows for an automatic compatibility of the shell model with beam models. The shell model is validated by comparing its predictions with several benchmark problems. In actual helicopter rotor blade problems, the shell model of the flex structure is shown to give very different results shown compared to beam models. The lead-lag and torsion modes in particular are strongly affected, whereas flapping modes seem to be less affected.

Multi-modal vibration amplitudes of taut inclined cables due to direct and/or parametric excitation

NASA Astrophysics Data System (ADS)

Macdonald, J. H. G.

2016-02-01

Cables are often prone to potentially damaging large amplitude vibrations. The dynamic excitation may be from external loading or motion of the cable ends, the latter including direct excitation, normally from components of end motion transverse to the cable, and parametric excitation induced by axial components of end motion causing dynamic tension variations. Geometric nonlinearity can be important, causing stiffening behaviour and nonlinear modal coupling. Previous analyses of the vibrations, often neglecting sag, have generally dealt with direct and parametric excitation separately or have reverted to numerical solutions of the responses. Here a nonlinear cable model is adopted, applicable to taut cables such as on cable-stayed bridges, that allows for cable inclination, small sag (such that the vibration modes are similar to those of a taut string), multiple modes in both planes and end motion and/or external forcing close to any natural frequency. Based on the method of scaling and averaging it is found that, for sinusoidal inputs and positive damping, non-zero steady state responses can only occur in the modes in each plane with natural frequencies close to the excitation frequency and those with natural frequencies close to half this frequency. Analytical solutions, in the form of non-dimensional polynomial equations, are derived for the steady state vibration amplitudes in up to three modes simultaneously: the directly excited mode, the corresponding nonlinearly coupled mode in the orthogonal plane and a parametrically excited mode with half the natural frequency. The stability of the solutions is also identified. The outputs of the equations are consistent with previous results, where available. Example results from the analytical solutions are presented for a typical inclined bridge cable subject to vertical excitation of the lower end, and they are validated by numerical integration of the equations of motion and against some previous experimental results. It is shown that the modal interactions and sag (although very small) affect the responses significantly.

A comparison between elastic network interpolation and MD simulation of 16S ribosomal RNA.

PubMed

Kim, Moon K; Li, Wen; Shapiro, Bruce A; Chirikjian, Gregory S

2003-12-01

In this paper a coarse-grained method called elastic network interpolation (ENI) is used to generate feasible transition pathways between two given conformations of the core central domain of 16S Ribosomal RNA (16S rRNA). The two given conformations are the extremes generated by a molecular dynamics (MD) simulation, which differ from each other by 10A in root-mean-square deviation (RMSD). It takes only several hours to build an ENI pathway on a 1.5GHz Pentium with 512 MB memory, while the MD takes several weeks on high-performance multi-processor servers such as the SGI ORIGIN 2000/2100. It is shown that multiple ENI pathways capture the essential anharmonic motions of millions of timesteps in a particular MD simulation. A coarse-grained normal mode analysis (NMA) is performed on each intermediate ENI conformation, and the lowest 1% of the normal modes (representing about 40 degrees of freedom (DOF)) are used to parameterize fluctuations. This combined ENI/NMA method captures all intermediate conformations in the MD run with 1.5A RMSD on average. In addition, if we restrict attention to the time interval of the MD run between the two extreme conformations, the RMSD between the closest ENI/NMA pathway and the MD results is about 1A. These results may serve as a paradigm for reduced-DOF dynamic simulations of large biological macromolecules as well as a method for the reduced-parameter interpretation of massive amounts of MD data.

Exciton transport in the PE545 complex: insight from atomistic QM/MM-based quantum master equations and elastic network models

NASA Astrophysics Data System (ADS)

Pouyandeh, Sima; Iubini, Stefano; Jurinovich, Sandro; Omar, Yasser; Mennucci, Benedetta; Piazza, Francesco

2017-12-01

In this paper, we work out a parameterization of environmental noise within the Haken-Strobl-Reinenker (HSR) model for the PE545 light-harvesting complex, based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of various auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments. Interestingly, several cross-correlations of the latter kind, together with coupling-coupling cross-correlations, display clear low-frequency signatures in their spectral densities in the 30-70 cm-1 region. These slow components lie at the limits of validity of the HSR approach, which requires that environmental fluctuations be faster than typical exciton transfer time scales. We show that a simple coarse-grained elastic-network-model (ENM) analysis of the PE545 protein naturally spotlights collective normal modes in this frequency range that represent specific concerted motions of the subnetwork of cysteines covalenty linked to the pigments. This analysis strongly suggests that protein scaffolds in light-harvesting complexes are able to express specific collective, low-frequency normal modes providing a fold-rooted blueprint of exciton transport pathways. We speculate that ENM-based mixed quantum classical methods, such as Ehrenfest dynamics, might be promising tools to disentangle the fundamental designing principles of these dynamical processes in natural and artificial light-harvesting structures.

Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes.

PubMed

Lima, Angelica Nakagawa; de Oliveira, Ronaldo Junio; Braz, Antônio Sérgio Kimus; de Souza Costa, Maurício Garcia; Perahia, David; Scott, Luis Paulo Barbour

2018-03-15

There are two different prion conformations: (1) the cellular natural (PrP C ) and (2) the scrapie (PrP Sc ), an infectious form that tends to aggregate under specific conditions. PrP C and PrP Sc are widely different regarding secondary and tertiary structures. PrP Sc contains more and longer β-strands compared to PrP C . The lack of solved PrP Sc structures precludes a proper understanding of the mechanisms related to the transition between cellular and scrapie forms, as well as the aggregation process. In order to investigate the conformational transition between PrP C and PrP Sc , we applied MDeNM (molecular dynamics with excited normal modes), an enhanced sampling simulation technique that has been recently developed to probe large structural changes. These simulations yielded new structural rearrangements of the cellular prion that would have been difficult to obtain with standard MD simulations. We observed an increase in β-sheet formation under low pH (≤ 4) and upon oligomerization, whose relevance was discussed on the basis of the energy landscape theory for protein folding. The characterization of intermediate structures corresponding to transition states allowed us to propose a conversion model from the cellular to the scrapie prion, which possibly ignites the fibril formation. This model can assist the design of new drugs to prevent neurological disorders related to the prion aggregation mechanism.

Adaptive track scheduling to optimize concurrency and vectorization in GeantV

DOE PAGES

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.; ...

2015-05-22

The GeantV project is focused on the R&D of new particle transport techniques to maximize parallelism on multiple levels, profiting from the use of both SIMD instructions and co-processors for the CPU-intensive calculations specific to this type of applications. In our approach, vectors of tracks belonging to multiple events and matching different locality criteria must be gathered and dispatched to algorithms having vector signatures. While the transport propagates tracks and changes their individual states, data locality becomes harder to maintain. The scheduling policy has to be changed to maintain efficient vectors while keeping an optimal level of concurrency. The modelmore » has complex dynamics requiring tuning the thresholds to switch between the normal regime and special modes, i.e. prioritizing events to allow flushing memory, adding new events in the transport pipeline to boost locality, dynamically adjusting the particle vector size or switching between vector to single track mode when vectorization causes only overhead. Lastly, this work requires a comprehensive study for optimizing these parameters to make the behaviour of the scheduler self-adapting, presenting here its initial results.« less

Excited-State Vibrational Coherence in Perylene Bisimide Probed by Femtosecond Broadband Pump-Probe Spectroscopy.

PubMed

Son, Minjung; Park, Kyu Hyung; Yoon, Min-Chul; Kim, Pyosang; Kim, Dongho

2015-06-18

Broadband laser pulses with ultrashort duration are capable of triggering impulsive excitation of the superposition of vibrational eigenstates, giving rise to quantum beating signals originating from coherent wave packet motions along the potential energy surface. In this work, coherent vibrational wave packet dynamics of an N,N'-bis(2,6-dimethylphenyl)perylene bisimide (DMP-PBI) were investigated by femtosecond broadband pump-probe spectroscopy which features fast and balanced data acquisition with a wide spectral coverage of >200 nm. Clear modulations were observed in the envelope of the stimulated emission decay profiles of DMP-PBI with the oscillation frequencies of 140 and 275 cm(-1). Fast Fourier transform analysis of each oscillatory mode revealed characteristic phase jumps near the maxima of the steady-state fluorescence, indicating that the observed vibrational coherence originates from an excited-state wave packet motion. Quantum calculations of the normal modes at the low-frequency region suggest that low-frequency C-C (C═C) stretching motions accompanied by deformation of the dimethylphenyl substituents are responsible for the manifestation of such coherent wave packet dynamics.

Quantized mode of a leaky cavity

NASA Astrophysics Data System (ADS)

Dutra, S. M.; Nienhuis, G.

2000-12-01

We use Thomson's classical concept of mode of a leaky cavity to develop a quantum theory of cavity damping. This theory generalizes the conventional system-reservoir theory of high-Q cavity damping to arbitrary Q. The small system now consists of damped oscillators corresponding to the natural modes of the leaky cavity rather than undamped oscillators associated with the normal modes of a fictitious perfect cavity. The formalism unifies semiclassical Fox-Li modes and the normal modes traditionally used for quantization. It also lays the foundations for a full quantum description of excess noise. The connection with Siegman's semiclassical work is straightforward. In a wider context, this theory constitutes a radical departure from present models of dissipation in quantum mechanics: unlike conventional models, system and reservoir operators no longer commute with each other. This noncommutability is an unavoidable consequence of having to use natural cavity modes rather than normal modes of a fictitious perfect cavity.

An approach to the quantization of black hole quasi-normal modes

NASA Astrophysics Data System (ADS)

Pal, Soham; Rajeev, Karthik; Shankaranarayanan, S.

2015-07-01

In this work, we derive the asymptotic quasi-normal modes of a Banados-Teitelboim-Zanelli (BTZ) black hole using a quantum field theoretic Lagrangian. The BTZ black hole is a very popular system in the context of 2 + 1-dimensional quantum gravity. However, to our knowledge the quasi-normal modes of the BTZ black hole have been studied only in the classical domain. Here we show a way to quantize the quasi-normal modes of the BTZ black hole by mapping it to the Bateman-Feschbach-Tikochinsky oscillator and the Caldirola-Kanai oscillator. We have also discussed a couple of other black hole potentials to which this method can be applied.

Tunable Mode Coupling in Nanocontact Spin-Torque Oscillators

DOE PAGES

Zhang, Steven S. -L.; Iacocca, Ezio; Heinonen, Olle

2017-07-27

Recent experiments on spin-torque oscillators have revealed interactions between multiple magneto-dynamic modes, including mode coexistence, mode hopping, and temperature-driven crossover between modes. The initial multimode theory indicates that a linear coupling between several dominant modes, arising from the interaction of the subdynamic system with a magnon bath, plays an essential role in the generation of various multimode behaviors, such as mode hopping and mode coexistence. In this work, we derive a set of rate equations to describe the dynamics of coupled magneto-dynamic modes in a nanocontact spin-torque oscillator. Here, expressions for both linear and nonlinear coupling terms are obtained, whichmore » allow us to analyze the dependence of the coupled dynamic behaviors of modes on external experimental conditions as well as intrinsic magnetic properties. For a minimal two-mode system, we further map the energy and phase difference of the two modes onto a two-dimensional phase space and demonstrate in the phase portraits how the manifolds of periodic orbits and fixed points vary with an external magnetic field as well as with the temperature.« less

Tunable Mode Coupling in Nanocontact Spin-Torque Oscillators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Steven S. -L.; Iacocca, Ezio; Heinonen, Olle

Recent experiments on spin-torque oscillators have revealed interactions between multiple magneto-dynamic modes, including mode coexistence, mode hopping, and temperature-driven crossover between modes. The initial multimode theory indicates that a linear coupling between several dominant modes, arising from the interaction of the subdynamic system with a magnon bath, plays an essential role in the generation of various multimode behaviors, such as mode hopping and mode coexistence. In this work, we derive a set of rate equations to describe the dynamics of coupled magneto-dynamic modes in a nanocontact spin-torque oscillator. Here, expressions for both linear and nonlinear coupling terms are obtained, whichmore » allow us to analyze the dependence of the coupled dynamic behaviors of modes on external experimental conditions as well as intrinsic magnetic properties. For a minimal two-mode system, we further map the energy and phase difference of the two modes onto a two-dimensional phase space and demonstrate in the phase portraits how the manifolds of periodic orbits and fixed points vary with an external magnetic field as well as with the temperature.« less

Confinement-induced alterations in the evaporation dynamics of sessile droplets.

PubMed

Bansal, Lalit; Chakraborty, Suman; Basu, Saptarshi

2017-02-07

Evaporation of sessile droplets has been a topic of extensive research. However, the effect of confinement on the underlying dynamics has not been well explored. Here, we report the evaporation dynamics of a sessile droplet in a confined fluidic environment. Our findings reveal that an increase in the channel length delays the completion of the evaporation process and leads to unique spatio-temporal evaporation flux and internal flow. The evaporation modes (constant contact angle and constant contact radius) during the droplet lifetime however exhibit global similarity when normalized by appropriate length and timescales. These results are explained in light of an increase in vapor concentration inside the channel due to greater accumulation of water vapor on account of increased channel length. We have formulated a theoretical framework which introduces two key parameters namely an enhanced concentration of the vapor field in the vicinity of the confined droplet and a corresponding accumulation lengthscale over which the accumulated vapor relaxes to the ambient concentration. Using these two parameters and modified diffusion based evaporation we are able to show that confined droplets exhibit a universal behavior in terms of the temporal evolution of each evaporation mode irrespective of the channel length. These results may turn out to be of profound importance in a wide variety of applications, ranging from surface patterning to microfluidic technology.

Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution

NASA Astrophysics Data System (ADS)

Schmitz, Matthias; Tavan, Paul

2004-12-01

The midinfrared (MIR) spectra of molecules in polar solvents exhibit inhomogeneously broadened bands whose spectral positions are shifted as compared to the gas phase. The shifts are caused by interactions with structured solvation shells and the broadenings by fluctuations of these interactions. The MIR spectra can be calculated from hybrid molecular dynamics (MD) simulations, which treat the solute molecule by density functional theory and the solvent by molecular mechanics by the so-called instantaneous normal mode analysis (INMA) or by Fourier transforming the time correlation function (FTTCF) of the molecular dipole moment. In Paper I of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12233 (2004)] we explored an alternative method based on generalized virial (GV) frequencies noting, however, that GV systematically underestimates frequencies. As shown by us these artifacts are caused by solvent-induced fluctuations of the (i) equilibrium geometry, (ii) force constants, and (iii) normal mode directions as well as by (iv) diagonal and (v) off-diagonal anharmonicities. Here we now show, by analyzing the time scales of fluctuations and sample MD trajectories of formaldehyde in the gas phase and in water, that all these sources of computational artifacts can be made visible by a Fourier analysis of the normal coordinates. Correspondingly, the error sources (i) and (iii)-(v) can be removed by bandpass filtering, as long as the spectral signatures of the respective effects are well separated from the fundamental band. Furthermore, the artifacts arising from effect (ii) can be strongly diminished by a time-resolved version of the GV approach (TF-GV). The TF-GV method then yields for each mode j a trajectory of the vibrational frequency ωj(t|τ) at a time resolution τ>τj, which is only limited by the corresponding oscillation time τj=2π/ωj and, thus, is in the femtosecond range. A correlation analysis of these trajectories clearly separates the librational motions from the conformational dynamics of the solvation shells and yields the inhomogeneously broadened MIR spectra, if the theory of motional narrowing is properly included. The MIR spectrum of formaldehyde in solution obtained by TF-GV agrees very well with the FTTCF result, if one applies the so-called "harmonic approximation" quantum correction factor and a temperature scaling to the FTTCF intensities. Also for INMA an excellent agreement is achieved if one disregards a slight INMA overestimate of linewidths.

Coherent control of double deflected anomalous modes in ultrathin trapezoid-shaped slit metasurface.

PubMed

Zhu, Z; Liu, H; Wang, D; Li, Y X; Guan, C Y; Zhang, H; Shi, J H

2016-11-22

Coherent light-matter interaction in ultrathin metamaterials has been demonstrated to dynamically modulate intensity, polarization and propagation direction of light. The gradient metasurface with a transverse phase variation usually exhibits an anomalous refracted beam of light dictated by so-called generalized Snell's law. However, less attention has been paid to coherent control of the metasurface with multiple anomalous refracted beams. Here we propose an ultrathin gradient metasurface with single trapezoid-shaped slot antenna as its building block that allows one normal and two deflected transmitted beams. It is numerically demonstrated that such metasurface with multiple scattering modes can be coherently controlled to modulate output intensities by changing the relative phase difference between two counterpropagating coherent beams. Each mode can be coherently switched on/off and two deflected anomalous beams can be synchronously dictated by the phase difference. The coherent control effect in the trapezoid-shaped slit metasurface will offer a promising opportunity for multichannel signals modulation, multichannel sensing and wave front shaping.

Coherent control of double deflected anomalous modes in ultrathin trapezoid-shaped slit metasurface

PubMed Central

Zhu, Z.; Liu, H.; Wang, D.; Li, Y. X.; Guan, C. Y.; Zhang, H.; Shi, J. H.

2016-01-01

Coherent light-matter interaction in ultrathin metamaterials has been demonstrated to dynamically modulate intensity, polarization and propagation direction of light. The gradient metasurface with a transverse phase variation usually exhibits an anomalous refracted beam of light dictated by so-called generalized Snell’s law. However, less attention has been paid to coherent control of the metasurface with multiple anomalous refracted beams. Here we propose an ultrathin gradient metasurface with single trapezoid-shaped slot antenna as its building block that allows one normal and two deflected transmitted beams. It is numerically demonstrated that such metasurface with multiple scattering modes can be coherently controlled to modulate output intensities by changing the relative phase difference between two counterpropagating coherent beams. Each mode can be coherently switched on/off and two deflected anomalous beams can be synchronously dictated by the phase difference. The coherent control effect in the trapezoid-shaped slit metasurface will offer a promising opportunity for multichannel signals modulation, multichannel sensing and wave front shaping. PMID:27874053

Terahertz Absorption and Circular Dichroism Spectroscopy of Solvated Biopolymers

NASA Astrophysics Data System (ADS)

Xu, Jing; Plaxco, Kevin; Allen, S. James

2006-03-01

Biopolymers are expected to exhibit broad spectral features in the terahertz frequency range, corresponding to their functionally relevant, global and sub-global collective vibrational modes with ˜ picosecond timescale. Recent advances in terahertz technology have stimulated researchers to employ terahertz absorption spectroscopy to directly probe these postulated collective modes. However, these pioneering studies have been limited to dry and, at best, moist samples. Successful isolation of low frequency vibrational activities of solvated biopolymers in their natural water environment has remained elusive, due to the overwhelming attenuation of the terahertz radiation by water. Here we have developed a terahertz absorption and circular dichroism spectrometer suitable for studying biopolymers in biologically relevant water solutions. We have precisely isolated, for the first time, the terahertz absorption of solvated prototypical proteins, Bovine Serum Albumin and Lysozyme, and made important direct comparison to the existing molecular dynamic simulations and normal mode calculations. We have also successfully demonstrated the magnetic circular dichroism in semiconductors, and placed upper bounds on the terahertz circular dichroism signatures of prototypical proteins in water solution.

Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?

PubMed Central

McLeish, Tom C.B.; Cann, Martin J.; Rodgers, Thomas L.

2015-01-01

We examine the contrast between mechanisms for allosteric signaling that involve structural change, and those that do not, from the perspective of allosteric pathways. In particular we treat in detail the case of fluctuation-allostery by which amplitude modulation of the thermal fluctuations of the elastic normal modes conveys the allosteric signal, and address the question of what an allosteric pathway means in this case. We find that a perturbation theory of thermal elastic solids and nonperturbative approach (by super-coarse-graining elasticity into internal bending modes) have opposite signatures in their structure of correlated pathways. We illustrate the effect from analysis of previous results from GlxR of Corynebacterium glutamicum, an example of the CRP/FNR transcription family of allosteric homodimers. We find that the visibility of both correlated pathways and disconnected sites of correlated motion in this protein suggests that mechanisms of local elastic stretch and bend are recruited for the purpose of creating and controlling allosteric cooperativity. PMID:26338443

Quantifying the Energy Landscape Statistics in Proteins - a Relaxation Mode Analysis

NASA Astrophysics Data System (ADS)

Cai, Zhikun; Zhang, Yang

Energy landscape, the hypersurface in the configurational space, has been a useful concept in describing complex processes that occur over a very long time scale, such as the multistep slow relaxations of supercooled liquids and folding of polypeptide chains into structured proteins. Despite extensive simulation studies, its experimental characterization still remains a challenge. To address this challenge, we developed a relaxation mode analysis (RMA) for liquids under a framework analogous to the normal mode analysis for solids. Using RMA, important statistics of the activation barriers of the energy landscape becomes accessible from experimentally measurable two-point correlation functions, e.g. using quasi-elastic and inelastic scattering experiments. We observed a prominent coarsening effect of the energy landscape. The results were further confirmed by direct sampling of the energy landscape using a metadynamics-like adaptive autonomous basin climbing computation. We first demonstrate RMA in a supercooled liquid when dynamical cooperativity emerges in the landscape-influenced regime. Then we show this framework reveals encouraging energy landscape statistics when applied to proteins.

