The Experts below are selected from a list of 38838 Experts worldwide ranked by ideXlab platform
Kuniaki Nagayama - One of the best experts on this subject based on the ideXlab platform.
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PROTEIN BACKBONE DYNAMICS REVEALED BY QUASI Spectral Density Function ANALYSIS OF AMIDE N-15 NUCLEI
Biochemistry, 1995Co-Authors: Riecko Ishima, Kuniaki NagayamaAbstract:Spectral Density Functions J(0), J(omega N), and J(omega H + omega N) of individual amide N-15 nuclei in proteins were approximated by a quasi Spectral Density Function (QSDF). Using this Function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega N) as the difference between the J(0) and the J(omega N) values, which describes motions slower than 50 (or 60) MHz, and J(omega N; omega H+N) as the difference between the J(omega N) and the J(omega H + omega N) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega N) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega N) and the J(omega N; omega H+N) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega N) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega N) was observed in two or three residues located between secondary structures.
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Application of the quasi-Spectral Density Function of (15)N nuclei to the selection of a motional model for model-free analysis.
Journal of biomolecular NMR, 1995Co-Authors: Rieko Ishima, Kazuhiko Yamasaki, Kuniaki NagayamaAbstract:Parameters used in model-free analysis were related to simulated Spectral Density Functions in a frequency region experimentally obtained by quasi-Spectral Density Function analysis of 15N nuclei. Five kinds of motional models used in recent model-free analyses were characterized by a simple classification of the experimental Spectral Density Function. We demonstrate advantages and limitations of each of the motional models. To verify the character of the models, model selection using experimental Spectral Density Functions was examined.
Rieko Ishima - One of the best experts on this subject based on the ideXlab platform.
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Model-free analysis for large proteins at high magnetic field strengths
Journal of Biomolecular NMR, 2007Co-Authors: Shou-lin Chang, Andrew P. Hinck, Rieko IshimaAbstract:Protein backbone dynamics is often characterized using model-free analysis of three sets of ^15N relaxation data: longitudinal relaxation rate ( R _1), transverse relaxation rate ( R _2), and ^15N–{H} NOE values. Since the experimental data is limited, a simplified model-free Spectral Density Function is often used that contains one Lorentzian describing overall rotational correlation but not one describing internal motion. The simplified Spectral Density Function may be also used in estimating the overall rotational correlation time, by making the R _2/ R _1 largely insensitive to internal motions, as well as used as one of the choices in the model selection protocol. However, such approximation may not be valid for analysis of relaxation data of large proteins recorded at high magnetic field strengths since the contribution to longitudinal relaxation from the Lorentzian describing the overall rotational diffusion of the molecule is comparably small relative to that describing internal motion. Here, we quantitatively estimate the errors introduced by the use of the simplified Spectral Density in model-free analysis for large proteins at high magnetic field strength.
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Application of the quasi-Spectral Density Function of (15)N nuclei to the selection of a motional model for model-free analysis.
Journal of biomolecular NMR, 1995Co-Authors: Rieko Ishima, Kazuhiko Yamasaki, Kuniaki NagayamaAbstract:Parameters used in model-free analysis were related to simulated Spectral Density Functions in a frequency region experimentally obtained by quasi-Spectral Density Function analysis of 15N nuclei. Five kinds of motional models used in recent model-free analyses were characterized by a simple classification of the experimental Spectral Density Function. We demonstrate advantages and limitations of each of the motional models. To verify the character of the models, model selection using experimental Spectral Density Functions was examined.
Christian Soize - One of the best experts on this subject based on the ideXlab platform.
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Identification of stochastic loads applied to a non-linear dynamical system using an uncertain computational model and experimental responses
Computational Mechanics, 2009Co-Authors: Anas Batou, Christian SoizeAbstract:The paper is devoted to the identification of stochastic loads applied to a non-linear dynamical system for which experimental dynamical responses are available. The identification of the stochastic load is performed using a simplified computational non-linear dynamical model containing both model uncertainties and data uncertainties. Uncertainties are taken into account in the context of the probability theory. The stochastic load which has to be identified is modelled by a stationary non-Gaussian stochastic process for which the matrix-valued Spectral Density Function is uncertain and is then modelled by a matrix-valued random Function. The parameters to be identified are the mean value of the random matrix-valued Spectral Density Function and its dispersion parameter. The identification problem is formulated as two optimization problems using the computational stochastic model and experimental responses. A validation of the theory proposed is presented in the context of tubes bundles in Pressurized Water Reactors.
