Models normal modes

Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods to analyze domain motions in proteins from simulation A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27 (1997) 425-437. 

An instability of the impulse MTS method for At slightly less than half the period of a normal mode is confirmed by an analytical study of a linear model problem [7]. For another analysis, see [2]. A special case of this model problem, which gives a more transparent description of the phenomenon, is as follows Consider a two-degree-of-freedom system with Hamiltonian p + 5P2 + + 4( 2 This models a system of two springs con-... 

Harmonic analysis (normal modes) at given temperature and curvature gives complete time behavior of the system in the harmonic limit [1, 2, 3]. Although the harmonic model may be incomplete because of the contribution of anharmonic terms to the potential energy, it is nevertheless of considerable importance because it serves as a first approximation for which the theory is highly developed. This model is also useful in SISM which uses harmonic analysis. 

It should be realized, though, that either model can be used for levels for all values of v for such stretching vibrations but the normal mode model is more practically useful at low v and the local mode model more useful at higher values of v. 

Many thermodynamic quantities can be calculated from the set of normal mode frequencies. In calculating these quantities, one must always be aware that the harmonic approximation may not provide an adequate physical model of a biological molecule under physiological conditions. 

In this paper, we review progress in the experimental detection and theoretical modeling of the normal modes of vibration of carbon nanotubes. Insofar as the theoretical calculations are concerned, a carbon nanotube is assumed to be an infinitely long cylinder with a mono-layer of hexagonally ordered carbon atoms in the tube wall. A carbon nanotube is, therefore, a one-dimensional system in which the cyclic boundary condition around the tube wall, as well as the periodic structure along the tube axis, determine the degeneracies and symmetry classes of the one-dimensional vibrational branches [1-3] and the electronic energy bands[4-12]. 

The Rouse model, as given by the system of Eq, (21), describes the dynamics of a connected body displaying local interactions. In the Zimm model, on the other hand, the interactions among the segments are delocalized due to the inclusion of long range hydrodynamic effects. For this reason, the solution of the system of coupled equations and its transformation into normal mode coordinates are much more laborious than with the Rouse model. In order to uncouple the system of matrix equations, Zimm replaced S2U by its average over the equilibrium distribution function ... 

He X, Bell AF, Tonge PJ (2002) Isotopic labeling and normal-mode analysis of a model green fluorescent protein chromophore. J Phys Chem B 106 6056-6066... 

Delarue, M. Sanejouand, Y.H., Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases the elastic network model, J. Mol. Biol. 2002, 320, 1011-1024... 

Schuyler, A. D., Chirikjian, G. S., Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA, J. Mol. Graph. Model. 2005, 24, 46-58... 

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