Structural Origin of Enhanced Dynamics at the Surface of a Glassy Alloy

NASA Astrophysics Data System (ADS)

Sun, Gang; Saw, Shibu; Douglass, Ian; Harrowell, Peter

2017-12-01

The enhancement of mobility at the surface of an amorphous alloy is studied using a combination of molecular dynamic simulations and normal mode analysis of the nonuniform distribution of Debye-Waller factors. The increased mobility at the surface is found to be associated with the appearance of Arrhenius temperature dependence. We show that the transverse Debye-Waller factor exhibits a peak at the surface. Over the accessible temperature range, we find that the bulk and surface diffusion coefficients obey the same empirical relationship with the respective Debye-Waller factors. Extrapolating this relationship to lower T , we argue that the observed decrease in the constraint at the surface is sufficient to account for the experimentally observed surface enhancement of mobility.

Magnetotail dynamics under isobaric constraints

NASA Technical Reports Server (NTRS)

Birn, Joachim; Schindler, Karl; Janicke, Lutz; Hesse, Michael

1994-01-01

Using linear theory and nonlinear MHD simulations, we investigate the resistive and ideal MHD stability of two-dimensional plasma configurations under the isobaric constraint dP/dt = 0, which in ideal MHD is equivalent to conserving the pressure function P = P(A), where A denotes the magnetic flux. This constraint is satisfied for incompressible modes, such as Alfven waves, and for systems undergoing energy losses. The linear stability analysis leads to a Schroedinger equation, which can be investigated by standard quantum mechanics procedures. We present an application to a typical stretched magnetotail configuration. For a one-dimensional sheet equilibrium characteristic properties of tearing instability are rediscovered. However, the maximum growth rate scales with the 1/7 power of the resistivity, which implies much faster growth than for the standard tearing mode (assuming that the resistivity is small). The same basic eigen-mode is found also for weakly two-dimensional equilibria, even in the ideal MHD limit. In this case the growth rate scales with the 1/4 power of the normal magnetic field. The results of the linear stability analysis are confirmed qualitatively by nonlinear dynamic MHD simulations. These results suggest the interesting possibility that substorm onset, or the thinning in the late growth phase, is caused by the release of a thermodynamic constraint without the (immediate) necessity of releasing the ideal MHD constraint. In the nonlinear regime the resistive and ideal developments differ in that the ideal mode does not lead to neutral line formation without the further release of the ideal MHD constraint; instead a thin current sheet forms. The isobaric constraint is critically discussed. Under perhaps more realistic adiabatic conditions the ideal mode appears to be stable but could be driven by external perturbations and thus generate the thin current sheet in the late growth phase, before a nonideal instability sets in.

Active polar two-fluid macroscopic dynamics.

PubMed

Pleiner, H; Svenšek, D; Brand, H R

2013-11-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria as well as shoals of fish, flocks of birds and migrating insects. Due to the fact that the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units, which are typically biological in nature. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to a second velocity as a variable. We analyze in detail how the macroscopic behavior of an active system with a polar dynamic preferred direction compares to other systems with two velocities including immiscible liquids and electrically neutral quantum liquids such as superfluid (4)He and (3)He . We critically discuss changes in the normal mode spectrum when comparing uncharged superfluids, immiscible liquids and active system with a polar dynamic preferred direction. We investigate the influence of a macroscopic hand (collective effects of chirality) on the macroscopic behavior of such active media.

Transient analysis mode participation for modal survey target mode selection using MSC/NASTRAN DMAP

NASA Technical Reports Server (NTRS)

Barnett, Alan R.; Ibrahim, Omar M.; Sullivan, Timothy L.; Goodnight, Thomas W.

1994-01-01

Many methods have been developed to aid analysts in identifying component modes which contribute significantly to component responses. These modes, typically targeted for dynamic model correlation via a modal survey, are known as target modes. Most methods used to identify target modes are based on component global dynamic behavior. It is sometimes unclear if these methods identify all modes contributing to responses important to the analyst. These responses are usually those in areas of hardware design concerns. One method used to check the completeness of target mode sets and identify modes contributing significantly to important component responses is mode participation. With this method, the participation of component modes in dynamic responses is quantified. Those modes which have high participation are likely modal survey target modes. Mode participation is most beneficial when it is used with responses from analyses simulating actual flight events. For spacecraft, these responses are generated via a structural dynamic coupled loads analysis. Using MSC/NASTRAN DMAP, a method has been developed for calculating mode participation based on transient coupled loads analysis results. The algorithm has been implemented to be compatible with an existing coupled loads methodology and has been used successfully to develop a set of modal survey target modes.

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

PubMed

Sorzano, Carlos Oscar S; de la Rosa-Trevín, José Miguel; Tama, Florence; Jonić, Slavica

2014-11-01

This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction. Copyright © 2014 Elsevier Inc. All rights reserved.

Normal mode Rossby waves observed in the upper stratosphere

NASA Technical Reports Server (NTRS)

Hirooka, T.; Hirota, I.

1985-01-01

In recent years, observational evidence has been obtained for westward traveling planetary waves in the middle atmosphere with the aid of global data from satellites. There is no doubt that the fair portion of the observed traveling waves can be understood as the manifestation of the normal mode Rossby waves which are theoretically derived from the tidal theory. Some observational aspects of the structure and behavior of the normal model Rossby waves in the upper stratosphere are reported. The data used are the global stratospheric geopotential thickness and height analyses which are derived mainly from the Stratospheric Sounding Units (SSUs) on board TIROS-N and NOAA satellites. A clear example of the influence of the normal mode Rossby wave on the mean flow is reported. The mechanism considered is interference between the normal mode Rossby wave and the quasi-stationary wave.

Observation of dynamic interactions between fundamental and second-harmonic modes in a high-power sub-terahertz gyrotron operating in regimes of soft and hard self-excitation.

PubMed

Saito, Teruo; Tatematsu, Yoshinori; Yamaguchi, Yuusuke; Ikeuchi, Shinji; Ogasawara, Shinya; Yamada, Naoki; Ikeda, Ryosuke; Ogawa, Isamu; Idehara, Toshitaka

2012-10-12

Dynamic mode interaction between fundamental and second-harmonic modes has been observed in high-power sub-terahertz gyrotrons [T. Notake et al., Phys. Rev. Lett. 103, 225002 (2009); T. Saito et al. Phys. Plasmas 19, 063106 (2012)]. Interaction takes place between a parasitic fundamental or first-harmonic (FH) mode and an operating second-harmonic (SH) mode, as well as among SH modes. In particular, nonlinear excitation of the parasitic FH mode in the hard self-excitation regime with assistance of a SH mode in the soft self-excitation regime was clearly observed. Moreover, both cases of stable two-mode oscillation and oscillation of the FH mode only were observed. These observations and theoretical analyses of the dynamic behavior of the mode interaction verify the nonlinear hard self-excitation of the FH mode.

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

ERIC Educational Resources Information Center

Dunn, Janette L.

2010-01-01

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

Acoustic-gravity waves in atmospheric and oceanic waveguides.

PubMed

Godin, Oleg A

2012-08-01

A theory of guided propagation of sound in layered, moving fluids is extended to include acoustic-gravity waves (AGWs) in waveguides with piecewise continuous parameters. The orthogonality of AGW normal modes is established in moving and motionless media. A perturbation theory is developed to quantify the relative significance of the gravity and fluid compressibility as well as sensitivity of the normal modes to variations in sound speed, flow velocity, and density profiles and in boundary conditions. Phase and group speeds of the normal modes are found to have certain universal properties which are valid for waveguides with arbitrary stratification. The Lamb wave is shown to be the only AGW normal mode that can propagate without dispersion in a layered medium.

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.

Turbine blade forced response prediction using FREPS

NASA Technical Reports Server (NTRS)

Murthy, Durbha, V.; Morel, Michael R.

1993-01-01

This paper describes a software system called FREPS (Forced REsponse Prediction System) that integrates structural dynamic, steady and unsteady aerodynamic analyses to efficiently predict the forced response dynamic stresses in axial flow turbomachinery blades due to aerodynamic and mechanical excitations. A flutter analysis capability is also incorporated into the system. The FREPS system performs aeroelastic analysis by modeling the motion of the blade in terms of its normal modes. The structural dynamic analysis is performed by a finite element code such as MSC/NASTRAN. The steady aerodynamic analysis is based on nonlinear potential theory and the unsteady aerodynamic analyses is based on the linearization of the non-uniform potential flow mean. The program description and presentation of the capabilities are reported herein. The effectiveness of the FREPS package is demonstrated on the High Pressure Oxygen Turbopump turbine of the Space Shuttle Main Engine. Both flutter and forced response analyses are performed and typical results are illustrated.

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2010-01-01

Summary The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease. PMID:20948980

Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-01-01

The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease.

Evaluation of the vibration-rotation-tunneling dynamics at the basis set superposition error corrected global minimum geometry of the ammonia dimer

NASA Astrophysics Data System (ADS)

Muguet, Francis F.; Robinson, G. Wilse; Bassez-Muguet, M. Palmyre

1995-03-01

With the help of a new scheme to correct for the basis set superposition error (BSSE), we find that an eclipsed nonlinear geometry becomes energetically favored over the eclipsed linear hydrogen-bonded geometry. From a normal mode analysis of the potential energy surface (PES) in the vicinity of the nonlinear geometry, we suggest that several dynamical interchange pathways must be taken into account. The minimal molecular symmetry group to be considered should be the double group of G36, but still larger multiple groups may be required. An interpretation of experimental vibration-rotation-tunneling (VRT) data in terms of the G144 group, which implies monomer inversions, may not be the only alternative. It appears that group theoretical considerations alone are insufficient for understanding the complex VRT dynamics of the ammonia dimer.

Rotor dynamic simulation and system identification methods for application to vacuum whirl data

NASA Technical Reports Server (NTRS)

Berman, A.; Giansante, N.; Flannelly, W. G.

1980-01-01

Methods of using rotor vacuum whirl data to improve the ability to model helicopter rotors were developed. The work consisted of the formulation of the equations of motion of elastic blades on a hub using a Galerkin method; the development of a general computer program for simulation of these equations; the study and implementation of a procedure for determining physical parameters based on measured data; and the application of a method for computing the normal modes and natural frequencies based on test data.

Low-noise pulse conditioner

DOEpatents

Bird, David A.

1983-01-01

A low-noise pulse conditioner is provided for driving electronic digital processing circuitry directly from differentially induced input pulses. The circuit uses a unique differential-to-peak detector circuit to generate a dynamic reference signal proportional to the input peak voltage. The input pulses are compared with the reference signal in an input network which operates in full differential mode with only a passive input filter. This reduces the introduction of circuit-induced noise, or jitter, generated in ground referenced input elements normally used in pulse conditioning circuits, especially speed transducer processing circuits.

A comparative numerical analysis of linear and nonlinear aerodynamic sound generation by vortex disturbances in homentropic constant shear flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hau, Jan-Niklas, E-mail: hau@fdy.tu-darmstadt.de; Oberlack, Martin; GSC CE, Technische Universität Darmstadt, Dolivostraße 15, 64293 Darmstadt

2015-12-15

Aerodynamic sound generation in shear flows is investigated in the light of the breakthrough in hydrodynamics stability theory in the 1990s, where generic phenomena of non-normal shear flow systems were understood. By applying the thereby emerged short-time/non-modal approach, the sole linear mechanism of wave generation by vortices in shear flows was captured [G. D. Chagelishvili, A. Tevzadze, G. Bodo, and S. S. Moiseev, “Linear mechanism of wave emergence from vortices in smooth shear flows,” Phys. Rev. Lett. 79, 3178-3181 (1997); B. F. Farrell and P. J. Ioannou, “Transient and asymptotic growth of two-dimensional perturbations in viscous compressible shear flow,” Phys.more » Fluids 12, 3021-3028 (2000); N. A. Bakas, “Mechanism underlying transient growth of planar perturbations in unbounded compressible shear flow,” J. Fluid Mech. 639, 479-507 (2009); and G. Favraud and V. Pagneux, “Superadiabatic evolution of acoustic and vorticity perturbations in Couette flow,” Phys. Rev. E 89, 033012 (2014)]. Its source is the non-normality induced linear mode-coupling, which becomes efficient at moderate Mach numbers that is defined for each perturbation harmonic as the ratio of the shear rate to its characteristic frequency. Based on the results by the non-modal approach, we investigate a two-dimensional homentropic constant shear flow and focus on the dynamical characteristics in the wavenumber plane. This allows to separate from each other the participants of the dynamical processes — vortex and wave modes — and to estimate the efficacy of the process of linear wave-generation. This process is analyzed and visualized on the example of a packet of vortex modes, localized in both, spectral and physical, planes. Further, by employing direct numerical simulations, the wave generation by chaotically distributed vortex modes is analyzed and the involved linear and nonlinear processes are identified. The generated acoustic field is anisotropic in the wavenumber plane, which results in highly directional linear sound radiation, whereas the nonlinearly generated waves are almost omni-directional. As part of this analysis, we compare the effectiveness of the linear and nonlinear mechanisms of wave generation within the range of validity of the rapid distortion theory and show the dominance of the linear aerodynamic sound generation. Finally, topological differences between the linear source term of the acoustic analogy equation and of the anisotropic non-normality induced linear mechanism of wave generation are found.« less

Nonlinear Tides in Close Binary Systems

NASA Astrophysics Data System (ADS)

Weinberg, Nevin N.; Arras, Phil; Quataert, Eliot; Burkart, Josh

2012-06-01

We study the excitation and damping of tides in close binary systems, accounting for the leading-order nonlinear corrections to linear tidal theory. These nonlinear corrections include two distinct physical effects: three-mode nonlinear interactions, i.e., the redistribution of energy among stellar modes of oscillation, and nonlinear excitation of stellar normal modes by the time-varying gravitational potential of the companion. This paper, the first in a series, presents the formalism for studying nonlinear tides and studies the nonlinear stability of the linear tidal flow. Although the formalism we present is applicable to binaries containing stars, planets, and/or compact objects, we focus on non-rotating solar-type stars with stellar or planetary companions. Our primary results include the following: (1) The linear tidal solution almost universally used in studies of binary evolution is unstable over much of the parameter space in which it is employed. More specifically, resonantly excited internal gravity waves in solar-type stars are nonlinearly unstable to parametric resonance for companion masses M' >~ 10-100 M ⊕ at orbital periods P ≈ 1-10 days. The nearly static "equilibrium" tidal distortion is, however, stable to parametric resonance except for solar binaries with P <~ 2-5 days. (2) For companion masses larger than a few Jupiter masses, the dynamical tide causes short length scale waves to grow so rapidly that they must be treated as traveling waves, rather than standing waves. (3) We show that the global three-wave treatment of parametric instability typically used in the astrophysics literature does not yield the fastest-growing daughter modes or instability threshold in many cases. We find a form of parametric instability in which a single parent wave excites a very large number of daughter waves (N ≈ 103[P/10 days] for a solar-type star) and drives them as a single coherent unit with growth rates that are a factor of ≈N faster than the standard three-wave parametric instability. These are local instabilities viewed through the lens of global analysis; the coherent global growth rate follows local rates in the regions where the shear is strongest. In solar-type stars, the dynamical tide is unstable to this collective version of the parametric instability for even sub-Jupiter companion masses with P <~ a month. (4) Independent of the parametric instability, the dynamical and equilibrium tides excite a wide range of stellar p-modes and g-modes by nonlinear inhomogeneous forcing; this coupling appears particularly efficient at draining energy out of the dynamical tide and may be more important than either wave breaking or parametric resonance at determining the nonlinear dissipation of the dynamical tide.

Continuous-wave to pulse regimes for a family of passively mode-locked lasers with saturable nonlinearity

NASA Astrophysics Data System (ADS)

Dikandé, Alain M.; Voma Titafan, J.; Essimbi, B. Z.

2017-10-01

The transition dynamics from continuous-wave to pulse regimes of operation for a generic model of passively mode-locked lasers with saturable absorbers, characterized by an active medium with non-Kerr nonlinearity, are investigated analytically and numerically. The system is described by a complex Ginzburg-Landau equation with a general m:n saturable nonlinearity (i.e {I}m/{(1+{{Γ }}I)}n, where I is the field intensity and m and n are two positive numbers), coupled to a two-level gain equation. An analysis of stability of continuous waves, following the modulational instability approach, provides a global picture of the self-starting dynamics in the system. The analysis reveals two distinct routes depending on values of the couple (m, n), and on the dispersion regime: in the normal dispersion regime, when m = 2 and n is arbitrary, the self-starting requires positive values of the fast saturable absorber and nonlinearity coefficients, but negative values of these two parameters for the family with m = 0. However, when the spectral filter is negative, the laser can self-start for certain values of the input field and the nonlinearity saturation coefficient Γ. The present work provides a general map for the self-starting mechanisms of rare-earth doped figure-eight fiber lasers, as well as Kerr-lens mode-locked solid-state lasers.

Local thermal energy as a structural indicator in glasses

NASA Astrophysics Data System (ADS)

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-01

Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

Interaction vs. observation: distinctive modes of social cognition in human brain and behavior? A combined fMRI and eye-tracking study.

PubMed

Tylén, Kristian; Allen, Micah; Hunter, Bjørk K; Roepstorff, Andreas

2012-01-01

Human cognition has usually been approached on the level of individual minds and brains, but social interaction is a challenging case. Is it best thought of as a self-contained individual cognitive process aiming at an "understanding of the other," or should it rather be approached as an collective, inter-personal process where individual cognitive components interact on a moment-to-moment basis to form coupled dynamics? In a combined fMRI and eye-tracking study we directly contrasted these models of social cognition. We found that the perception of situations affording social contingent responsiveness (e.g., someone offering or showing you an object) elicited activations in regions of the right posterior temporal sulcus and yielded greater pupil dilation corresponding to a model of coupled dynamics (joint action). In contrast, the social-cognitive perception of someone "privately" manipulating an object elicited activation in medial prefrontal cortex, the right inferior frontal gyrus and right inferior parietal lobus, regions normally associated with Theory of Mind and with the mirror neuron system. Our findings support a distinction in social cognition between social observation and social interaction, and demonstrate that simple ostensive cues may shift participants' experience, behavior, and brain activity between these modes. The identification of a distinct, interactive mode has implications for research on social cognition, both in everyday life and in clinical conditions.

A flexible docking scheme to explore the binding selectivity of PDZ domains.

PubMed

Gerek, Z Nevin; Ozkan, S Banu

2010-05-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 A. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

A flexible docking scheme to explore the binding selectivity of PDZ domains

PubMed Central

Gerek, Z Nevin; Ozkan, S Banu

2010-01-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using RosettaLigand, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately. PMID:20196074

Insight into structural phase transitions from the decoupled anharmonic mode approximation

NASA Astrophysics Data System (ADS)

Adams, Donat J.; Passerone, Daniele

2016-08-01

We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

Insight into structural phase transitions from the decoupled anharmonic mode approximation.

PubMed

Adams, Donat J; Passerone, Daniele

2016-08-03

We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

Modes and emergent time scales of embayed beach dynamics

NASA Astrophysics Data System (ADS)

Ratliff, Katherine M.; Murray, A. Brad

2014-10-01

In this study, we use a simple numerical model (the Coastline Evolution Model) to explore alongshore transport-driven shoreline dynamics within generalized embayed beaches (neglecting cross-shore effects). Using principal component analysis (PCA), we identify two primary orthogonal modes of shoreline behavior that describe shoreline variation about its unchanging mean position: the rotation mode, which has been previously identified and describes changes in the mean shoreline orientation, and a newly identified breathing mode, which represents changes in shoreline curvature. Wavelet analysis of the PCA mode time series reveals characteristic time scales of these modes (typically years to decades) that emerge within even a statistically constant white-noise wave climate (without changes in external forcing), suggesting that these time scales can arise from internal system dynamics. The time scales of both modes increase linearly with shoreface depth, suggesting that the embayed beach sediment transport dynamics exhibit a diffusive scaling.

Very highly excited vibrational states of LiCN using a discrete variable representation

NASA Astrophysics Data System (ADS)

Henderson, James R.; Tennyson, Jonathan

Calculations are presented for the lowest 900 vibrational (J = 0) states of the LiCN floppy system for a two dimensional potential energy surface (rCN frozen). Most of these states lie well above the barrier separating the two linear isomers of the molecule and the point where the classical dynamics of the system becomes chaotic. Analysis of the wavefunctions of individual states in the high energy region shows that while most have an irregular nodal structure, a significant number of states appear regular - corresponding to solutions of standard, 'mode localized' hamiltonians. Motions corresponding in zero-order to Li-CN and Li-NC normal modes as well as free rotor states are identified. The distribution of level spacings is also studied and yields results in good agreement with those obtained by analysing nodal structures.

Progesterone and testosterone studies by neutron scattering and nuclear magnetic resonance methods and quantum chemistry calculations

NASA Astrophysics Data System (ADS)

Szyczewski, A.; Hołderna-Natkaniec, K.; Natkaniec, I.

2004-05-01

Inelastic incoherent neutron scattering spectra of progesterone and testosterone measured at 20 and 290 K were compared with the IR spectra measured at 290 K. The Phonon Density of States spectra display well resolved peaks of low frequency internal vibration modes up to 1200 cm -1. The quantum chemistry calculations were performed by semiempirical PM3 method and by the density functional theory method with different basic sets for isolated molecule, as well as for the dimer system of testosterone. The proposed assignment of internal vibrations of normal modes enable us to conclude about the sequence of the onset of the torsion movements of the CH 3 groups. These conclusions were correlated with the results of proton molecular dynamics studies performed by NMR method. The GAUSSIAN program had been used for calculations.