Steven Pruess - One of the best experts on this subject based on the ideXlab platform.
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Algorithms for estimating Spectral Density Functions for periodic potentials on the half line
arXiv: Numerical Analysis, 2013Co-Authors: Charles T. Fulton, David Pearson, Steven PruessAbstract:For Hill's equation on [0,infinity) we prove new characterizations of the Spectral Function rho(lambda) and the Spectral Density Function f(lambda) based on analysis involving a companion system of first order differential equations in [6,7]. A numerical algorithm is derived and implemented based on coefficient approximation. Results for several examples, including the Mathieu equation, are presented.
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Estimating Spectral Density Functions for Sturm-Liouville problems with two singular endpoints
arXiv: Numerical Analysis, 2013Co-Authors: Charles T. Fulton, David Pearson, Steven PruessAbstract:In this paper we consider the Sturm-Liouville equation -y"+qy = lambda*y on the half line (0,infinity) under the assumptions that x=0 is a regular singular point and nonoscillatory for all real lambda, and that either (i) q is L_1 near x=infinity, or (ii) q' is L_1 near infinity with q(x) --> 0 as x --> infinity, so that there is absolutely continuous spectrum in (0,infinity). Characterizations of the Spectral Density Function for this doubly singular problem, similar to those obtained in [12] and [13] (when the left endpoint is regular) are established; corresponding approximants from the two algorithms in [12] and [13] are then utilized, along with the Frobenius recurrence relations and piecewise trigonometric - hyperbolic splines, to generate numerical approximations to the Spectral Density Function associated with the doubly singular problem on (0,infinity). In the case of the radial part of the separated hydrogen atom problem, the new algorithms are capable of achieving near machine precision accuracy over the range of lambda from 0.1 to 10000, accuracies which could not be achieved using the SLEDGE software package.
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Characterization of the Spectral Density Function for a one-sided tridiagonalJacobi matrix operator
Conference Publications, 2013Co-Authors: Charles T. Fulton, David Pearson, Steven PruessAbstract:In this paper we give a first order system of difference equations which provides a useful companion system in the study of Jacobi matrix operators and make use of it to obtain a characterization of the Spectral Density Function for a simple case involving absolutely continuous spectrum on the stability intervals.
Ge Nan - One of the best experts on this subject based on the ideXlab platform.
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A Solution for the Spectral Density Function of Across Wind Load Fluctuation
Building Science, 2006Co-Authors: Ge NanAbstract:A basic idea of the evaluation of Spectral Density Function of across-wind load(non-eddy dropping induced across-wind fluctuation load)fluctuation is presented in this paper from the original fluid movement equation in turbulence theory.The wind load fluctuation Spectral Density Function could be derviated from the wind average velocity and fluctuating velocity distribution.This could provide useful reference for defining the whole across-wind load acting on the structure.
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An Analytical Solution to the Spectral Density Function of Across-Wind Load Fluctuation on Rectangle High Rise Buildings
Journal of Shenyang Architectural and Civil Engineering Institute, 2005Co-Authors: Ge NanAbstract:An analytical solution to Spectral Density Function of across-wind load fluctuation acting on the structure flank is presented from the original fluid movement equation in turbulence theory under certain assumptions.The Spectral Density Function of wind load fluctuation could be derived from the CFD wind average velocity and fluctuating velocity distribution according to Taylor's Frozen Assumption of turbulence.All the T-M contributions have been taken into account in the analysis process.This could be regarded as an effective verification of the datum from wind tunnel test and datum from full scale observation.The analysis of structure dynamic response induced by this kind of wind load fluctuation could then be achieved without the expensive wind tunnel test.