Polyad breaking phenomenon associated with a local-to-normal mode transition and suitability to estimate force constants

NASA Astrophysics Data System (ADS)

Bermúdez-Montaña, M.; Lemus, R.; Castaños, O.

2017-12-01

In a system of two interacting harmonic oscillators a local-to-normal mode transition is manifested as a polyad breaking phenomenon. This phenomenon is associated with the suitability to estimate zeroth-order force constants in the framework of a local mode description. This transition is also exhibited in two interacting Morse oscillators. To study this case, an appropriate parameterisation going from a molecule with local mode behaviour (H2O) to a molecule presenting a normal mode behaviour (CO2) is introduced. Concepts from quantum mechanics like fidelity, entropy and probability density, as well from nonlinear classical mechanics like Poincaré sections are used to detect the transition region. It is found that fidelity and entropy are sensitive complementary properties to detect the local-to-normal transition. Poincaré sections allow the local-to-normal transition to be detected through the appearance of chaos as a consequence of the polyad breaking phenomenon. In addition, two kinds of avoided energy crossings are identified in accordance with the different regions of the spectrum.

Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

NASA Astrophysics Data System (ADS)

Williams, Robert W.; Schlücker, Sebastian; Hudson, Bruce S.

2008-01-01

A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.

The dynamics and control of large flexible space structures, 3. Part A: Shape and orientation control of a platform in orbit using point actuators

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Reddy, A. S. S. R.; Krishna, R.; James, P. K.

1980-01-01

The dynamics, attitude, and shape control of a large thin flexible square platform in orbit are studied. Attitude and shape control are assumed to result from actuators placed perpendicular to the main surface and one edge and their effect on the rigid body and elastic modes is modelled to first order. The equations of motion are linearized about three different nominal orientations: (1) the platform following the local vertical with its major surface perpendicular to the orbital plane; (2) the platform following the local horizontal with its major surface normal to the local vertical; and (3) the platform following the local vertical with its major surface perpendicular to the orbit normal. The stability of the uncontrolled system is investigated analytically. Once controllability is established for a set of actuator locations, control law development is based on decoupling, pole placement, and linear optimal control theory. Frequencies and elastic modal shape functions are obtained using a finite element computer algorithm, two different approximate analytical methods, and the results of the three methods compared.

On Three-dimensional Structures in Relativistic Hydrodynamic Jets

NASA Astrophysics Data System (ADS)

Hardee, Philip E.

2000-04-01

The appearance of wavelike helical structures on steady relativistic jets is studied using a normal mode analysis of the linearized fluid equations. Helical structures produced by the normal modes scale relative to the resonant (most unstable) wavelength and not with the absolute wavelength. The resonant wavelength of the normal modes can be less than the jet radius even on highly relativistic jets. High-pressure regions helically twisted around the jet beam may be confined close to the jet surface, penetrate deeply into the jet interior, or be confined to the jet interior. The high-pressure regions range from thin and ribbon-like to thick and tubelike depending on the mode and wavelength. The wave speeds can be significantly different at different wavelengths but are less than the flow speed. The highest wave speed for the jets studied has a Lorentz factor somewhat more than half that of the underlying flow speed. A maximum pressure fluctuation criterion found through comparison between theory and a set of relativistic axisymmetric jet simulations is applied to estimate the maximum amplitudes of the helical, elliptical, and triangular normal modes. Transverse velocity fluctuations for these asymmetric modes are up to twice the amplitude of those associated with the axisymmetric pinch mode. The maximum amplitude of jet distortions and the accompanying velocity fluctuations at, for example, the resonant wavelength decreases as the Lorentz factor increases. Long-wavelength helical surface mode and shorter wavelength helical first body mode generated structures should be the most significant. Emission from high-pressure regions as they twist around the jet beam can vary significantly as a result of angular variation in the flow direction associated with normal mode structures if they are viewed at about the beaming angle θ=1/γ. Variation in the Doppler boost factor can lead to brightness asymmetries by factors up to 6 as long-wavelength helical structure produced by the helical surface mode winds around the jet. Higher order surface modes and first body modes produce less variation. Angular variation in the flow direction associated with the helical mode appears consistent with precessing jet models that have been proposed to explain the variability in 3C 273 and BL Lac object AO 0235+164. In particular, cyclic angular variation in the flow direction produced by the normal modes could produce the activity seen in BL Lac object OJ 287. Jet precession provides a mechanism for triggering the helical modes on multiple length scales, e.g., the galactic superluminal GRO J1655-40.

Quasi-Normal Modes of Stars and Black Holes.

PubMed

Kokkotas, Kostas D; Schmidt, Bernd G

1999-01-01

Perturbations of stars and black holes have been one of the main topics of relativistic astrophysics for the last few decades. They are of particular importance today, because of their relevance to gravitational wave astronomy. In this review we present the theory of quasi-normal modes of compact objects from both the mathematical and astrophysical points of view. The discussion includes perturbations of black holes (Schwarzschild, Reissner-Nordström, Kerr and Kerr-Newman) and relativistic stars (non-rotating and slowly-rotating). The properties of the various families of quasi-normal modes are described, and numerical techniques for calculating quasi-normal modes reviewed. The successes, as well as the limits, of perturbation theory are presented, and its role in the emerging era of numerical relativity and supercomputers is discussed.

Atmospheric resonances of the Rayleigh and tsunami normal modes and its sensitivity to local time and geographical location.

NASA Astrophysics Data System (ADS)

Rakoto, V.; Astafyeva, E.; Lognonne, P. H.

2017-12-01

It is known that natural hazard events, such as earthquakes, tsunamis, volcano eruptions, etc. can generate atmospheric/ionospheric perturbations. During earthquakes, vertical displacements of the ground or of the ocean floor generate acoustic-gravity waves that further propagate upward in the upper atmosphere and ionosphere. In turn, tsunamis propagating in the open sea, generate gravity waves which propagate obliquely and reach the ionosphere in 45-60 min. The properties of the atmospheric "channel" in the vertical and oblique propagation depend on a variety of factors such as solar and geomagnetic conditions, latitude, local time, season, and their influence on propagation and properties of co-seismic and co-tsunamic perturbations is not well understood yet. In this work, we use present a detailed study of the coupling efficiency between solid earth, ocean and atmosphere. For this purpose, we use the normal mode technique extended to the whole solid Earth-ocean-atmosphere system. In our study, we focus on the Rayleigh modes (solid modes) and tsunami modes (oceanic modes). As the normal modes amplitude are also depending on the spatial and temporal variation of the structure of the atmosphere, we also performed a sensitivity study location of the normal modes amplitude with local time and geographical position.

Off-axis fishbone-like instability and excitation of resistive wall modes in JT-60U and DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okabayashi, M.; Solomon, W. M.; Budny, R. V.

2011-05-15

An energetic-particle (EP)-driven ''off-axis-fishbone-like mode (OFM)'' often triggers a resistive wall mode (RWM) in JT-60U and DIII-D devices, preventing long-duration high-{beta}{sub N} discharges. In these experiments, the EPs are energetic ions (70-85 keV) injected by neutral beams to produce high-pressure plasmas. EP-driven bursting events reduce the EP density and the plasma rotation simultaneously. These changes are significant in high-{beta}{sub N} low-rotation plasmas, where the RWM stability is predicted to be strongly influenced by the EP precession drift resonance and by the plasma rotation near the q=2 surface (kinetic effects). Analysis of these effects on stability with a self-consistent perturbation tomore » the mode structure using the MARS-K code showed that the impact of EP losses and rotation drop is sufficient to destabilize the RWM in low-rotation plasmas, when the plasma rotation normalized by Alfven frequency is only a few tenths of a percent near the q=2 surface. The OFM characteristics are very similar in JT-60U and DIII-D, including nonlinear mode evolution. The modes grow initially like a classical fishbone, and then the mode structure becomes strongly distorted. The dynamic response of the OFM to an applied n=1 external field indicates that the mode retains its external kink character. These comparative studies suggest that an energetic particle-driven 'off-axis-fishbone-like mode' is a new EP-driven branch of the external kink mode in wall-stabilized plasmas, analogous to the relationship of the classical fishbone branch to the internal kink mode.« less

Identification of Dynamic Patterns of Speech-Evoked Auditory Brainstem Response Based on Ensemble Empirical Mode Decomposition and Nonlinear Time Series Analysis Methods

NASA Astrophysics Data System (ADS)

Mozaffarilegha, Marjan; Esteki, Ali; Ahadi, Mohsen; Nazeri, Ahmadreza

The speech-evoked auditory brainstem response (sABR) shows how complex sounds such as speech and music are processed in the auditory system. Speech-ABR could be used to evaluate particular impairments and improvements in auditory processing system. Many researchers used linear approaches for characterizing different components of sABR signal, whereas nonlinear techniques are not applied so commonly. The primary aim of the present study is to examine the underlying dynamics of normal sABR signals. The secondary goal is to evaluate whether some chaotic features exist in this signal. We have presented a methodology for determining various components of sABR signals, by performing Ensemble Empirical Mode Decomposition (EEMD) to get the intrinsic mode functions (IMFs). Then, composite multiscale entropy (CMSE), the largest Lyapunov exponent (LLE) and deterministic nonlinear prediction are computed for each extracted IMF. EEMD decomposes sABR signal into five modes and a residue. The CMSE results of sABR signals obtained from 40 healthy people showed that 1st, and 2nd IMFs were similar to the white noise, IMF-3 with synthetic chaotic time series and 4th, and 5th IMFs with sine waveform. LLE analysis showed positive values for 3rd IMFs. Moreover, 1st, and 2nd IMFs showed overlaps with surrogate data and 3rd, 4th and 5th IMFs showed no overlap with corresponding surrogate data. Results showed the presence of noisy, chaotic and deterministic components in the signal which respectively corresponded to 1st, and 2nd IMFs, IMF-3, and 4th and 5th IMFs. While these findings provide supportive evidence of the chaos conjecture for the 3rd IMF, they do not confirm any such claims. However, they provide a first step towards an understanding of nonlinear behavior of auditory system dynamics in brainstem level.

Topography-coupled resonance between Mars normal-modes and the tidal force of the Phobos

NASA Astrophysics Data System (ADS)

Tian, Y.; Zheng, Y.

2016-12-01

Phobos is the largest moon of Mars. The gravity attraction of Phobos to Mars is a periodic force, which may excite seismic waves inside Mars. Since Phobos is below the synchronous orbit, its orbit is continuously decreasing due to the tidal effect. This will result in a monotonic increase in its orbital frequency, which may eventually intrude into the seismic normal-mode frequency range to cause resonance. The objective of this research is to investigate whether such a resonance phenomenon can occur and what the consequence is. As we know, resonance happens when the periodic tidal force has a similar frequency as that of martian normal modes. It can be shown that such a resonance will not occur if Mars is perfectly spherical because the tidal force can only excite modes of the same angular order. For the same angular order, the tidal force frequencies are always smaller than those of the normal modes. However, when we consider the effect of topography of Mars, the resonance can occur because of coupling of normal modes. We use numerical method to calculate when the resonance will occur. We firstly solve for the normal modes of Mars by idealizing it as a solid elastic sphere. At the second step, we calculate the excitation effect of gravitational force from Phobos on each individual normal mode. For example, the gravity tidal force F at L=5, m=5 F55 can excite a normal mode 0S5 which can be coupled to 0T2. The third step is to calculate the frequency that the resonance will happen. For example, when the rotation frequency of Phobos increase to 0.8 mRad/s, the tidal force at L=5, m=5 can reach 4mRad/s which is the eigen-frequency of 0T2. Since we have calculated the coupling factors between each individual mode, the amplitude coefficients can be solved by a linear equation. We can observe a 100 times of amplitude increase of mode 0T2, which convince us the resonance will happen. The resonance may cause large amplitude of ground vibration of Mars. From our calculation, when the resonance happen, the energy dissipation rate will be greatly increased, which will make Phobos falling much faster. Eventually, Phobos will hit Mars in a very short time. Our research may give us a new prospective on early formation of planets.

Dynamic elementary mode modelling of non-steady state flux data.

PubMed

Folch-Fortuny, Abel; Teusink, Bas; Hoefsloot, Huub C J; Smilde, Age K; Ferrer, Alberto

2018-06-18

A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the time point of the experiment. Two methods are introduced here: dynamic elementary mode analysis (dynEMA) and dynamic elementary mode regression discriminant analysis (dynEMR-DA). The former is an extension of the recently proposed principal elementary mode analysis (PEMA) method from steady state to non-steady state scenarios. The latter is a discriminant model that permits to identify which dynEMs behave strongly different depending on the experimental conditions. Two case studies of Saccharomyces cerevisiae, with fluxes derived from simulated and real concentration data sets, are presented to highlight the benefits of this dynamic modelling. This methodology permits to analyse metabolic fluxes at early stages with the aim of i) creating reduced dynamic models of flux data, ii) combining many experiments in a single biologically meaningful model, and iii) identifying the metabolic pathways that drive the organism from one state to another when changing the environmental conditions.

Computational modeling of intrinsic dissipation in nano-structure

NASA Astrophysics Data System (ADS)

Kunal, Kumar

In this work, using computational modeling, we study the different mechanisms of intrinsic dissipation in nano-electro mechanical systems (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important applications. A few examples include the sensing of atomic mass, detection of biological molecules and observation of quantum effects in macroscopic objects. For all these potential applications, dissipation plays a limiting role. While a number of experimental and theoretical studies have been performed, the individual role of different mechanisms remains unclear. In this work, we attempt to isolate and understand the surface and size effect on some of the intrinsic mechanisms. We, first, consider the case of the Akhiezer damping. The Akhiezer dynamics is expected to play an important role in nano-resonators with frequencies in the GHz range. Using a judiciously devised MD set-up, we isolate Akhiezer dynamics. We show that the surfaces aid in reducing the dissipation rate through increasing the rate of thermalization of the phonons. We, next, study damping under the flexure mode of operation. A comparative analysis with the stretching mode shows that the flexure mode is less dissipative. A reduced order model is considered to understand this novel behavior. We, also, investigate the role of tension on the Q factor, a measure of the inverse of dissipation rate. From these studies, we conclude that Akhiezer dynamics plays a dominant role in nano-resonators. We, then, develop a quasi-harmonic based multi-scale method to model Akhiezer damping. A stress component, that characterizes the non-equilibrium phonon population, is derived. We obtain constitutive relation that governs the time evolution of the non-equilibrium stress. Different methods to parametrize the constitutive relation are discussed. Using the proposed formulation, we compute the dissipation rate for different cases. The results are compared with those obtained using MD. Next, we use the Boltzmann transport equation and investigate the Q factor due to the thermo-elastic dissipation (TED). The Q factor obtained shows deviations from the classical theory of TED. Correction to the classical formula, for the case of longitudinal modes, is provided. We, then, study damping is low dimensional structure. We first consider the case of two dimensional graphene sheet and under in-plane stretching. We show that the coupling between the in-plane and the out-of-plane motions plays an important role in the loss of mechanical energy. Further, a hysteresis behavior in the out-of-plane dynamics is observed. Next, we investigate the stretching motion of graphene nano-ribbon. A normal mode Langevin dynamics is devised to understand the results from the MD simulation.

Adaptive Actor-Critic Design-Based Integral Sliding-Mode Control for Partially Unknown Nonlinear Systems With Input Disturbances.

PubMed

Fan, Quan-Yong; Yang, Guang-Hong

2016-01-01

This paper is concerned with the problem of integral sliding-mode control for a class of nonlinear systems with input disturbances and unknown nonlinear terms through the adaptive actor-critic (AC) control method. The main objective is to design a sliding-mode control methodology based on the adaptive dynamic programming (ADP) method, so that the closed-loop system with time-varying disturbances is stable and the nearly optimal performance of the sliding-mode dynamics can be guaranteed. In the first step, a neural network (NN)-based observer and a disturbance observer are designed to approximate the unknown nonlinear terms and estimate the input disturbances, respectively. Based on the NN approximations and disturbance estimations, the discontinuous part of the sliding-mode control is constructed to eliminate the effect of the disturbances and attain the expected equivalent sliding-mode dynamics. Then, the ADP method with AC structure is presented to learn the optimal control for the sliding-mode dynamics online. Reconstructed tuning laws are developed to guarantee the stability of the sliding-mode dynamics and the convergence of the weights of critic and actor NNs. Finally, the simulation results are presented to illustrate the effectiveness of the proposed method.

Comparative study of various normal mode analysis techniques based on partial Hessians.

PubMed

Ghysels, An; Van Speybroeck, Veronique; Pauwels, Ewald; Catak, Saron; Brooks, Bernard R; Van Neck, Dimitri; Waroquier, Michel

2010-04-15

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. 2009 Wiley Periodicals, Inc.

Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians

PubMed Central

GHYSELS, AN; VAN SPEYBROECK, VERONIQUE; PAUWELS, EWALD; CATAK, SARON; BROOKS, BERNARD R.; VAN NECK, DIMITRI; WAROQUIER, MICHEL

2014-01-01

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein. PMID:19813181

Infrared vibrational spectroscopy of [Ru(bpy)2(bpm)]2+ and [Ru(bpy)3]2+ in the excited triplet state.

PubMed

Mukuta, Tatsuhiko; Fukazawa, Naoto; Murata, Kei; Inagaki, Akiko; Akita, Munetaka; Tanaka, Sei'ichi; Koshihara, Shin-ya; Onda, Ken

2014-03-03

This work involved a detailed investigation into the infrared vibrational spectra of ruthenium polypyridyl complexes, specifically heteroleptic [Ru(bpy)2(bpm)](2+) (bpy = 2,2'-bipyridine and bpm = 2,2'-bipyrimidine) and homoleptic [Ru(bpy)3](2+), in the excited triplet state. Transient spectra were acquired 500 ps after photoexcitation, corresponding to the vibrational ground state of the excited triplet state, using time-resolved infrared spectroscopy. We assigned the observed bands to specific ligands in [Ru(bpy)2(bpm)](2+) based on the results of deuterium substitution and identified the corresponding normal vibrational modes using quantum-chemical calculations. Through this process, the more complex vibrational bands of [Ru(bpy)3](2+) were assigned to normal vibrational modes. The results are in good agreement with the model in which excited electrons are localized on a single ligand. We also found that the vibrational bands of both complexes associated with the ligands on which electrons are little localized appear at approximately 1317 and 1608 cm(-1). These assignments should allow the study of the reaction dynamics of various photofunctional systems including ruthenium polypyridyl complexes.

The System Power Control Unit Based on the On-Chip Wireless Communication System

PubMed Central

Li, Tiefeng; Ma, Caiwen; Li, WenHua

2013-01-01

Currently, the on-chip wireless communication system (OWCS) includes 2nd-generation (2G), 3rd-generation (3G), and long-term evolution (LTE) communication subsystems. To improve the power consumption of OWCS, a typical architecture design of system power control unit (SPCU) is given in this paper, which can not only make a 2G, a 3G, and an LTE subsystems enter sleep mode, but it can also wake them up from sleep mode via the interrupt. During the sleep mode period, either the real-time sleep timer or the global system for mobile (GSM) communication sleep timer can be used individually to arouse the corresponding subsystem. Compared to previous sole voltage supplies on the OWCS, a 2G, a 3G, or an LTE subsystem can be independently configured with three different voltages and frequencies in normal work mode. In the meantime, the voltage supply monitor, which is an important part in the SPCU, can significantly guard the voltage of OWCS in real time. Finally, the SPCU may implement dynamic voltage and frequency scaling (DVFS) for a 2G, a 3G, or an LTE subsystem, which is automatically accomplished by the hardware. PMID:23818835

The system power control unit based on the on-chip wireless communication system.

PubMed

Li, Tiefeng; Ma, Caiwen; Li, WenHua

2013-01-01

Currently, the on-chip wireless communication system (OWCS) includes 2nd-generation (2G), 3rd-generation (3G), and long-term evolution (LTE) communication subsystems. To improve the power consumption of OWCS, a typical architecture design of system power control unit (SPCU) is given in this paper, which can not only make a 2G, a 3G, and an LTE subsystems enter sleep mode, but it can also wake them up from sleep mode via the interrupt. During the sleep mode period, either the real-time sleep timer or the global system for mobile (GSM) communication sleep timer can be used individually to arouse the corresponding subsystem. Compared to previous sole voltage supplies on the OWCS, a 2G, a 3G, or an LTE subsystem can be independently configured with three different voltages and frequencies in normal work mode. In the meantime, the voltage supply monitor, which is an important part in the SPCU, can significantly guard the voltage of OWCS in real time. Finally, the SPCU may implement dynamic voltage and frequency scaling (DVFS) for a 2G, a 3G, or an LTE subsystem, which is automatically accomplished by the hardware.

Deconvolution of reacting-flow dynamics using proper orthogonal and dynamic mode decompositions

NASA Astrophysics Data System (ADS)

Roy, Sukesh; Hua, Jia-Chen; Barnhill, Will; Gunaratne, Gemunu H.; Gord, James R.

2015-01-01

Analytical and computational studies of reacting flows are extremely challenging due in part to nonlinearities of the underlying system of equations and long-range coupling mediated by heat and pressure fluctuations. However, many dynamical features of the flow can be inferred through low-order models if the flow constituents (e.g., eddies or vortices) and their symmetries, as well as the interactions among constituents, are established. Modal decompositions of high-frequency, high-resolution imaging, such as measurements of species-concentration fields through planar laser-induced florescence and of velocity fields through particle-image velocimetry, are the first step in the process. A methodology is introduced for deducing the flow constituents and their dynamics following modal decomposition. Proper orthogonal (POD) and dynamic mode (DMD) decompositions of two classes of problems are performed and their strengths compared. The first problem involves a cellular state generated in a flat circular flame front through symmetry breaking. The state contains two rings of cells that rotate clockwise at different rates. Both POD and DMD can be used to deconvolve the state into the two rings. In POD the contribution of each mode to the flow is quantified using the energy. Each DMD mode can be associated with an energy as well as a unique complex growth rate. Dynamic modes with the same spatial symmetry but different growth rates are found to be combined into a single POD mode. Thus, a flow can be approximated by a smaller number of POD modes. On the other hand, DMD provides a more detailed resolution of the dynamics. Two classes of reacting flows behind symmetric bluff bodies are also analyzed. In the first, symmetric pairs of vortices are released periodically from the two ends of the bluff body. The second flow contains von Karman vortices also, with a vortex being shed from one end of the bluff body followed by a second shedding from the opposite end. The way in which DMD can be used to deconvolve the second flow into symmetric and von Karman vortices is demonstrated. The analyses performed illustrate two distinct advantages of DMD: (1) Unlike proper orthogonal modes, each dynamic mode is associated with a unique complex growth rate. By comparing DMD spectra from multiple nominally identical experiments, it is possible to identify "reproducible" modes in a flow. We also find that although most high-energy modes are reproducible, some are not common between experimental realizations; in the examples considered, energy fails to differentiate between reproducible and nonreproducible modes. Consequently, it may not be possible to differentiate reproducible and nonreproducible modes in POD. (2) Time-dependent coefficients of dynamic modes are complex. Even in noisy experimental data, the dynamics of the phase of these coefficients (but not their magnitude) are highly regular. The phase represents the angular position of a rotating ring of cells and quantifies the downstream displacement of vortices in reacting flows. Thus, it is suggested that the dynamical characterizations of complex flows are best made through the phase dynamics of reproducible DMD modes.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

NASA Astrophysics Data System (ADS)

Lin, Hui-Chi; Yang, Meng-Ru; Tsai, Sheng-Feng; Yan, Shih-Chiang

2014-01-01

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Hui-Chi, E-mail: huichilin@nfu.edu.tw; Yang, Meng-Ru; Tsai, Sheng-Feng

2014-01-06

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Nuclear quantum effects on adsorption of H 2 and isotopologues on metal ions

DOE PAGES

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; ...

2017-01-03

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of Hmore » $$_2$$ and isotopologues on metal ions, are examined in this study using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. To estimate for the anharmonicity, a nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) have been employed for complexes of Li$^+$ and Cu$$^{+2}$$ with H$$_2$$, D$$_2$$, HD. The dynamics analysis shows that incorporation of the PES anharmonicity changes the ZPE by up to 9%. Finally, the lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions.« less

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

Interference effects on guided Cherenkov emission in silicon from perpendicular, oblique, and parallel boundaries

NASA Astrophysics Data System (ADS)

Couillard, M.; Yurtsever, A.; Muller, D. A.

2010-05-01

Waveguide electromagnetic modes excited by swift electrons traversing Si slabs at normal and oblique incidence are analyzed using monochromated electron energy-loss spectroscopy and interpreted using a local dielectric theory that includes relativistic effects. At normal incidence, sharp spectral features in the visible/near-infrared optical domain are directly assigned to p -polarized modes. When the specimen is tilted, s -polarized modes, which are completely absent at normal incidence, become visible in the loss spectra. In the tilted configuration, the dispersion of p -polarized modes is also modified. For tilt angles higher than ˜50° , Cherenkov radiation, the phenomenon responsible for the excitation of waveguide modes, is expected to partially escape the silicon slab and the influence of this effect on experimental measurements is discussed. Finally, we find evidence for an interference effect at parallel Si/SiO2 interfaces, as well as a delocalized excitation of guided Cherenkov modes.

Generalized global symmetries in states with dynamical defects: The case of the transverse sound in field theory and holography

NASA Astrophysics Data System (ADS)

Grozdanov, Sašo; Poovuttikul, Napat

2018-05-01

In this work, we show how states with conserved numbers of dynamical defects (strings, domain walls, etc.) can be understood as possessing generalized global symmetries even when the microscopic origins of these symmetries are unknown. Using this philosophy, we build an effective theory of a 2 +1 -dimensional fluid state with two perpendicular sets of immersed elastic line defects. When the number of defects is independently conserved in each set, then the state possesses two one-form symmetries. Normally, such viscoelastic states are described as fluids coupled to Goldstone bosons associated with spontaneous breaking of translational symmetry caused by the underlying microscopic structure—the principle feature of which is a transverse sound mode. At the linear, nondissipative level, we verify that our theory, based entirely on symmetry principles, is equivalent to a viscoelastic theory. We then build a simple holographic dual of such a state containing dynamical gravity and two two-form gauge fields, and use it to study its hydrodynamic and higher-energy spectral properties characterized by nonhydrodynamic, gapped modes. Based on the holographic analysis of transverse two-point functions, we study consistency between low-energy predictions of the bulk theory and the effective boundary theory. Various new features of the holographic dictionary are explained in theories with higher-form symmetries, such as the mixed-boundary-condition modification of the quasinormal mode prescription that depends on the running coupling of the boundary double-trace deformations. Furthermore, we examine details of low- and high-energy parts of the spectrum that depend on temperature, line defect densities and the renormalization group scale.

Quantum localization for a kicked rotor with accelerator mode islands.

PubMed

Iomin, A; Fishman, S; Zaslavsky, G M

2002-03-01

Dynamical localization of classical superdiffusion for the quantum kicked rotor is studied in the semiclassical limit. Both classical and quantum dynamics of the system become more complicated under the conditions of mixed phase space with accelerator mode islands. Recently, long time quantum flights due to the accelerator mode islands have been found. By exploration of their dynamics, it is shown here that the classical-quantum duality of the flights leads to their localization. The classical mechanism of superdiffusion is due to accelerator mode dynamics, while quantum tunneling suppresses the superdiffusion and leads to localization of the wave function. Coupling of the regular type dynamics inside the accelerator mode island structures to dynamics in the chaotic sea proves increasing the localization length. A numerical procedure and an analytical method are developed to obtain an estimate of the localization length which, as it is shown, has exponentially large scaling with the dimensionless Planck's constant (tilde)h<1 in the semiclassical limit. Conditions for the validity of the developed method are specified.

A reduced-order model for compressible flows with buffeting condition using higher order dynamic mode decomposition with a mode selection criterion

NASA Astrophysics Data System (ADS)

Kou, Jiaqing; Le Clainche, Soledad; Zhang, Weiwei

2018-01-01

This study proposes an improvement in the performance of reduced-order models (ROMs) based on dynamic mode decomposition to model the flow dynamics of the attractor from a transient solution. By combining higher order dynamic mode decomposition (HODMD) with an efficient mode selection criterion, the HODMD with criterion (HODMDc) ROM is able to identify dominant flow patterns with high accuracy. This helps us to develop a more parsimonious ROM structure, allowing better predictions of the attractor dynamics. The method is tested in the solution of a NACA0012 airfoil buffeting in a transonic flow, and its good performance in both the reconstruction of the original solution and the prediction of the permanent dynamics is shown. In addition, the robustness of the method has been successfully tested using different types of parameters, indicating that the proposed ROM approach is a tool promising for using in both numerical simulations and experimental data.

Deconvolution of azimuthal mode detection measurements

NASA Astrophysics Data System (ADS)

Sijtsma, Pieter; Brouwer, Harry

2018-05-01

Unequally spaced transducer rings make it possible to extend the range of detectable azimuthal modes. The disadvantage is that the response of the mode detection algorithm to a single mode is distributed over all detectable modes, similarly to the Point Spread Function of Conventional Beamforming with microphone arrays. With multiple modes the response patterns interfere, leading to a relatively high "noise floor" of spurious modes in the detected mode spectrum, in other words, to a low dynamic range. In this paper a deconvolution strategy is proposed for increasing this dynamic range. It starts with separating the measured sound into shaft tones and broadband noise. For broadband noise modes, a standard Non-Negative Least Squares solver appeared to be a perfect deconvolution tool. For shaft tones a Matching Pursuit approach is proposed, taking advantage of the sparsity of dominant modes. The deconvolution methods were applied to mode detection measurements in a fan rig. An increase in dynamic range of typically 10-15 dB was found.

Helicon normal modes in Proto-MPEX

NASA Astrophysics Data System (ADS)

Piotrowicz, P. A.; Caneses, J. F.; Green, D. L.; Goulding, R. H.; Lau, C.; Caughman, J. B. O.; Rapp, J.; Ruzic, D. N.

2018-05-01

The Proto-MPEX helicon source has been operating in a high electron density ‘helicon-mode’. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the ‘helicon-mode’. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besides directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region. ).

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

NASA Astrophysics Data System (ADS)

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

1998-10-01

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

Quantum-to-classical crossover near quantum critical point

DOE PAGES

Vasin, M.; Ryzhov, V.; Vinokur, V. M.

2015-12-21

A quantum phase transition (QPT) is an inherently dynamic phenomenon. However, while non-dissipative quantum dynamics is described in detail, the question, that is not thoroughly understood is how the omnipresent dissipative processes enter the critical dynamics near a quantum critical point (QCP). Here we report a general approach enabling inclusion of both adiabatic and dissipative processes into the critical dynamics on the same footing. We reveal three distinct critical modes, the adiabatic quantum mode (AQM), the dissipative classical mode [classical critical dynamics mode (CCDM)], and the dissipative quantum critical mode (DQCM). We find that as a result of the transitionmore » from the regime dominated by thermal fluctuations to that governed by the quantum ones, the system acquires effective dimension d+zΛ(T), where z is the dynamical exponent, and temperature-depending parameter Λ(T)ε[0, 1] decreases with the temperature such that Λ(T=0) = 1 and Λ(T →∞) = 0. Lastly, our findings lead to a unified picture of quantum critical phenomena including both dissipation- and dissipationless quantum dynamic effects and offer a quantitative description of the quantum-to-classical crossover.« less

Age-Related Changes in Dynamic Postural Control and Attentional Demands are Minimally Affected by Local Muscle Fatigue

PubMed Central

Remaud, Anthony; Thuong-Cong, Cécile; Bilodeau, Martin

2016-01-01

Normal aging results in alterations in the visual, vestibular and somtaosensory systems, which in turn modify the control of balance. Muscle fatigue may exacerbate these age-related changes in sensory and motor functions, and also increase the attentional demands associated with dynamic postural control. The purpose of this study was to investigate the effect of aging on dynamic postural control and posture-related attentional demands before and after a plantar flexor fatigue protocol. Participants (young adults: n = 15; healthy seniors: n = 13) performed a dynamic postural task along the antero-posterior (AP) and the medio-lateral (ML) axes, with and without the addition of a simple reaction time (RT) task. The dynamic postural task consisted in following a moving circle on a computer screen with the representation of the center of pressure (COP). This protocol was repeated before and after a fatigue task where ankle plantar flexor muscles were targeted. The mean COP-target distance and the mean COP velocity were calculated for each trial. Cross-correlation analyses between the COP and target displacements were also performed. RTs were recorded during dual-task trials. Results showed that while young adults adopted an anticipatory control mode to move their COP as close as possible to the target center, seniors adopted a reactive control mode, lagging behind the target center. This resulted in longer COP-target distance and higher COP velocity in the latter group. Concurrently, RT increased more in seniors when switching from static stance to dynamic postural conditions, suggesting potential alterations in the central nervous system (CNS) functions. Finally, plantar flexor muscle fatigue and dual-tasking had only minor effects on dynamic postural control of both young adults and seniors. Future studies should investigate why the fatigue-induced changes in quiet standing postural control do not seem to transfer to dynamic balance tasks. PMID:26834626

Fluid involvement in normal faulting

NASA Astrophysics Data System (ADS)

Sibson, Richard H.

2000-04-01

Evidence of fluid interaction with normal faults comes from their varied role as flow barriers or conduits in hydrocarbon basins and as hosting structures for hydrothermal mineralisation, and from fault-rock assemblages in exhumed footwalls of steep active normal faults and metamorphic core complexes. These last suggest involvement of predominantly aqueous fluids over a broad depth range, with implications for fault shear resistance and the mechanics of normal fault reactivation. A general downwards progression in fault rock assemblages (high-level breccia-gouge (often clay-rich) → cataclasites → phyllonites → mylonite → mylonitic gneiss with the onset of greenschist phyllonites occurring near the base of the seismogenic crust) is inferred for normal fault zones developed in quartzo-feldspathic continental crust. Fluid inclusion studies in hydrothermal veining from some footwall assemblages suggest a transition from hydrostatic to suprahydrostatic fluid pressures over the depth range 3-5 km, with some evidence for near-lithostatic to hydrostatic pressure cycling towards the base of the seismogenic zone in the phyllonitic assemblages. Development of fault-fracture meshes through mixed-mode brittle failure in rock-masses with strong competence layering is promoted by low effective stress in the absence of thoroughgoing cohesionless faults that are favourably oriented for reactivation. Meshes may develop around normal faults in the near-surface under hydrostatic fluid pressures to depths determined by rock tensile strength, and at greater depths in overpressured portions of normal fault zones and at stress heterogeneities, especially dilational jogs. Overpressures localised within developing normal fault zones also determine the extent to which they may reutilise existing discontinuities (for example, low-angle thrust faults). Brittle failure mode plots demonstrate that reactivation of existing low-angle faults under vertical σ1 trajectories is only likely if fluid overpressures are localised within the fault zone and the surrounding rock retains significant tensile strength. Migrating pore fluids interact both statically and dynamically with normal faults. Static effects include consideration of the relative permeability of the faults with respect to the country rock, and juxtaposition effects which determine whether a fault is transmissive to flow or acts as an impermeable barrier. Strong directional permeability is expected in the subhorizontal σ2 direction parallel to intersections between minor faults, extension fractures, and stylolites. Three dynamic mechanisms tied to the seismic stress cycle may contribute to fluid redistribution: (i) cycling of mean stress coupled to shear stress, sometimes leading to postfailure expulsion of fluid from vertical fractures; (ii) suction pump action at dilational fault jogs; and, (iii) fault-valve action when a normal fault transects a seal capping either uniformly overpressured crust or overpressures localised to the immediate vicinity of the fault zone at depth. The combination of σ2 directional permeability with fluid redistribution from mean stress cycling may lead to hydraulic communication along strike, contributing to the protracted earthquake sequences that characterise normal fault systems.

Dynamic fracture mechanics analysis for an edge delamination crack

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Doyle, James F.

1994-01-01

A global/local analysis is applied to the problem of a panel with an edge delamination crack subject to an impulse loading to ascertain the dynamic J integral. The approach uses the spectral element method to obtain the global dynamic response and local resultants to obtain the J integral. The variation of J integral along the crack front is shown. The crack behavior is mixed mode (Mode 2 and Mode 3), but is dominated by the Mode 2 behavior.

Calculation of structural dynamic forces and stresses using mode acceleration

NASA Technical Reports Server (NTRS)

Blelloch, Paul

1989-01-01

While the standard mode acceleration formulation in structural dynamics has often been interpreted to suggest that the reason for improved convergence obtainable is that the dynamic correction factor is divided by the modal frequencies-squared, an alternative formulation is presented which clearly indicates that the only difference between mode acceleration and mode displacement data recovery is the addition of a static correction term. Attention is given to the advantages in numerical implementation associated with this alternative, as well as to an illustrative example.

Effects of lithium insertion on thermal conductivity of silicon nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Wen; Institute of High Performance Computing, A*STAR, Singapore, Singapore 138632; Zhang, Gang, E-mail: zhangg@ihpc.a-star.edu.sg

2015-04-27

Recently, silicon nanowires (SiNWs) have been applied as high-performance Li battery anodes, since they can overcome the pulverization and mechanical fracture during lithiation. Although thermal stability is one of the most important parameters that determine safety of Li batteries, thermal conductivity of SiNWs with Li insertion remains unclear. In this letter, using molecular dynamics simulations, we study room temperature thermal conductivity of SiNWs with Li insertion. It is found that compared with the pristine SiNW, there is as much as 60% reduction in thermal conductivity with 10% concentration of inserted Li atoms, while under the same impurity concentration the reductionmore » in thermal conductivity of the mass-disordered SiNW is only 30%. With lattice dynamics calculations and normal mode decomposition, it is revealed that the phonon lifetimes in SiNWs decrease greatly due to strong scattering of phonons by vibrational modes of Li atoms, especially for those high frequency phonons. The observed strong phonon scattering phenomenon in Li-inserted SiNWs is similar to the phonon rattling effect. Our study serves as an exploration of thermal properties of SiNWs as Li battery anodes or weakly coupled with impurity atoms.« less

Finite Element Model Development and Validation for Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results. The increased frequency range results in a corresponding increase in the number of modes, modal density and spatial resolution requirements. In this study, conventional modal tests using accelerometers are complemented with Scanning Laser Doppler Velocimetry and Electro-Optic Holography measurements to further resolve the spatial response characteristics. Whenever possible, component and subassembly modal tests are used to validate the finite element models at lower levels of assembly. Normal mode predictions for different finite element representations of components and assemblies are compared with experimental results to assess the most accurate techniques for modeling aircraft fuselage type structures.

Multivariable Techniques for High-Speed Research Flight Control Systems

NASA Technical Reports Server (NTRS)

Newman, Brett A.

1999-01-01

This report describes the activities and findings conducted under contract with NASA Langley Research Center. Subject matter is the investigation of suitable multivariable flight control design methodologies and solutions for large, flexible high-speed vehicles. Specifically, methodologies are to address the inner control loops used for stabilization and augmentation of a highly coupled airframe system possibly involving rigid-body motion, structural vibrations, unsteady aerodynamics, and actuator dynamics. Design and analysis techniques considered in this body of work are both conventional-based and contemporary-based, and the vehicle of interest is the High-Speed Civil Transport (HSCT). Major findings include: (1) control architectures based on aft tail only are not well suited for highly flexible, high-speed vehicles, (2) theoretical underpinnings of the Wykes structural mode control logic is based on several assumptions concerning vehicle dynamic characteristics, and if not satisfied, the control logic can break down leading to mode destabilization, (3) two-loop control architectures that utilize small forward vanes with the aft tail provide highly attractive and feasible solutions to the longitudinal axis control challenges, and (4) closed-loop simulation sizing analyses indicate the baseline vane model utilized in this report is most likely oversized for normal loading conditions.

Effects of lithium insertion on thermal conductivity of silicon nanowires

NASA Astrophysics Data System (ADS)

Xu, Wen; Zhang, Gang; Li, Baowen

2015-04-01

Recently, silicon nanowires (SiNWs) have been applied as high-performance Li battery anodes, since they can overcome the pulverization and mechanical fracture during lithiation. Although thermal stability is one of the most important parameters that determine safety of Li batteries, thermal conductivity of SiNWs with Li insertion remains unclear. In this letter, using molecular dynamics simulations, we study room temperature thermal conductivity of SiNWs with Li insertion. It is found that compared with the pristine SiNW, there is as much as 60% reduction in thermal conductivity with 10% concentration of inserted Li atoms, while under the same impurity concentration the reduction in thermal conductivity of the mass-disordered SiNW is only 30%. With lattice dynamics calculations and normal mode decomposition, it is revealed that the phonon lifetimes in SiNWs decrease greatly due to strong scattering of phonons by vibrational modes of Li atoms, especially for those high frequency phonons. The observed strong phonon scattering phenomenon in Li-inserted SiNWs is similar to the phonon rattling effect. Our study serves as an exploration of thermal properties of SiNWs as Li battery anodes or weakly coupled with impurity atoms.

A low-order model of the equatorial ocean-atmosphere system

NASA Astrophysics Data System (ADS)

Legnani, Roberto

A low order model of the equatorial ocean-atmosphere coupled system is presented. The model atmosphere includes a hydrological cycle with cloud-radiation interaction. The model ocean is based on mixed layer dynamics with a parameterization of entrainment processes. The coupling takes place via transfer to momentum, sensible heat, latent heat and short wave and long wave radiation through the ocean surface. The dynamical formulation is that of the primitive equations of an equatorial beta-plane, with zonally periodic and meridionally infinite geometry. The system is expanded into the set of normal modes pertinent to the linear problem and severly truncated to a few modes; 54 degrees of freedom are retained. Some nonlinear terms of the equations are evaluated in physical space and then projected onto the functional space; other terms are evaluated directly in the functional space. Sensitivity tests to variations of the parameters are performed, and some results from 10-year initial value simulations are presented. The model is capable of supporting oscillations of different time scales, ranging from a few days to a few years; it prefers a particular zonally asymmetric state, but temporarily switches to a different (opposite) zonally asymmetric state in an event-like fashion.

a Low-Order Model of the Equatorial Ocean-Atmosphere System.

NASA Astrophysics Data System (ADS)

Legnani, Roberto

A low order model of the equatorial ocean-atmosphere coupled system is presented. The model atmosphere includes a hydrological cycle with cloud-radiation interaction. The model ocean is based on mixed layer dynamics with a parameterization of entrainment processes. The coupling takes place via transfer to momentum, sensible heat, latent heat and short -wave and long-wave radiation through the ocean surface. The dynamical formulation is that of the primitive equations of an equatorial beta-plane, with zonally periodic and meridionally infinite geometry. The system is expanded into the set of normal modes pertinent to the linear problem and severely truncated to a few modes; 54 degrees of freedom are retained. Some nonlinear terms of the equations are evaluated in physical space and then projected onto the functional space; other terms are evaluated directly in the functional space. Sensitivity tests to variations of the parameters are performed, and some results from 10-year initial value simulations are presented. The model is capable of supporting oscillations of different time scales, ranging from a few days to a few years; it prefers a particular zonally asymmetric state, but temporarily switches to a different (opposite) zonally asymmetric state in an event-like fashion.

Free-Surface flow dynamics and its effect on travel time distribution in unsaturated fractured zones - findings from analogue percolation experiments

NASA Astrophysics Data System (ADS)

Noffz, Torsten; Kordilla, Jannes; Dentz, Marco; Sauter, Martin

2017-04-01

Flow in unsaturated fracture networks constitutes a high potential for rapid mass transport and can therefore possibly contributes to the vulnerability of aquifer systems. Numerical models are generally used to predict flow and transport and have to reproduce various complex effects of gravity-driven flow dynamics. However, many classical volume-effective modelling approaches often do not grasp the non-linear free surface flow dynamics and partitioning behaviour at fracture intersections in unsaturated fracture networks. Better process understanding can be obtained by laboratory experiments, that isolate single aspects of the mass partitioning process, which influence travel time distributions and allow possible cross-scale applications. We present a series of percolation experiments investigating partitioning dynamics of unsaturated multiphase flow at an individual horizontal fracture intersection. A high precision multichannel dispenser is used to establish gravity-driven free surface flow on a smooth and vertical PMMA (poly(methyl methacrylate)) surface at rates ranging from 1.5 to 4.5 mL/min to obtain various flow modes (droplets; rivulets). Cubes with dimensions 20 x 20 x 20 cm are used to create a set of simple geometries. A digital balance provides continuous real-time cumulative mass bypassing the network. The influence of variable flow rate, atmospheric pressure and temperature on the stability of flow modes is shown in single-inlet experiments. Droplet and rivulet flow are delineated and a transition zone exhibiting mixed flow modes can be determined. Furthermore, multi-inlet setups with constant total inflow rates are used to reduce variance and the effect of erratic free-surface flow dynamics. Investigated parameters include: variable aperture widths df, horizontal offsets dv of the vertical fracture surface and alternating injection methods for both droplet and rivulet flow. Repetitive structures with several horizontal fractures extend arrival times but also complexity and variance. Finally, impacts of variable geometric features and flow modes on partitioning dynamics are highlighted by normalized fracture inflow rates. For higher flow rates, i.e. rivulet flows dominates, the effectiveness of filling horizontal fractures strongly increases. We demonstrate that the filling can be described by plug flow, which transitions into a Washburn-type flow at later times, and derive an analytical solution for the case of rivulet flows. Droplet flow dominated flow experiments exhibit a high bypass efficiency, which cannot be described by plug-flow, however, they also transition into a Washburn stage.

Tearing mode dynamics and sawtooth oscillation in Hall-MHD

NASA Astrophysics Data System (ADS)

Ma, Zhiwei; Zhang, Wei; Wang, Sheng

2017-10-01

Tearing mode instability is one of the most important dynamic processes in space and laboratory plasmas. Hall effects, resulted from the decoupling of electron and ion motions, could cause the fast development and perturbation structure rotation of the tearing mode and become non-negligible. We independently developed high accuracy nonlinear MHD code (CLT) to study Hall effects on the dynamic evolution of tearing modes with Tokamak geometries. It is found that the rotation frequency of the mode in the electron diamagnetic direction is in a good agreement with analytical prediction. The linear growth rate increases with increase of the ion inertial length, which is contradictory to analytical solution in the slab geometry. We further find that the self-consistently generated rotation largely alters the dynamic behavior of the double tearing mode and the sawtooth oscillation. National Magnetic Confinement Fusion Science Program of China under Grant No. 2013GB104004 and 2013GB111004.

"I Treat Him as a Normal Patient": Unveiling the Normalization Coping Strategy Among Formal Caregivers of Persons With Dementia and Its Implications for Person-Centered Care.

PubMed

Bentwich, Miriam Ethel; Dickman, Nomy; Oberman, Amitai; Bokek-Cohen, Ya'arit

2017-11-01

Currently, 47 million people have dementia, worldwide, often requiring paid care by formal caregivers. Research regarding family caregivers suggests normalization as a model for coping with negative emotional outcomes in caring for a person with dementia (PWD). The study aims to explore whether normalization coping mechanism exists among formal caregivers, reveal differences in its application among cross-cultural caregivers, and examine how this coping mechanism may be related to implementing person-centered care for PWDs. Content analysis of interviews with 20 formal caregivers from three cultural groups (Jews born in Israel [JI], Arabs born in Israel [AI], Russian immigrants [RI]), attending to PWDs. We extracted five normalization modes, revealing AI caregivers had substantially more utterances of normalization expressions than their colleagues. The normalization modes most commonly expressed by AI caregivers relate to the personhood of PWDs. These normalization modes may enhance formal caregivers' ability to employ person-centered care.

Secular instabilities of Keplerian stellar discs

NASA Astrophysics Data System (ADS)

Kaur, Karamveer; Kazandjian, Mher V.; Sridhar, S.; Touma, Jihad R.

2018-05-01

We present idealized models of a razor-thin, axisymmetric, Keplerian stellar disc around a massive black hole, and study non-axisymmetric secular instabilities in the absence of either counter-rotation or loss cones. These discs are prograde mono-energetic waterbags, whose phase-space distribution functions are constant for orbits within a range of eccentricities (e) and zero outside this range. The linear normal modes of waterbags are composed of sinusoidal disturbances of the edges of distribution function in phase space. Waterbags that include circular orbits (polarcaps) have one stable linear normal mode for each azimuthal wavenumber m. The m = 1 mode always has positive pattern speed and, for polarcaps consisting of orbits with e < 0.9428, only the m = 1 mode has positive pattern speed. Waterbags excluding circular orbits (bands) have two linear normal modes for each m, which can be stable or unstable. We derive analytical expressions for the instability condition, pattern speeds, growth rates, and normal mode structure. Narrow bands are unstable to modes with a wide range in m. Numerical simulations confirm linear theory and follow the non-linear evolution of instabilities. Long-time integration suggests that instabilities of different m grow, interact non-linearly, and relax collisionlessly to a coarse-grained equilibrium with a wide range of eccentricities.

FIBER AND INTEGRATED OPTICS: Propagation of radiation in a light-induced active waveguide

NASA Astrophysics Data System (ADS)

Afanas'ev, Anatolii A.; Samson, B. A.; Drits, V. V.; Yukhimenko, S. I.; Yakite, R. V.

1990-10-01

An investigation is reported of the properties of the normal modes of an active light-induced waveguide. It is shown that, in contrast to a dielectric waveguide, the presence of the active component may increase considerably the number of the normal modes and the angles of their scattering. In the case of an active light-induced waveguide in the form of a thin filament the normal modes exist and are amplified only in the case when the nonlinear correction to the refractive index is positive.

Normal-Mode Splitting in a Weakly Coupled Optomechanical System

NASA Astrophysics Data System (ADS)

Rossi, Massimiliano; Kralj, Nenad; Zippilli, Stefano; Natali, Riccardo; Borrielli, Antonio; Pandraud, Gregory; Serra, Enrico; Di Giuseppe, Giovanni; Vitali, David

2018-02-01

Normal-mode splitting is the most evident signature of strong coupling between two interacting subsystems. It occurs when two subsystems exchange energy between themselves faster than they dissipate it to the environment. Here we experimentally show that a weakly coupled optomechanical system at room temperature can manifest normal-mode splitting when the pump field fluctuations are antisquashed by a phase-sensitive feedback loop operating close to its instability threshold. Under these conditions the optical cavity exhibits an effectively reduced decay rate, so that the system is effectively promoted to the strong coupling regime.

A modal aeroelastic analysis scheme for turbomachinery blading. M.S. Thesis - Case Western Reserve Univ. Final Report

NASA Technical Reports Server (NTRS)

Smith, Todd E.

1991-01-01

An aeroelastic analysis is developed which has general application to all types of axial-flow turbomachinery blades. The approach is based on linear modal analysis, where the blade's dynamic response is represented as a linear combination of contributions from each of its in-vacuum free vibrational modes. A compressible linearized unsteady potential theory is used to model the flow over the oscillating blades. The two-dimensional unsteady flow is evaluated along several stacked axisymmetric strips along the span of the airfoil. The unsteady pressures at the blade surface are integrated to result in the generalized force acting on the blade due to simple harmonic motions. The unsteady aerodynamic forces are coupled to the blade normal modes in the frequency domain using modal analysis. An iterative eigenvalue problem is solved to determine the stability of the blade when the unsteady aerodynamic forces are included in the analysis. The approach is demonstrated by applying it to a high-energy subsonic turbine blade from a rocket engine turbopump power turbine. The results indicate that this turbine could undergo flutter in an edgewise mode of vibration.

Power inverter implementing phase skipping control

DOEpatents

Somani, Utsav; Amirahmadi, Ahmadreza; Jourdan, Charles; Batarseh, Issa

2016-10-18

A power inverter includes a DC/AC inverter having first, second and third phase circuitry coupled to receive power from a power source. A controller is coupled to a driver for each of the first, second and third phase circuitry (control input drivers). The controller includes an associated memory storing a phase skipping control algorithm, wherein the controller is coupled to receive updating information including a power level generated by the power source. The drivers are coupled to control inputs of the first, second and third phase circuitry, where the drivers are configured for receiving phase skipping control signals from the controller and outputting mode selection signals configured to dynamically select an operating mode for the DC/AC inverter from a Normal Control operation and a Phase Skipping Control operation which have different power injection patterns through the first, second and third phase circuitry depending upon the power level.

A reduced order, test verified component mode synthesis approach for system modeling applications

NASA Astrophysics Data System (ADS)

Butland, Adam; Avitabile, Peter

2010-05-01

Component mode synthesis (CMS) is a very common approach used for the generation of large system models. In general, these modeling techniques can be separated into two categories: those utilizing a combination of constraint modes and fixed interface normal modes and those based on a combination of free interface normal modes and residual flexibility terms. The major limitation of the methods utilizing constraint modes and fixed interface normal modes is the inability to easily obtain the required information from testing; the result of this limitation is that constraint mode-based techniques are primarily used with numerical models. An alternate approach is proposed which utilizes frequency and shape information acquired from modal testing to update reduced order finite element models using exact analytical model improvement techniques. The connection degrees of freedom are then rigidly constrained in the test verified, reduced order model to provide the boundary conditions necessary for constraint modes and fixed interface normal modes. The CMS approach is then used with this test verified, reduced order model to generate the system model for further analysis. A laboratory structure is used to show the application of the technique with both numerical and simulated experimental components to describe the system and validate the proposed approach. Actual test data is then used in the approach proposed. Due to typical measurement data contaminants that are always included in any test, the measured data is further processed to remove contaminants and is then used in the proposed approach. The final case using improved data with the reduced order, test verified components is shown to produce very acceptable results from the Craig-Bampton component mode synthesis approach. Use of the technique with its strengths and weaknesses are discussed.

Improvement of analytical dynamic models using modal test data

NASA Technical Reports Server (NTRS)

Berman, A.; Wei, F. S.; Rao, K. V.

1980-01-01

A method developed to determine maximum changes in analytical mass and stiffness matrices to make them consistent with a set of measured normal modes and natural frequencies is presented. The corrected model will be an improved base for studies of physical changes, boundary condition changes, and for prediction of forced responses. The method features efficient procedures not requiring solutions of the eigenvalue problem, and the ability to have more degrees of freedom than the test data. In addition, modal displacements are obtained for all analytical degrees of freedom, and the frequency dependence of the coordinate transformations is properly treated.

Test procedures and performance measures sensitive to automobile steering dynamics. [considering operator/vehicle responses

NASA Technical Reports Server (NTRS)

Klein, R. H.; Mcruer, D. T.; Weir, D.

1975-01-01

A maneuver complex and related performance measures used to evaluate driver/vehicle system responses as effected by variations in the directional response characteristics of passenger cars are described. The complex consists of normal and emergency maneuvers (including random and discrete disturbances) which, taken as a whole, represent all classes of steering functions and all modes of driver response behavior. Measures of driver/vehicle system response and performance in regulation tasks included direct describing function measurements and rms yaw velocity. In transient maneuvers, measures such as steering activity and cone strikes were used.

Epitaxial Growths of m-Plane AlGaN/GaN and AlInN/GaN Heterostructures Applicable for Normally-Off Mode High Power Field Effect Transistors on Freestanding GaN Substrates

DTIC Science & Technology

2011-08-17

cathodoluminescence (CL), and Hall effect measurement. We will disclose how structural and point defects affect the internal quantum efficiency. We have a complete...18. S. F. Chichibu, A. Uedono, T. Onuma, S. P. DenBaars, U. K. Mishra, J. S. Speck, and S. Nakamura, “Impact of Point Defects on the Luminescence...A. Uedono, “Major impacts of point defects and impurities on the carrier recombination dynamics in AlN,” Appl. Phys. Lett. 97(20), 201904 (2010

Prediction of novel alloy phases of Al with Sc or Ta

PubMed Central

Bilić, Ante; Gale, Julian D.; Gibson, Mark A.; Wilson, Nick; McGregor, Kathie

2015-01-01

Using the evolutionary optimization algorithm, as implemented in the USPEX crystal predictor program, and first principles total energy calculations, the compositional phase diagrams for Al-Sc and Al-Ta alloy systems at zero temperature and pressure have been calculated. In addition to the known binary intermetallic phases, new potentially stable alloys, AlSc3 and AlTa7, have been identified in the Al-poor region of the phase diagram. The dynamic and thermal stability of their lattices has been confirmed from the calculated vibrational normal mode spectra in the harmonic approximation. PMID:25950915

On Magnetic Dynamos in Thin Accretion Disks around Compact and Young Stars

NASA Technical Reports Server (NTRS)

Stepinski, T. F.

1993-01-01

A variety of geometrically thin accretion disks commonly associated with such astronomical objects as X-ray binaries, cataclysmic variables, and protostars are likely to be seats of MHD dynamo actions. Thin disk geometry and the particular physical environment make accretion disk dynamos different from stellar, planetary, or even galactic dynamos. We discuss those particular features of disk dynamos with emphasis on the difference between protoplanetary disk dynamos and those associated with compact stars. We then describe normal mode solutions for thin disk dynamos and discuss implications for the dynamical behavior of dynamo-magnetized accretion disks.

Motion-mode energy method for vehicle dynamics analysis and control

NASA Astrophysics Data System (ADS)

Zhang, Nong; Wang, Lifu; Du, Haiping

2014-01-01

Vehicle motion and vibration control is a fundamental motivation for the development of advanced vehicle suspension systems. In a vehicle-fixed coordinate system, the relative motions of the vehicle between body and wheel can be classified into several dynamic stages based on energy intensity, and can be decomposed into sets of uncoupled motion-modes according to modal parameters. Vehicle motions are coupled, but motion-modes are orthogonal. By detecting and controlling the predominating vehicle motion-mode, the system cost and energy consumption of active suspensions could be reduced. A motion-mode energy method (MEM) is presented in this paper to quantify the energy contribution of each motion-mode to vehicle dynamics in real time. The control of motion-modes is prioritised according to the level of motion-mode energy. Simulation results on a 10 degree-of-freedom nonlinear full-car model with the magic-formula tyre model illustrate the effectiveness of the proposed MEM. The contribution of each motion-mode to the vehicle's dynamic behaviour is analysed under different excitation inputs from road irregularities, directional manoeuvres and braking. With the identified dominant motion-mode, novel cost-effective suspension systems, such as active reconfigurable hydraulically interconnected suspension, can possibly be used to control full-car motions with reduced energy consumption. Finally, discussion, conclusions and suggestions for future work are provided.

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 that full coupling of normal modes, rather than group coupling, is necessary for accurate predictions of the body tide response.

On-chip optical mode conversion based on dynamic grating in photonic-phononic hybrid waveguide

PubMed Central

Chen, Guodong; Zhang, Ruiwen; Sun, Junqiang

2015-01-01

We present a scheme for reversible and tunable on-chip optical mode conversion based on dynamic grating in a hybrid photonic-phononic waveguide. The dynamic grating is built up through the acousto-optic effect and the theoretical model of the optical mode conversion is developed by considering the geometrical deformation and refractive index change. Three kinds of mode conversions are able to be realized using the same hybrid waveguide structure in a large bandwidth by only changing the launched acoustic frequency. The complete mode conversion can be achieved by choosing a proper acoustic power under a given waveguide length. PMID:25996236

Modal analysis of the thermal conductivity of nanowires: examining unique thermal transport features.

PubMed

Samaraweera, Nalaka; Larkin, Jason M; Chan, Kin L; Mithraratne, Kumar

2018-06-06

In this study, unique thermal transport features of nanowires over bulk materials are investigated using a combined analysis based on lattice dynamics and equilibrium molecular dynamics (EMD). The evaluation of the thermal conductivity (TC) of Lenard-Jones nanowires becomes feasible due to the multi-step normal mode decomposition (NMD) procedure implemented in the study. A convergence issue of the TC of nanowires is addressed by the NMD implementation for two case studies, which employ pristine nanowires (PNW) and superlattice nanowires. Interestingly, mode relaxation times at low frequencies of acoustic branches exhibit signs of approaching constant values, thus indicating the convergence of TC. The TC evaluation procedure is further verified by implementing EMD-based Green-Kubo analysis, which is based on a fundamentally different physical perspective. Having verified the NMD procedure, the non-monotonic trend of the TC of nanowires is addressed. It is shown that the principal cause for the observed trend is due to the competing effects of long wavelength phonons and phonon-surface scatterings as the nanowire's cross-sectional width is changed. A computational procedure is developed to decompose the different modal contribution to the TC of shell alloy nanowires (SANWs) using virtual crystal NMD and the Allen-Feldman theory. Several important conclusions can be drawn from the results. A propagons to non-propagons boundary appeared, resulting in a cut-off frequency (ω cut ); moreover, as alloy atomic mass is increased, ω cut shifts to lower frequencies. The existence of non-propagons partly causes the low TC of SANWs. It can be seen that modes with low frequencies demonstrate a similar behavior to corresponding modes of PNWs. Moreover, lower group velocities associated with higher alloy atomic mass resulted in a lower TC of SANWs.

Modal analysis of the thermal conductivity of nanowires: examining unique thermal transport features

NASA Astrophysics Data System (ADS)

Samaraweera, Nalaka; Larkin, Jason M.; Chan, Kin L.; Mithraratne, Kumar

2018-06-01

In this study, unique thermal transport features of nanowires over bulk materials are investigated using a combined analysis based on lattice dynamics and equilibrium molecular dynamics (EMD). The evaluation of the thermal conductivity (TC) of Lenard–Jones nanowires becomes feasible due to the multi-step normal mode decomposition (NMD) procedure implemented in the study. A convergence issue of the TC of nanowires is addressed by the NMD implementation for two case studies, which employ pristine nanowires (PNW) and superlattice nanowires. Interestingly, mode relaxation times at low frequencies of acoustic branches exhibit signs of approaching constant values, thus indicating the convergence of TC. The TC evaluation procedure is further verified by implementing EMD-based Green–Kubo analysis, which is based on a fundamentally different physical perspective. Having verified the NMD procedure, the non-monotonic trend of the TC of nanowires is addressed. It is shown that the principal cause for the observed trend is due to the competing effects of long wavelength phonons and phonon–surface scatterings as the nanowire’s cross-sectional width is changed. A computational procedure is developed to decompose the different modal contribution to the TC of shell alloy nanowires (SANWs) using virtual crystal NMD and the Allen–Feldman theory. Several important conclusions can be drawn from the results. A propagons to non-propagons boundary appeared, resulting in a cut-off frequency (ω cut); moreover, as alloy atomic mass is increased, ω cut shifts to lower frequencies. The existence of non-propagons partly causes the low TC of SANWs. It can be seen that modes with low frequencies demonstrate a similar behavior to corresponding modes of PNWs. Moreover, lower group velocities associated with higher alloy atomic mass resulted in a lower TC of SANWs.

Flow Mode Dependent Partitioning Processes of Preferential Flow Dynamics in Unsaturated Fractures - Findings From Analogue Percolation Experiments

NASA Astrophysics Data System (ADS)

Kordilla, J.; Noffz, T.; Dentz, M.; Sauter, M.

2017-12-01

To assess the vulnerability of an aquifer system it is of utmost importance to recognize the high potential for a rapid mass transport offered by ow through unsaturated fracture networks. Numerical models have to reproduce complex effects of gravity-driven flow dynamics to generate accurate predictions of flow and transport. However, the non-linear characteristics of free surface flow dynamics and partitioning behaviour at unsaturated fracture intersections often exceed the capacity of classical volume-effective modelling approaches. Laboratory experiments that manage to isolate single aspects of the mass partitioning process can enhance the understanding of underlying dynamics, which ultimately influence travel time distributions on multiple scales. Our analogue fracture network consists of synthetic cubes with dimensions of 20 x 20 x 20 cm creating simple geometries of a single or a cascade of consecutive horizontal fractures. Gravity-driven free surface flow (droplets; rivulets) is established via a high precision multichannel dispenser at flow rates ranging from 1.5 to 4.5 ml/min. Single-inlet experiments show the influence of variable flow rate, atmospheric pressure and temperature on the stability of flow modes and allow to delineate a droplet and rivulet regime. The transition between these regimes exhibits mixed flow characteristics. In addition, multi-inlet setups with constant total infow rates decrease the variance induced by erratic free-surface flow dynamics. We investigate the impacts of variable aperture widths, horizontal offsets of vertical fracture surfaces, and alternating injection methods for both flow regimes. Normalized fracture inflow rates allow to demonstrate and compare the effects of variable geometric features. Firstly, the fracture filling can be described by plug flow. At later stages it transitions into a Washburn-type flow, which we compare to an analytical solution for the case of rivulet flow. Observations show a considerably higher bypass effciency of droplet flow. This behaviour may not be recovered by plug flow but also transitions into a Washburn stage. Furthermore, we study the effect of additional cubes, i.e. increasing amount of horizontal fractures, on the bulk arrival times and associated importance of flow mode dependent partitioning processes.

Interaction vs. observation: distinctive modes of social cognition in human brain and behavior? A combined fMRI and eye-tracking study

PubMed Central

Tylén, Kristian; Allen, Micah; Hunter, Bjørk K.; Roepstorff, Andreas

2012-01-01

Human cognition has usually been approached on the level of individual minds and brains, but social interaction is a challenging case. Is it best thought of as a self-contained individual cognitive process aiming at an “understanding of the other,” or should it rather be approached as an collective, inter-personal process where individual cognitive components interact on a moment-to-moment basis to form coupled dynamics? In a combined fMRI and eye-tracking study we directly contrasted these models of social cognition. We found that the perception of situations affording social contingent responsiveness (e.g., someone offering or showing you an object) elicited activations in regions of the right posterior temporal sulcus and yielded greater pupil dilation corresponding to a model of coupled dynamics (joint action). In contrast, the social-cognitive perception of someone “privately” manipulating an object elicited activation in medial prefrontal cortex, the right inferior frontal gyrus and right inferior parietal lobus, regions normally associated with Theory of Mind and with the mirror neuron system. Our findings support a distinction in social cognition between social observation and social interaction, and demonstrate that simple ostensive cues may shift participants' experience, behavior, and brain activity between these modes. The identification of a distinct, interactive mode has implications for research on social cognition, both in everyday life and in clinical conditions. PMID:23267322

Modal Substructuring of Geometrically Nonlinear Finite Element Models with Interface Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Substructuring methods have been widely used in structural dynamics to divide large, complicated finite element models into smaller substructures. For linear systems, many methods have been developed to reduce the subcomponents down to a low order set of equations using a special set of component modes, and these are then assembled to approximate the dynamics of a large scale model. In this paper, a substructuring approach is developed for coupling geometrically nonlinear structures, where each subcomponent is drastically reduced to a low order set of nonlinear equations using a truncated set of fixedinterface and characteristic constraint modes. The method usedmore » to extract the coefficients of the nonlinear reduced order model (NLROM) is non-intrusive in that it does not require any modification to the commercial FEA code, but computes the NLROM from the results of several nonlinear static analyses. The NLROMs are then assembled to approximate the nonlinear differential equations of the global assembly. The method is demonstrated on the coupling of two geometrically nonlinear plates with simple supports at all edges. The plates are joined at a continuous interface through the rotational degrees-of-freedom (DOF), and the nonlinear normal modes (NNMs) of the assembled equations are computed to validate the models. The proposed substructuring approach reduces a 12,861 DOF nonlinear finite element model down to only 23 DOF, while still accurately reproducing the first three NNMs of the full order model.« less

Modal Substructuring of Geometrically Nonlinear Finite Element Models with Interface Reduction

DOE PAGES

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

2017-03-29

Substructuring methods have been widely used in structural dynamics to divide large, complicated finite element models into smaller substructures. For linear systems, many methods have been developed to reduce the subcomponents down to a low order set of equations using a special set of component modes, and these are then assembled to approximate the dynamics of a large scale model. In this paper, a substructuring approach is developed for coupling geometrically nonlinear structures, where each subcomponent is drastically reduced to a low order set of nonlinear equations using a truncated set of fixedinterface and characteristic constraint modes. The method usedmore » to extract the coefficients of the nonlinear reduced order model (NLROM) is non-intrusive in that it does not require any modification to the commercial FEA code, but computes the NLROM from the results of several nonlinear static analyses. The NLROMs are then assembled to approximate the nonlinear differential equations of the global assembly. The method is demonstrated on the coupling of two geometrically nonlinear plates with simple supports at all edges. The plates are joined at a continuous interface through the rotational degrees-of-freedom (DOF), and the nonlinear normal modes (NNMs) of the assembled equations are computed to validate the models. The proposed substructuring approach reduces a 12,861 DOF nonlinear finite element model down to only 23 DOF, while still accurately reproducing the first three NNMs of the full order model.« less

Fibonacci family of dynamical universality classes.

PubMed

Popkov, Vladislav; Schadschneider, Andreas; Schmidt, Johannes; Schütz, Gunter M

2015-10-13

Universality is a well-established central concept of equilibrium physics. However, in systems far away from equilibrium, a deeper understanding of its underlying principles is still lacking. Up to now, a few classes have been identified. Besides the diffusive universality class with dynamical exponent [Formula: see text], another prominent example is the superdiffusive Kardar-Parisi-Zhang (KPZ) class with [Formula: see text]. It appears, e.g., in low-dimensional dynamical phenomena far from thermal equilibrium that exhibit some conservation law. Here we show that both classes are only part of an infinite discrete family of nonequilibrium universality classes. Remarkably, their dynamical exponents [Formula: see text] are given by ratios of neighboring Fibonacci numbers, starting with either [Formula: see text] (if a KPZ mode exist) or [Formula: see text] (if a diffusive mode is present). If neither a diffusive nor a KPZ mode is present, all dynamical modes have the Golden Mean [Formula: see text] as dynamical exponent. The universal scaling functions of these Fibonacci modes are asymmetric Lévy distributions that are completely fixed by the macroscopic current density relation and compressibility matrix of the system and hence accessible to experimental measurement.

Dynamic Investigation of Static Divergence: Analysis and Testing

NASA Technical Reports Server (NTRS)

Heeg, Jennifer

2000-01-01

The phenomenon known as aeroelastic divergence is the focus of this work. The analyses and experiment presented here show that divergence can occur without a structural dynamic mode losing its oscillatory nature. Aeroelastic divergence occurs when the structural restorative capability or stiffness of a structure is overwhelmed by the static aerodynamic moment. This static aeroelastic coupling does not require the structural dynamic system behavior to cease, however. Aeroelastic changes in the dynamic mode behavior are governed not only by the stiffness, but by damping and inertial properties. The work presented here supports these fundamental assertions by examining a simple system: a typical section airfoil with only a rotational structural degree of freedom. Analytical results identified configurations that exhibit different types of dynamic mode behavior as the system encounters divergence. A wind tunnel model was designed and tested to examine divergence experimentally. The experimental results validate the analytical calculations and explicitly examine the divergence phenomenon where the dynamic mode persists. Three configurations of the wind tunnel model were tested. The experimental results agree very well with the analytical predictions of subcritical characteristics, divergence velocity, and behavior of the noncritical dynamic mode at divergence.

Simulating structure and dynamics in small droplets of 1-ethyl-3-methylimidazolium acetate

NASA Astrophysics Data System (ADS)

Brehm, Martin; Sebastiani, Daniel

2018-05-01

To investigate the structure and dynamics of small ionic liquid droplets in gas phase, we performed a DFT-based ab initio molecular dynamics study of several 1-ethyl-3-methylimidazolium acetate clusters in vacuum as well as a bulk phase simulation. We introduce an unbiased criterion for average droplet diameter and density. By extrapolation of the droplet densities, we predict the experimental bulk phase density with a deviation of only a few percent. The hydrogen bond geometry between cations and anions is very similar in droplets and bulk, but the hydrogen bond dynamics is significantly slower in the droplets, becoming slower with increasing system size, with hydrogen bond lifetimes up to 2000 ps. From a normal mode analysis of the trajectories, we identify the modes of the ring proton C-H stretching, which are strongly affected by hydrogen bonding. From analyzing these, we find that the hydrogen bond becomes weaker with increasing system size. The cations possess an increased concentration inside the clusters, whereas the anions show an excess concentration on the outside. Almost all anions point towards the droplet center with their carboxylic groups. Ring stacking is found to be a very important structural motif in the droplets (as in the bulk), but side chain interactions are only of minor importance. By using Voronoi tessellation, we define the exposed droplet surface and find that it consists mainly of hydrogen atoms from the cation's and anion's methyl and ethyl groups. Polar atoms are rarely found on the surface, such that the droplets appear completely hydrophobic on the outside.

Phonons on fcc (100), (110), and (111) surfaces using Lennard-Jones potentials. II. Temperature dependence of surface phonons studied with molecular dynamics

NASA Astrophysics Data System (ADS)

Koleske, D. D.; Sibener, S. J.

In this paper we present temperature dependent studies of the surface phonon dispersion relations for fcc (100), (110), and (111) faces using molecular dynamics (MD) simulations and Lennard-Jones potentials. This study was conducted in order to investigate how anharmonic potential terms influence the dynamical properties of the surface. This was accomplished by examining the temperature dependence of the Q-resolved phonon spectral density function. All phonon frequencies were found to decrease linearly in T as the temperature was increased, while at low temperatures the phonon linewidths increased linearly with T. At higher temperatures, some of the phonon linewidths changed from having a linear to a quadratic dependence on T. The temperature at which this T to T2 change occurs is surface dependent and occurs at the lowest temperature on the (110) surface. The T2 dependence arises from the increasing importance of higher-order phonon-phonon scattering terms. The phonons which exhibit T2 dependence tend to be modes which propagate perpendicularly or nearly perpendicularly to the direction of maximum root-mean-squared displacement (RMSD). This is especially true for the linewidth of the S 1 mode at overlineX on the (110) surface where, at T ≈ 15-23% of the melting temperature, the RMSD perpendicular to the atomic rows become larger than the RMSD normal to the surface. Our results indicate that the dynamics on the (110) surface may be significantly influenced by anharmonic potential terms at temperatures as low as 15% of the melting temperature.

Recovering Intrinsic Fragmental Vibrations Using the Generalized Subsystem Vibrational Analysis.

PubMed

Tao, Yunwen; Tian, Chuan; Verma, Niraj; Zou, Wenli; Wang, Chao; Cremer, Dieter; Kraka, Elfi

2018-05-08

Normal vibrational modes are generally delocalized over the molecular system, which makes it difficult to assign certain vibrations to specific fragments or functional groups. We introduce a new approach, the Generalized Subsystem Vibrational Analysis (GSVA), to extract the intrinsic fragmental vibrations of any fragment/subsystem from the whole system via the evaluation of the corresponding effective Hessian matrix. The retention of the curvature information with regard to the potential energy surface for the effective Hessian matrix endows our approach with a concrete physical basis and enables the normal vibrational modes of different molecular systems to be legitimately comparable. Furthermore, the intrinsic fragmental vibrations act as a new link between the Konkoli-Cremer local vibrational modes and the normal vibrational modes.

Nonlinear normal modes in electrodynamic systems: A nonperturbative approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kudrin, A. V., E-mail: kud@rf.unn.ru; Kudrina, O. A.; Petrov, E. Yu.

2016-06-15

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 tomore » hold only for linear oscillations and fields, can also be observed in a nonlinear oscillatory system.« less

Influence of Mixed Mode I-Mode II Loading on Fatigue Delamination Growth Characteristics of a Graphite Epoxy Tape Laminate

NASA Technical Reports Server (NTRS)

Ratcliffe, James G.; Johnston, William M., Jr.

2014-01-01

Mixed mode I-mode II interlaminar tests were conducted on IM7/8552 tape laminates using the mixed-mode bending test. Three mixed mode ratios, G(sub II)/G(sub T) = 0.2, 0.5, and 0.8, were considered. Tests were performed at all three mixed-mode ratios under quasi-static and cyclic loading conditions, where the former static tests were used to determine initial loading levels for the latter fatigue tests. Fatigue tests at each mixed-mode ratio were performed at four loading levels, Gmax, equal to 0.5G(sub c), 0.4G(sub c), 0.3G(sub c), and 0.2G(sub c), where G(sub c) is the interlaminar fracture toughness of the corresponding mixed-mode ratio at which a test was performed. All fatigue tests were performed using constant-amplitude load control and delamination growth was automatically documented using compliance solutions obtained from the corresponding quasi-static tests. Static fracture toughness data yielded a mixed-mode delamination criterion that exhibited monotonic increase in Gc with mixed-mode ratio, G(sub II)/G(sub T). Fatigue delamination onset parameters varied monotonically with G(sub II)/G(sub T), which was expected based on the fracture toughness data. Analysis of non-normalized data yielded a monotonic change in Paris law exponent with mode ratio. This was not the case when normalized data were analyzed. Fatigue data normalized by the static R-curve were most affected in specimens tested at G(sub II)/G(sub T)=0.2 (this process has little influence on the other data). In this case, the normalized data yielded a higher delamination growth rate compared to the raw data for a given loading level. Overall, fiber bridging appeared to be the dominant mechanism, affecting delamination growth rates in specimens tested at different load levels and differing mixed-mode ratios.

Quantum dynamics of Kerr optical frequency combs below and above threshold: Spontaneous four-wave mixing, entanglement, and squeezed states of light

NASA Astrophysics Data System (ADS)

Chembo, Yanne K.

2016-03-01

The dynamical behavior of Kerr optical frequency combs is very well understood today from the perspective of the semiclassical approximation. These combs are obtained by pumping an ultrahigh-Q whispering-gallery mode resonator with a continuous-wave laser. The long-lifetime photons are trapped within the toruslike eigenmodes of the resonator, where they interact nonlinearly via the Kerr effect. In this article, we use quantum Langevin equations to provide a theoretical understanding of the nonclassical behavior of these combs when pumped below and above threshold. In the configuration where the system is under threshold, the pump field is the unique oscillating mode inside the resonator, and it triggers the phenomenon of spontaneous four-wave mixing, where two photons from the pump are symmetrically up- and down-converted in the Fourier domain. This phenomenon, also referred to as parametric fluorescence, can only be understood and analyzed from a fully quantum perspective as a consequence of the coupling between the field of the central (pumped) mode and the vacuum fluctuations of the various side modes. We analytically calculate the power spectra of the spontaneous emission noise, and we show that these spectra can be either single- or double-peaked depending on the value of the laser frequency, chromatic dispersion, pump power, and spectral distance between the central mode and the side mode of interest. We also calculate as well the overall spontaneous noise power per side mode and propose simplified analytical expressions for some particular cases. In the configuration where the system is pumped above threshold, we investigate the phenomena of quantum correlations and multimode squeezed states of light that can occur in the Kerr frequency combs originating from stimulated four-wave mixing. We show that for all stationary spatiotemporal patterns, the side modes that are symmetrical relative to the pumped mode in the frequency domain display quantum correlations that can lead to squeezed states of light under some optimal conditions that are analytically determined. These quantum correlations can persist regardless the dynamical state of the system (rolls or solitons), regardless of the spectral extension of the comb (number side modes) and regardless of the dispersion regime (normal or anomalous). We also explicitly determine the phase quadratures leading to photon entanglement and analytically calculate their quantum-noise spectra. For both the below- and above-threshold cases, we study with particular emphasis the two principal architectures for Kerr comb generation, namely the add-through and add-drop configurations. It is found that regardless of the configuration, an essential parameter is the ratio between out-coupling and total losses, which plays a key role as it directly determines the efficiency of the detected fluorescence or squeezing spectra. We finally discuss the relevance of Kerr combs for quantum information systems at optical telecommunication wavelengths below and above threshold.

Dynamic model updating based on strain mode shape and natural frequency using hybrid pattern search technique

NASA Astrophysics Data System (ADS)

Guo, Ning; Yang, Zhichun; Wang, Le; Ouyang, Yan; Zhang, Xinping

2018-05-01

Aiming at providing a precise dynamic structural finite element (FE) model for dynamic strength evaluation in addition to dynamic analysis. A dynamic FE model updating method is presented to correct the uncertain parameters of the FE model of a structure using strain mode shapes and natural frequencies. The strain mode shape, which is sensitive to local changes in structure, is used instead of the displacement mode for enhancing model updating. The coordinate strain modal assurance criterion is developed to evaluate the correlation level at each coordinate over the experimental and the analytical strain mode shapes. Moreover, the natural frequencies which provide the global information of the structure are used to guarantee the accuracy of modal properties of the global model. Then, the weighted summation of the natural frequency residual and the coordinate strain modal assurance criterion residual is used as the objective function in the proposed dynamic FE model updating procedure. The hybrid genetic/pattern-search optimization algorithm is adopted to perform the dynamic FE model updating procedure. Numerical simulation and model updating experiment for a clamped-clamped beam are performed to validate the feasibility and effectiveness of the present method. The results show that the proposed method can be used to update the uncertain parameters with good robustness. And the updated dynamic FE model of the beam structure, which can correctly predict both the natural frequencies and the local dynamic strains, is reliable for the following dynamic analysis and dynamic strength evaluation.

Zonal Acoustic Velocimetry in 30-cm, 60-cm, and 3-m Laboratory Models of the Outer Core

NASA Astrophysics Data System (ADS)

Rojas, R.; Doan, M. N.; Adams, M. M.; Mautino, A. R.; Stone, D.; Lekic, V.; Lathrop, D. P.

2016-12-01

A knowledge of zonal flows and shear is key in understanding magnetic field dynamics in the Earth and laboratory experiments with Earth-like geometries. Traditional techniques for measuring fluid flow using visualization and particle tracking are not well-suited to liquid metal flows. This has led us to develop a flow measurement technique based on acoustic mode velocimetry adapted from helioseismology. As a first step prior to measurements in the liquid sodium experiments, we implement this technique in our 60-cm diameter spherical Couette experiment in air. To account for a more realistic experimental geometry, including deviations from spherical symmetry, we compute predicted frequencies of acoustic normal modes using the finite element method. The higher accuracy of the predicted frequencies allows the identification of over a dozen acoustic modes, and mode identification is further aided by the use of multiple microphones and by analyzing spectra together with those obtained at a variety of nearby Rossby numbers. Differences between the predicted and observed mode frequencies are caused by differences in flow patterns present in the experiment. We compare acoustic mode frequency splittings with theoretical predictions for stationary fluid and solid body flow condition with excellent agreement. We also use this technique to estimate the zonal shear in those experiments across a range of Rossby numbers. Finally, we report on initial attempts to use this in liquid sodium in the 3-meter diameter experiment and parallel experiments performed in water in the 30-cm diameter experiment.

A femtosecond Yb-doped fiber laser with generalized vector vortex beams output (Conference Presentation)

NASA Astrophysics Data System (ADS)

Huo, Tiancheng; Qi, Li; Zhang, Buyun; Chen, Zhongping

2017-03-01

Light carries both spin and orbital angular momentum (OAM) and the superpositions of these two dynamical properties have found many applications. Many techniques exist to create such light sources but none allow their creation at the femtosecond fiber laser. Here we report on a novel mode-locked Ytterbium-doped fiber laser that generates femtosecond pulses with generalized vector vortex states. The controlled generation of such pulses such as azimuthally and radially polarized light with definite orbital angular momentum modes are demonstrated. A unidirectional ring cavity constructed with the Yb-doped fiber placed at the end of the fiber section to reduces unnecessary nonlinear effects is employed for self-starting operation. Pairs of diffraction gratings are used for compensating the normal group velocity dispersion of the fiber and other elements. Mode-locked operation is achieved based on nonlinear polarization evolution, which is mainly implemented with the single mode fiber, the bulk wave plates and the variable spiral plates (q-plate with topological charge q=0.5). The conversion from spin angular momentum to the OAM and reverse inside the laser cavity are realized by means of a quarter-wave plate and a q-plate so that the polarization control was mapped to OAM mode control. The fiber laser is diode pumped by a wavelength-division multiplexing coupler, which leads to excellent stability and portability.

Galileo radio science investigations

NASA Technical Reports Server (NTRS)

Howard, H. T.; Eshleman, V. R.; Hinson, D. P.; Kliore, A. J.; Lindal, G. F.; Woo, R.; Bird, M. K.; Volland, H.; Edenhoffer, P.; Paetzold, M.

1992-01-01

Galileo radio-propagation experiments are based on measurements of absolute and differential propagation time delay, differential phase delay, Doppler shift, signal strength, and polarization. These measurements can be used to study: the atmospheric and ionospheric structure, constituents, and dynamics of Jupiter; the magnetic field of Jupiter; the diameter of Io, its ionospheric structure, and the distribution of plasma in the Io torus; the diameters of the other Galilean satellites, certain properties of their surfaces, and possibly their atmospheres and ionospheres; and the plasma dynamics and magnetic field of the solar corona. The spacecraft system provides linear rather than circular polarization on the S-band downlink signal, the capability to receive X-band uplink signals, and a differential downlink ranging mode. A highly-stable, dual-frequency, spacecraft radio system is developed that is suitable for simultaneous measurements of all the parameters normally attributed to radio waves.

A real-time guidance algorithm for aerospace plane optimal ascent to low earth orbit

NASA Technical Reports Server (NTRS)

Calise, A. J.; Flandro, G. A.; Corban, J. E.

1989-01-01

Problems of onboard trajectory optimization and synthesis of suitable guidance laws for ascent to low Earth orbit of an air-breathing, single-stage-to-orbit vehicle are addressed. A multimode propulsion system is assumed which incorporates turbojet, ramjet, Scramjet, and rocket engines. An algorithm for generating fuel-optimal climb profiles is presented. This algorithm results from the application of the minimum principle to a low-order dynamic model that includes angle-of-attack effects and the normal component of thrust. Maximum dynamic pressure and maximum aerodynamic heating rate constraints are considered. Switching conditions are derived which, under appropriate assumptions, govern optimal transition from one propulsion mode to another. A nonlinear transformation technique is employed to derived a feedback controller for tracking the computed trajectory. Numerical results illustrate the nature of the resulting fuel-optimal climb paths.

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

Polaritonic Rabi and Josephson Oscillations

PubMed Central

Rahmani, Amir; Laussy, Fabrice P.

2016-01-01

The dynamics of coupled condensates is a wide-encompassing problem with relevance to superconductors, BECs in traps, superfluids, etc. Here, we provide a unified picture of this fundamental problem that includes i) detuning of the free energies, ii) different self-interaction strengths and iii) finite lifetime of the modes. At such, this is particularly relevant for the dynamics of polaritons, both for their internal dynamics between their light and matter constituents, as well as for the more conventional dynamics of two spatially separated condensates. Polaritons are short-lived, interact only through their material fraction and are easily detuned. At such, they bring several variations to their atomic counterpart. We show that the combination of these parameters results in important twists to the phenomenology of the Josephson effect, such as the behaviour of the relative phase (running or oscillating) or the occurence of self-trapping. We undertake a comprehensive stability analysis of the fixed points on a normalized Bloch sphere, that allows us to provide a generalized criterion to identify the Rabi and Josephson regimes in presence of detuning and decay. PMID:27452872

Rupture dynamics along bimaterial interfaces: a parametric study of the coupling between interfacial sliding and normal traction perturbation

NASA Astrophysics Data System (ADS)

Scala, Antonio; Festa, Gaetano; Vilotte, Jean-Pierre

2017-04-01

Earthquake ruptures often develop along faults separating materials with dissimilar elastic properties. Due to the broken symmetry, the propagation of the rupture along the bimaterial interface is driven by the coupling between interfacial sliding and normal traction perturbations. We numerically investigate in-plane rupture growth along a planar interface, under slip weakening friction, separating two dissimilar isotropic linearly elastic half-spaces. We perform a parametric study of the classical Prakash-Clifton regularisation for different material contrasts. In particular mesh-dependence and regularisation-dependence of the numerical solutions are analysed in this parameter space. When regularisation involves a slip-rate dependent relaxation time, a characteristic sliding distance is identified below which numerical solutions no longer depend on the regularisation parameter, i.e. they are consistent solutions of the same physical problem. Such regularisation provides an adaptive high-frequency filter of the slip-induced normal traction perturbations, following the dynamic shrinking of the dissipation zone during the acceleration phase. In contrast, regularisation involving a constant relaxation time leads to numerical solutions that always depend on the regularisation parameter since it fails adapting to the shrinking of the process zone. Dynamic regularisation is further investigated using a non-local regularisation based on a relaxation time that depends on the dynamic length of the dissipation zone. Such reformulation is shown to provide similar results as the dynamic time scale regularisation proposed by Prakash-Clifton when slip rate is replaced by the maximum slip rate along the sliding interface. This leads to the identification of a dissipative length scale associated with the coupling between interfacial sliding and normal traction perturbations, together with a scaling law between the maximum slip rate and the dynamic size of the process zone during the rupture propagation. Dynamic time scale regularisation is show to provide mesh-independent and physically well-posed numerical solutions during the acceleration phase toward an asymptotic speed. When generalised Rayleigh wave does not exist, numerical solutions are shown to tend toward an asymptotic velocity higher than the slowest shear wave speed. When generalised Rayleigh wave speed exists, as numerical solutions tend toward this velocity, increasing spurious oscillations develop and solutions become unstable. In this regime regularisation dependent and unstable finite-size pulses may be generated. This instability is associated with the singular behaviour of the slip-induced normal traction perturbations, and of the slip rate at the rupture front, in relation with complete shrinking of the dissipation zone. This phase requires to be modelled either by more complex interface constitutive laws involving velocity-strengthening effects that may stabilize short wavelength interfacial propagating modes or by considering non-ideal interfaces that introduce a new length scale in the problem that may promote selection and stabilization of the slip pulses.

Rotational diffusion of a molecular cat

NASA Astrophysics Data System (ADS)

Katz-Saporta, Ori; Efrati, Efi

We show that a simple isolated system can perform rotational random walk on account of internal excitations alone. We consider the classical dynamics of a ''molecular cat'': a triatomic molecule connected by three harmonic springs with non-zero rest lengths, suspended in free space. In this system, much like for falling cats, the angular momentum constraint is non-holonomic allowing for rotations with zero overall angular momentum. The geometric nonlinearities arising from the non-zero rest lengths of the springs suffice to break integrability and lead to chaotic dynamics. The coupling of the non-integrability of the system and its non-holonomic nature results in an angular random walk of the molecule. We study the properties and dynamics of this angular motion analytically and numerically. For low energy excitations the system displays normal-mode-like motion, while for high enough excitation energy we observe regular random-walk. In between, at intermediate energies we observe an angular Lévy-walk type motion associated with a fractional diffusion coefficient interpolating between the two regimes.

Buckling of circular cylindrical shells under dynamically applied axial loads

NASA Technical Reports Server (NTRS)

Tulk, J. D.

1972-01-01

A theoretical and experimental study was made of the buckling characteristics of perfect and imperfect circular cylindrical shells subjected to dynamic axial loading. Experimental data included dynamic buckling loads (124 data points), high speed photographs of buckling mode shapes and observations of the dynamic stability of shells subjected to rapidly applied sub-critical loads. A mathematical model was developed to describe the dynamic behavior of perfect and imperfect shells. This model was based on the Donnell-Von Karman compatibility and equilibrium equations and had a wall deflection function incorporating five separate modes of deflection. Close agreement between theory and experiment was found for both dynamic buckling strength and buckling mode shapes.

Normal Modes of a Lagrangian System Constrained in a Potential Well.

DTIC Science & Technology

1983-12-01

A’ -137 948 NORMAL MODES OF A LFHbRANGIAN SYSTEM CONSTRAINED INvi P0TENTIAL WELL(U WISCONSNN UNIV-MADISON MATHEMATICS RESEARCH CENTER V EN DEC F1...Carolina 27709 DT FLE OP Y UNIVERSITY OF WISCONSIN-MADISON MATHEMATICS RESEARCH CENTER NORMAL MODES OF A LAGRANGIAN SYSTEM CONSTRAINED IN A POTENTIAL WELL...respect to the norm lYE [f i + 2 yi )dtl/ 0 Since H I(S’ 1 n’) C CO(S, fle ), then the set A 1 0 is an open set in H1 (lf’) The periodic solution of

Experimental investigation of internal tides generated by finite-height topography

NASA Astrophysics Data System (ADS)

Wang, Shuya; Chen, Xu; Wang, Jinhu; Meng, Jing

2018-06-01

Internal tides generated by finite-height topography are investigated in the laboratory, and the particle image velocimetry (PIV) technique is applied to measure the velocity fields. The energy, energy flux, and vertical mode structure of the internal tides are calculated and analyzed. The experimental results indicate that the strength of the wave field is mainly affected by the normalized topography height. The rays radiated from the taller topography are wider than those radiated from the lower topography. Both the experimental and theoretical results indicate that the normalized energy and energy flux of the internal tides are mainly determined by the normalized topography height, and the increase of the two quantities follows a quadratic function, and they almost remain unchanged with different normalized frequencies except for higher frequency. The percentage of energy for mode-1 and mode-2 internal tides is determined not only by frequency but also by topography height. In addition, an "inherent normalized frequency" is observed in the experiment, at which the percentage of energy for mode 1 and mode 2 does not vary with topography height. The decay rate of internal tide energy in the near field and far field is also estimated, with average values of 36.5 and 7.5%, respectively.

Theory of psychological adaptive modes.

PubMed

Lehti, Juha

2016-05-01

When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of low velocity impact damage on the natural frequency of composite plates

NASA Astrophysics Data System (ADS)

Chok, E. Y. L.; Majid, D. L. A. A.; Harmin, M. Y.

2017-12-01

Biodegradable natural fibers have been suggested to replace the hazardous synthetic fibers in many aerospace applications. However, this notion has been limited due to their low mechanical properties, which leads to the idea of hybridizing the two materials. Many aircraft components such as radome, aft body and wing are highly susceptible to low velocity impact damage while in-service. The damages degrade the structural integrity of the components and change their dynamic characteristics. In worst case scenario, the changes can lead to resonance, which is an excessive vibration. This research is conducted to study the dynamic characteristic changes of low velocity impact damaged hybrid composites that is designed for aircraft radome applications. Three materials, which are glass fiber, kenaf fiber and kenaf/glass fiber hybrid composites, have been impacted with 3J, 6J and 9J of energy. Cantilevered and also vertically clamped boundary conditions are used and the natural frequencies are extracted for each of the specimens. The obtained results show that natural frequency decreases with increasing impact level. Cantilevered condition is found to induce lower modes due to the gravitational pull. To eliminate mass and geometrical effects, normalized modes are computed. Among the three materials considered, glass fiber composites have displayed the highest normalized frequency that reflects on its higher stiffness compared to the other two materials. As the damage level is increased, glass fiber composites have shown the highest frequency reduction to a maximum of 35% while kenaf composites have the least frequency reduction in the range of 1 - 18%. Thus, kenaf fiber is taken to be helpful in stalling the damage progression and reducing the effect of damage. This has been proven when the percentage frequency decrement shown by kenaf/glass fiber composite lies between glass fiber and kenaf fiber composites.

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

PubMed

Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

2014-01-09

Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.

Surface-wave potential for triggering tectonic (nonvolcanic) tremor

USGS Publications Warehouse

Hill, D.P.

2010-01-01

Source processes commonly posed to explain instances of remote dynamic triggering of tectonic (nonvolcanic) tremor by surface waves include frictional failure and various modes of fluid activation. The relative potential for Love- and Rayleigh-wave dynamic stresses to trigger tectonic tremor through failure on critically stressed thrust and vertical strike-slip faults under the Coulomb-Griffith failure criteria as a function of incidence angle is anticorrelated over the 15- to 30-km-depth range that hosts tectonic tremor. Love-wave potential is high for strike-parallel incidence on low-angle reverse faults and null for strike-normal incidence; the opposite holds for Rayleigh waves. Love-wave potential is high for both strike-parallel and strike-normal incidence on vertical, strike-slip faults and minimal for ~45?? incidence angles. The opposite holds for Rayleigh waves. This pattern is consistent with documented instances of tremor triggered by Love waves incident on the Cascadia mega-thrust and the San Andreas fault (SAF) in central California resulting from shear failure on weak faults (apparent friction, ????? 0.2). However, documented instances of tremor triggered by surface waves with strike-parallel incidence along the Nankai megathrust beneath Shikoku, Japan, is associated primarily with Rayleigh waves. This is consistent with the tremor bursts resulting from mixed-mode failure (crack opening and shear failure) facilitated by near-lithostatic ambient pore pressure, low differential stress, with a moderate friction coefficient (?? ~ 0.6) on the Nankai subduction interface. Rayleigh-wave dilatational stress is relatively weak at tectonic tremor source depths and seems unlikely to contribute significantly to the triggering process, except perhaps for an indirect role on the SAF in sustaining tremor into the Rayleigh-wave coda that was initially triggered by Love waves.

Surface-wave potential for triggering tectonic (nonvolcanic) tremor-corrected

USGS Publications Warehouse

Hill, David P.

2012-01-01

Source processes commonly posed to explain instances of remote dynamic triggering of tectonic (nonvolcanic) tremor by surface waves include frictional failure and various modes of fluid activation. The relative potential for Love- and Rayleigh-wave dynamic stresses to trigger tectonic tremor through failure on critically stressed thrust and vertical strike-slip faults under the Coulomb-Griffith failure criteria as a function of incidence angle are anticorrelated over the 15- to 30-km-depth range that hosts tectonic tremor. Love-wave potential is high for strike-parallel incidence on low-angle reverse faults and null for strike-normal incidence; the opposite holds for Rayleigh waves. Love-wave potential is high for both strike-parallel and strike-normal incidence on vertical, strike-slip faults and minimal for ~45° incidence angles. The opposite holds for Rayleigh waves. This pattern is consistent with documented instances of tremor triggered by Love waves incident on the Cascadia megathrust and the San Andreas fault (SAF) in central California resulting from shear failure on weak faults (apparent friction is μ* ≤ 0:2). Documented instances of tremor triggered by surface waves with strike-parallel incidence along the Nankai megathrust beneath Shikoku, Japan, however, are associated primarily with Rayleigh waves. This is consistent with the tremor bursts resulting from mixed-mode failure (crack opening and shear failure) facilitated by near-lithostatic ambient pore pressure, low differential stress, with a moderate friction coefficient (μ ~ 0:6) on the Nankai subduction interface. Rayleigh-wave dilatational stress is relatively weak at tectonic tremor source depths and seems unlikely to contribute significantly to the triggering process, except perhaps for an indirect role on the SAF in sustaining tremor into the Rayleigh-wave coda that was initially triggered by Love waves.

Derivation of equations of motion for multi-blade rotors employing coupled modes and including high twist capability

NASA Technical Reports Server (NTRS)

Sopher, R.

1975-01-01

The equations of motion are derived for a multiblade rotor. A high twist capability and coupled flatwise-edgewise assumed normal modes are employed instead of uncoupled flatwise - edgewise assumed normal models. The torsion mode is uncoupled. Support system models, consisting of complete helicopters in free flight, or grounded flexible supports, arbitrary rotor-induced inflow, and arbitrary vertical gust models are also used.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanz, Alejandro; Ezquerra, Tiberio A.; Nogales, Aurora, E-mail: aurora.nogales@csic.es

The dynamics of lower disorder-order temperature diblock copolymer leading to phase separation has been observed by X ray photon correlation spectroscopy. Two different modes have been characterized. A non-diffusive mode appears at temperatures below the disorder to order transition, which can be associated to compositional fluctuations, that becomes slower as the interaction parameter increases, in a similar way to the one observed for diblock copolymers exhibiting phase separation upon cooling. At temperatures above the disorder to order transition T{sub ODT}, the dynamics becomes diffusive, indicating that after phase separation in Lower Disorder-Order Transition (LDOT) diblock copolymers, the diffusion of chainmore » segments across the interface is the governing dynamics. As the segregation is stronger, the diffusive process becomes slower. Both observed modes have been predicted by the theory describing upper order-disorder transition systems, assuming incompressibility. However, the present results indicate that the existence of these two modes is more universal as they are present also in compressible diblock copolymers exhibiting a lower disorder-order transition. No such a theory describing the dynamics in LDOT block copolymers is available, and these experimental results may offer some hints to understanding the dynamics in these systems. The dynamics has also been studied in the ordered state, and for the present system, the non-diffusive mode disappears and only a diffusive mode is observed. This mode is related to the transport of segment in the interphase, due to the weak segregation on this system.« less

Thermal transport dynamics in the quasi-single helicity state

NASA Astrophysics Data System (ADS)

McKinney, I. J.; Terry, P. W.

2017-06-01

A dynamical model describing oscillations between multiple and single helicity configurations in the quasi-single helicity (QSH) state of the reversed field pinch [P. W. Terry and G. G. Whelan, Plasma Phys. Controlled Fusion 56, 094003 (2014)] is extended to include electron temperature profile dynamics. It is shown that QSH dynamics is linked to the electron temperature profile because the suppression of mode coupling between tearing modes proposed to underlie QSH also suppresses magnetic-fluctuation-induced thermal transport. Above the threshold of dominant-mode shear that marks the transition to QSH, the model produces temperature-gradient steepening in the strong shear region. Oscillations of the dominant and secondary mode amplitudes give rise to oscillations of the temperature gradient. The phasing and amplitude of temperature gradient oscillations relative to those of the dominant mode are in agreement with experiment. This provides further evidence that the model, while heuristic, captures key physical aspects of the QSH state.

On the Use of Material-Dependent Damping in ANSYS for Mode Superposition Transient Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nie, J.; Wei, X.

The mode superposition method is often used for dynamic analysis of complex structures, such as the seismic Category I structures in nuclear power plants, in place of the less efficient full method, which uses the full system matrices for calculation of the transient responses. In such applications, specification of material-dependent damping is usually desirable because complex structures can consist of multiple types of materials that may have different energy dissipation capabilities. A recent review of the ANSYS manual for several releases found that the use of material-dependent damping is not clearly explained for performing a mode superposition transient dynamic analysis.more » This paper includes several mode superposition transient dynamic analyses using different ways to specify damping in ANSYS, in order to determine how material-dependent damping can be specified conveniently in a mode superposition transient dynamic analysis.« less

Active Polar Two-Fluid Macroscopic Dynamics

NASA Astrophysics Data System (ADS)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

Dynamic Response and Failure Mechanism of Brittle Rocks Under Combined Compression-Shear Loading Experiments

NASA Astrophysics Data System (ADS)

Xu, Yuan; Dai, Feng

2018-03-01

A novel method is developed for characterizing the mechanical response and failure mechanism of brittle rocks under dynamic compression-shear loading: an inclined cylinder specimen using a modified split Hopkinson pressure bar (SHPB) system. With the specimen axis inclining to the loading direction of SHPB, a shear component can be introduced into the specimen. Both static and dynamic experiments are conducted on sandstone specimens. Given carefully pulse shaping, the dynamic equilibrium of the inclined specimens can be satisfied, and thus the quasi-static data reduction is employed. The normal and shear stress-strain relationships of specimens are subsequently established. The progressive failure process of the specimen illustrated via high-speed photographs manifests a mixed failure mode accommodating both the shear-dominated failure and the localized tensile damage. The elastic and shear moduli exhibit certain loading-path dependence under quasi-static loading but loading-path insensitivity under high loading rates. Loading rate dependence is evidently demonstrated through the failure characteristics involving fragmentation, compression and shear strength and failure surfaces based on Drucker-Prager criterion. Our proposed method is convenient and reliable to study the dynamic response and failure mechanism of rocks under combined compression-shear loading.

Plasma Modes

NASA Astrophysics Data System (ADS)

Dubin, D. H. E.

This chapter explores several aspects of the linear electrostatic normal modes of oscillation for a single-species non-neutral plasma in a Penning trap. Linearized fluid equations of motion are developed, assuming the plasma is cold but collisionless, which allow derivation of the cold plasma dielectric tensor and the electrostatic wave equation. Upper hybrid and magnetized plasma waves in an infinite uniform plasma are described. The effect of the plasma surface in a bounded plasma system is considered, and the properties of surface plasma waves are characterized. The normal modes of a cylindrical plasma column are discussed, and finally, modes of spheroidal plasmas, and finite temperature effects on the modes, are briefly described.

Inflow/Outflow Conditions for Unsteady Aerodynamics and Aeroacoustics in Nonuniform Flow

NASA Technical Reports Server (NTRS)

Atassi, Oliver V.; Grady, Joseph E. (Technical Monitor)

2003-01-01

The effect of a nonuniform mean flow on the normal modes; the inflow/outflow nonreflecting boundary conditions; and the sound power are studied. The normal modes in an annular duct are computed using a spectral method in combination with a shooting method. The swirl causes force imbalance which couples the acoustic and vortical modes. The acoustic modes are distinguished from the vortical modes by their large pressure and small vorticity content. The mean swirl also produces a Doppler shift in frequency. This results in more counter-spinning modes cut-on at a given frequency than modes spinning with the swirl. Nonreflecting boundary conditions are formulated using the normal mode solutions. The inflow/outflow boundary conditions are implemented in a linearized Euler scheme and validated by computing the propagation of acoustic and vortical waves in a duct for a variety of swirling mean flows. Numerical results show that the evolution of the vortical disturbances is sensitive to the inflow conditions and the details of the wake excitations. All three components of the wake velocity must be considered to correctly compute the wake evolution and the blade upwash. For high frequencies, the acoustic-vortical mode coupling is weak and a conservation equation for the acoustic energy can be derived. Sound power calculations show significant mean flow swirl effects, but mode interference effects are small.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Statistical mechanics of monatomic liquids

NASA Astrophysics Data System (ADS)

Wallace, Duane C.

1997-10-01

Two key experimental properties of elemental liquids, together with an analysis of the condensed-system potential-energy surface, lead us logically to the dynamical theory of monatomic liquids. Experimentally, the ion motional specific heat is approximately 3Nk for N ions, implying the normal modes of motion are approximately 3N independent harmonic oscillators. This implies the potential surface contains nearly harmonic valleys. The equilibrium configuration at the bottom of each valley is a ``structure.'' Structures are crystalline or amorphous, and amorphous structures can have a remnant of local crystal symmetry, or can be random. The random structures are by far the most numerous, and hence dominate the statistical mechanics of the liquid state, and their macroscopic properties are uniform over the structure class, for large-N systems. The Hamiltonian for any structural valley is the static structure potential, a sum of harmonic normal modes, and an anharmonic correction. Again from experiment, the constant-density entropy of melting contains a universal disordering contribution of NkΔ, suggesting the random structural valleys are of universal number wN, where lnw=Δ. Our experimental estimate for Δ is 0.80. In quasiharmonic approximation, the liquid theory for entropy agrees with experiment, for all currently analyzable experimental data at elevated temperatures, to within 1-2% of the total entropy. Further testable predictions of the theory are mentioned.

Conformational Analysis of Stiff Chiral Polymers with End-Constraints

PubMed Central

Kim, Jin Seob; Chirikjian, Gregory S.

2010-01-01

We present a Lie-group-theoretic method for the kinematic and dynamic analysis of chiral semi-flexible polymers with end constraints. The first is to determine the minimum energy conformations of semi-flexible polymers with end constraints, and the second is to perform normal mode analysis based on the determined minimum energy conformations. In this paper, we use concepts from the theory of Lie groups and principles of variational calculus to model such polymers as inextensible or extensible chiral elastic rods with coupling between twisting and bending stiffnesses, and/or between twisting and extension stiffnesses. This method is general enough to include any stiffness and chirality parameters in the context of elastic filament models with the quadratic elastic potential energy function. As an application of this formulation, the analysis of DNA conformations is discussed. We demonstrate our method with examples of DNA conformations in which topological properties such as writhe, twist, and linking number are calculated from the results of the proposed method. Given these minimum energy conformations, we describe how to perform the normal mode analysis. The results presented here build both on recent experimental work in which DNA mechanical properties have been measured, and theoretical work in which the mechanics of non-chiral elastic rods has been studied. PMID:20198114

Sad and happy emotion discrimination in music by children with cochlear implants.

PubMed

Hopyan, Talar; Manno, Francis A M; Papsin, Blake C; Gordon, Karen A

2016-01-01

Children using cochlear implants (CIs) develop speech perception but have difficulty perceiving complex acoustic signals. Mode and tempo are the two components used to recognize emotion in music. Based on CI limitations, we hypothesized children using CIs would have impaired perception of mode cues relative to their normal hearing peers and would rely more heavily on tempo cues to distinguish happy from sad music. Study participants were children with 13 right CIs and 3 left CIs (M = 12.7, SD = 2.6 years) and 16 normal hearing peers. Participants judged 96 brief piano excerpts from the classical genre as happy or sad in a forced-choice task. Music was randomly presented with alterations of transposed mode, tempo, or both. When music was presented in original form, children using CIs discriminated between happy and sad music with accuracy well above chance levels (87.5%) but significantly below those with normal hearing (98%). The CI group primarily used tempo cues, whereas normal hearing children relied more on mode cues. Transposing both mode and tempo cues in the same musical excerpt obliterated cues to emotion for both groups. Children using CIs showed significantly slower response times across all conditions. Children using CIs use tempo cues to discriminate happy versus sad music reflecting a very different hearing strategy than their normal hearing peers. Slower reaction times by children using CIs indicate that they found the task more difficult and support the possibility that they require different strategies to process emotion in music than normal.

Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

DOE PAGES

Somnath, Suhas; Collins, Liam; Matheson, Michael A.; ...

2016-09-08

We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify themore » findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.« less

Intrinsic hybrid modes in a corrugated conical horn

NASA Astrophysics Data System (ADS)

Dendane, A.; Arnold, J. M.

1988-08-01

Computational requirements for the generation of intrinsic modes in a nonseparable waveguide geometry requiring a full vector field description with anistropic impedance boundaries were derived. Good agreement is shown between computed and measured radiation patterns in copolar and crosspolar configurations. This agreement establishes that the intrinsic mode correctly accounts for the local normal mode conversion which takes place along the horn in a conventional mode coupling scheme, at least for cone semiangles up to 15 deg. The advantage of the intrinsic mode formulation over the conventional mode-coupling theory is that, to construct a single intrinsic mode throughout the horn, only one local normal mode field is required at each cross section, whereas mode conversion from the HE11 mode would require all the HE1n modes to be known at each cross section. The intrinsic mode accounts also for fields which would appear as backward modes in coupled-mode theory. A complete coupled-mode theory solution requires the inversion of a large matrix at each cross section, whereas the intrinsic mode can be constructed explicitly using a simple Fourier-like integral; the perturbation solution of Dragone (1977) is difficult to make rigorous.

Spectral statistics of the acoustic stadium

NASA Astrophysics Data System (ADS)

Méndez-Sánchez, R. A.; Báez, G.; Leyvraz, F.; Seligman, T. H.

2014-01-01

We calculate the normal-mode frequencies and wave amplitudes of the two-dimensional acoustical stadium. We also obtain the statistical properties of the acoustical spectrum and show that they agree with the results given by random matrix theory. Some normal-mode wave amplitudes showing scarring are presented.

75 FR 62476 - Ultra-Wideband Transmission Systems

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-12

... would be obtained from measurements taken with the system operating in its normal operating mode. At the... with the transmitter operating continuously at a fundamental transmission frequency. 9. Subsequent to... systems, measured in their normal operating modes, is less than that of a UWB transmitter employing...

Fibonacci family of dynamical universality classes

PubMed Central

Popkov, Vladislav; Schadschneider, Andreas; Schmidt, Johannes; Schütz, Gunter M.

2015-01-01

Universality is a well-established central concept of equilibrium physics. However, in systems far away from equilibrium, a deeper understanding of its underlying principles is still lacking. Up to now, a few classes have been identified. Besides the diffusive universality class with dynamical exponent z=2, another prominent example is the superdiffusive Kardar−Parisi−Zhang (KPZ) class with z=3/2. It appears, e.g., in low-dimensional dynamical phenomena far from thermal equilibrium that exhibit some conservation law. Here we show that both classes are only part of an infinite discrete family of nonequilibrium universality classes. Remarkably, their dynamical exponents zα are given by ratios of neighboring Fibonacci numbers, starting with either z1=3/2 (if a KPZ mode exist) or z1=2 (if a diffusive mode is present). If neither a diffusive nor a KPZ mode is present, all dynamical modes have the Golden Mean z=(1+5)/2 as dynamical exponent. The universal scaling functions of these Fibonacci modes are asymmetric Lévy distributions that are completely fixed by the macroscopic current density relation and compressibility matrix of the system and hence accessible to experimental measurement. PMID:26424449

Even and odd normalized zero modes in random interacting Majorana models respecting the parity P and the time-reversal-symmetry T

NASA Astrophysics Data System (ADS)

Monthus, Cécile

2018-06-01

For random interacting Majorana models where the only symmetries are the parity P and the time-reversal-symmetry T, various approaches are compared to construct exact even and odd normalized zero modes Γ in finite size, i.e. Hermitian operators that commute with the Hamiltonian, that square to the identity, and that commute (even) or anticommute (odd) with the parity P. Even normalized zero-modes are well known under the name of ‘pseudo-spins’ in the field of many-body-localization or more precisely ‘local integrals of motion’ (LIOMs) in the many-body-localized-phase where the pseudo-spins happens to be spatially localized. Odd normalized zero-modes are popular under the name of ‘Majorana zero modes’ or ‘strong zero modes’. Explicit examples for small systems are described in detail. Applications to real-space renormalization procedures based on blocks containing an odd number of Majorana fermions are also discussed.

Theoretical DFT study on spectroscopic signature and molecular dynamics of neurotransmitter and effect of hydrogen removal

NASA Astrophysics Data System (ADS)

Mukherjee, V.; Singh, N. P.; Yadav, R. A.

2013-04-01

Vibrational spectroscopic study has been made for the serotonin molecule and its deprotonated form. The Infrared and Raman spectra in optimum geometry of these two molecules are calculated using density functional theorem and the normal modes are assigned using potential energy distributions (PEDs) which are calculated using normal coordinate analysis method. The vibrational frequencies of these two molecules are reported and a comparison has been made. The effect of removal of the hydrogen atom from the serotonin molecule upon its geometry and vibrational frequencies are studied. Electronic structures of these two molecules are also studied using natural bond orbital (NBO) analysis. Theoretical Raman spectrum of serotonin at different exciting laser frequencies and at different temperatures are obtained and the results are discussed. Present study reveals that some wrong assignments had been made for serotonin molecule in earlier study.

Capillary waves' dynamics at the nanoscale

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Chacón, Enrique; Tarazona, Pedro

2008-12-01

We study the dynamics of thermally excited capillary waves (CW) at molecular scales, using molecular dynamics simulations of simple liquid slabs. The analysis is based on the Fourier modes of the liquid surface, constructed via the intrinsic sampling method (Chacón and Tarazona 2003 Phys. Rev. Lett. 91 166103). We obtain the time autocorrelation of the Fourier modes to get the frequency and damping rate Γd(q) of each mode, with wavenumber q. Continuum hydrodynamics predicts \\Gamma (q) \\propto q\\gamma (q) and thus provides a dynamic measure of the q-dependent surface tension, γd(q). The dynamical estimation is much more robust than the structural prediction based on the amplitude of the Fourier mode, γs(q). Using the optimal estimation of the intrinsic surface, we obtain quantitative agreement between the structural and dynamic pictures. Quite surprisingly, the hydrodynamic prediction for CW remains valid up to wavelengths of about four molecular diameters. Surface tension hydrodynamics break down at shorter scales, whereby a transition to a molecular diffusion regime is observed.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Electron temperature gradient mode instability and stationary vortices with elliptic and circular boundary conditions in non-Maxwellian plasmas

NASA Astrophysics Data System (ADS)

Haque, Q.; Zakir, U.; Qamar, A.

2015-12-01

Linear and nonlinear dynamics of electron temperature gradient mode along with parallel electron dynamics is investigated by considering hydrodynamic electrons and non-Maxwellian ions. It is noticed that the growth rate of ηe-mode driven linear instability decreases by increasing the value of spectral index and increases by reducing the ion/electron temperature ratio along the magnetic field lines. The eigen mode dispersion relation is also found in the ballooning mode limit. Stationary solutions in the form of dipolar vortices are obtained for both circular and elliptic boundary conditions. It is shown that the dynamics of both circular and elliptic vortices changes with the inclusion of inhomogeneity and non-Maxwellian effects.

Quasiparticle Coherence, Collective Modes, and Competing Order in Cuprate Superconductors

NASA Astrophysics Data System (ADS)

Hinton, James Patrick

In recent years, the study of cuprate superconductors has been dominated by the investigation of normal state properties. Of particular interest is the nature of interactions between superconductivity and other incipient orders which emerge above the superconducting transition temperature, Tc. The discovery of charge density wave (CDW) correlations in YBa2Cu3O6+x (YBCO) and HgBa2CuO 4+d (Hg-1201) has established that some form of charge order is ubiquitous in the cuprates. In this work, we explore the non-equilibrium dynamics of systems which sit near the boundary between superconductivity and competing orders. Ultrafast pump-probe spectroscopy is ideally suited to the study of competing order. Exciting the sample with an optical pulse perturbs the system from equilibrium, altering the balance between the co-existing orders. The return to equilibrium is then monitored by a time-delayed probe pulse, revealing multiple decay processes as well as collective excitations. We first apply this technique to Hg-1201, conducting a detailed study of the phase diagram. At temperatures near Tc, the pump pulse induces a non-equilibrium quasiparticle population. At Tc we observe a doping-dependent peak in the relaxation time of these quasiparticles which we associate with a divergence in the coherence time of the fluctuating CDW. Using heterodyne probing in the transient grating geometry, we are able to disentangle the transient reflectivity components associated with superconductivity and the pseudogap, domonstrating competition across the phase diagram. We also discuss the observation of a sharp transition in the nature of the pseudogap signal at ˜ 11% doping. In YBCO, we explore the temperature and doping dependence of coherent oscillations excited by the pump pulse. We associate these oscillations with the excitation of the CDW amplitude mode, and model their temperature dependence within the framework of a Landau model of competing orders. We conclude with an investigation of pseudogap dynamics in the electron doped compound Nd2-xCexCuO4+d as a function of temperature and doping. Near optimal doping, we observe the impulsive excitation of a critically damped mode, with time-temperature scaling consistent with quantum-critical fluctuations. This mode competes with superconductivity in a dynamical fashion, such that the suppression of this mode below T c can be lifted via photo-evaporation of the superconducting condensate.

Comparative analysis of guide mode of government - oriented industry guidance funds under china’s new normal of economic growth

NASA Astrophysics Data System (ADS)

Sun, Chunling; Cheng, Xuemei

2017-11-01

The government-oriented industry guidance Funds solve the problem of financing difficulty and high innovation under the background of China’s new normal. Through the provinces and cities of the policies and regulations of the collation and comparative analysis, it will be divided into three modes. And then compare among three modes and analyze applicability to guide the construction of provinces and cities.

Modeling Pulse Transmission in the Monterey Bay Using Parabolic Equation Methods

DTIC Science & Technology

1991-12-01

Collins 9-13 was chosen for this purpose due its energy conservation scheme , and its ability to efficiently incorporate higher order terms in its...pressure field generated by the PE model into normal modes. Additionally, this process provides increased physical understanding of mode coupling and...separation of variables (i.e. normal modes or fast field), as well as pure numerical schemes such as the parabolic equation methods, can be used. However, as

On the identification of normal modes of oscillation from observations of the solar periphery

NASA Technical Reports Server (NTRS)

Gough, D. D.; Latour, J.

1984-01-01

The decomposition of solar oscillations into their constituent normal modes requires a knowledge of both the spatial and temporal variation of the perturbation to the Sun's surface. The task is especially difficult when only limited spatial information is available. Observations of the limb darkening function, for example, are probably sensitive to too large a number of modes to permit most of the modes to be identified in a power spectrum of measurements at only a few points on the limb, unless the results are combined with other data. A procedure was considered by which the contributions from quite small groups of modes to spatially well resolved data obtained at any instant can be extracted from the remaining modes. Combining these results with frequency information then permits the modes to be identified, at least if their frequencies are low enough to ensure that modes of high degree do not contribute substantially to the signal.

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

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.

The internal model: A study of the relative contribution of proprioception and visual information to failure detection in dynamic systems. [sensitivity of operators versus monitors to failures

NASA Technical Reports Server (NTRS)

Kessel, C.; Wickens, C. D.

1978-01-01

The development of the internal model as it pertains to the detection of step changes in the order of control dynamics is investigated for two modes of participation: whether the subjects are actively controlling those dynamics or are monitoring an autopilot controlling them. A transfer of training design was used to evaluate the relative contribution of proprioception and visual information to the overall accuracy of the internal model. Sixteen subjects either tracked or monitored the system dynamics as a 2-dimensional pursuit display under single task conditions and concurrently with a sub-critical tracking task at two difficulty levels. Detection performance was faster and more accurate in the manual as opposed to the autopilot mode. The concurrent tracking task produced a decrement in detection performance for all conditions though this was more marked for the manual mode. The development of an internal model in the manual mode transferred positively to the automatic mode producing enhanced detection performance. There was no transfer from the internal model developed in the automatic mode to the manual mode.

Nonlinear normal modes modal interactions and isolated resonance curves

DOE PAGES

Kuether, Robert J.; Renson, L.; Detroux, T.; ...

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

Stiffening of flexible SUMO1 protein upon peptide-binding: Analysis with anisotropic network model.

PubMed

Sarkar, Ranja

2018-01-01

SUMO (small ubiquitin-like modifier) proteins interact with a large number of target proteins via a key regulatory event called sumoylation that encompasses activation, conjugation and ligation of SUMO proteins through specific E1, E2, and E3-type enzymes respectively. Single-molecule atomic force microscopic (AFM) experiments performed to unravel bound SUMO1 along its NC termini direction reveal that E3-ligases (in the form of small peptides) increase mechanical stability (along the axis) of the flexible protein upon binding. The experimental results are expected to correlate with the intrinsic flexibility of bound SUMO1 protein in the native state i.e., the bound conformation of SUMO1 without the binding peptide. The native protein flexibility/stiffness can be measured as a spring constant by normal mode analysis. In the present study, protein normal modes are computed from the protein structural data (as input from protein databank) via a simple anisotropic network model (ANM). ANM is computationally inexpensive and hence, can be explored to investigate and compare the native conformational dynamics of unbound and bound (without the binding partner) structures, if the corresponding structural data (NMR/X-ray) are available. The paper illustrates that SUMO1 stiffens (native flexibility decreases) along the NC termini (end-to-end) direction of the protein upon binding to small peptides; however, the degree of stiffening is peptide sequence-specific. The theoretical results are demonstrated for NMR structures of unbound SUMO1 and that bound to two peptides having short amino acid motifs and of similar size, one being an M-IR2 peptide derived from RanBP2 protein and the other one derived from PIASX protein. The peptide derived from PIASX stiffens SUMO1 remarkably which is evident from an atomic-level normal mode analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Determination of stress intensity factors for interface cracks under mixed-mode loading

NASA Technical Reports Server (NTRS)

Naik, Rajiv A.; Crews, John H., Jr.

1992-01-01

A simple technique was developed using conventional finite element analysis to determine stress intensity factors, K1 and K2, for interface cracks under mixed-mode loading. This technique involves the calculation of crack tip stresses using non-singular finite elements. These stresses are then combined and used in a linear regression procedure to calculate K1 and K2. The technique was demonstrated by calculating three different bimaterial combinations. For the normal loading case, the K's were within 2.6 percent of an exact solution. The normalized K's under shear loading were shown to be related to the normalized K's under normal loading. Based on these relations, a simple equation was derived for calculating K1 and K2 for mixed-mode loading from knowledge of the K's under normal loading. The equation was verified by computing the K's for a mixed-mode case with equal and normal shear loading. The correlation between exact and finite element solutions is within 3.7 percent. This study provides a simple procedure to compute K2/K1 ratio which has been used to characterize the stress state at the crack tip for various combinations of materials and loadings. Tests conducted over a range of K2/K1 ratios could be used to fully characterize interface fracture toughness.

Nonlinear interaction of strong S-waves with the rupture front in the shallow subsurface

NASA Astrophysics Data System (ADS)

Sleep, N. H.

2017-12-01

Shallow deformation in moderate to large earthquakes is sometimes distributed rather than being concentrated on a single fault plane. Strong high-frequency S-waves interact with the rupture front to produce this effect. For strike-slip faults, the rupture propagation velocity is a fraction of the S-wave velocity. The rupture propagation vector refracts essentially vertically in the low (S-wave) velocity shallow subsurface. So does the propagation direction of S-waves. The shallow rupture front is essentially mode 3 near the surface. Strong S-waves arrive before the rupture front. They continue to arrive for several seconds in a large event. There are simple scaling relationships. The dynamic Coulomb stress ratio of horizontal stress on horizontal planes from S-waves is the normalized acceleration in g's. For fractured rock and gravel, frictional failure occurs when the normalized acceleration exceeds the effective coefficient of friction. Acceleration tends to saturate at that level as the anelastic strain rate increases rapidly with stress. For muddy materials, failure begins at a low normalized acceleration but increases slowly with dynamic stress. Dynamic accelerations sometimes exceed 1 g. In both cases, the rupture tip finds the shallow subsurface already in nonlinear failure down to a few to tens of meters depth. The material does not distinguish between S-wave and rupture tip stresses. Both stresses add to the stress invariant and hence to the anelastic strain rate tensor. Surface anelastic strain from fault slip is thus distributed laterally over a distance scaling to the depth of nonlinearity from S-waves. The environs of the fault anelastically accommodate the fault slip at depth. This process differs from blind faults where the shallow coseismic strain is mostly elastic and interseismic anelastic processes accommodate the long-term shallow deformation.

Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase

PubMed Central

Harijan, Rajesh K.; Zoi, Ioanna; Antoniou, Dimitri; Schwartz, Steven D.; Schramm, Vern L.

2017-01-01

Heavy-enzyme isotope effects (15N-, 13C-, and 2H-labeled protein) explore mass-dependent vibrational modes linked to catalysis. Transition path-sampling (TPS) calculations have predicted femtosecond dynamic coupling at the catalytic site of human purine nucleoside phosphorylase (PNP). Coupling is observed in heavy PNPs, where slowed barrier crossing caused a normal heavy-enzyme isotope effect (kchem light/kchem heavy > 1.0). We used TPS to design mutant F159Y PNP, predicted to improve barrier crossing for heavy F159Y PNP, an attempt to generate a rare inverse heavy-enzyme isotope effect (kchem light/kchem heavy < 1.0). Steady-state kinetic comparison of light and heavy native PNPs to light and heavy F159Y PNPs revealed similar kinetic properties. Pre–steady-state chemistry was slowed 32-fold in F159Y PNP. Pre–steady-state chemistry compared heavy and light native and F159Y PNPs and found a normal heavy-enzyme isotope effect of 1.31 for native PNP and an inverse effect of 0.75 for F159Y PNP. Increased isotopic mass in F159Y PNP causes more efficient transition state formation. Independent validation of the inverse isotope effect for heavy F159Y PNP came from commitment to catalysis experiments. Most heavy enzymes demonstrate normal heavy-enzyme isotope effects, and F159Y PNP is a rare example of an inverse effect. Crystal structures and TPS dynamics of native and F159Y PNPs explore the catalytic-site geometry associated with these catalytic changes. Experimental validation of TPS predictions for barrier crossing establishes the connection of rapid protein dynamics and vibrational coupling to enzymatic transition state passage. PMID:28584087