Harmonic average correlation time

In the three bond jump model for segmental motion there are two parameters. The time scale is set by the harmonic average correlation time, Tjj and the effective distribution of correlation times is set by the number of coupled bonds m. The sharp cut off of coupling solution of the three bond jump model is employed here. The composite spectral density for internal rotation by jumps or stochastic diffusion plus segmental motion by three bond jump is... 

A similar result was obtained In a related study of frog muscle labeled with enriched glycine (46) and Chinese hamster ovary cells loaded with phosphoryl [Me- C] choline (50). These values are considerably less than that (>500 cp) obtained by Keith and Snipes (53) for chlamydomonas on the basis of an EPR spin label Study. The validity of the latter result has been questioned by Finch and Harmon (54) who suggested that the correlation time of the spin label probe could be a weighted average of Its predominant occupation of a "mobile" site and a small occupation of a highly immobilized one. 

The unperturbed harmonic vibration of an Isolated bond of length b would lead to a correlation function, Cv(t), which oscillates without decay for all times. However, shifts in either the frequency or phase of the oscillation results in an eventual decay of C (t) to zero after a time when the phase of Ab(t) is, on the average, completely random with respect to that of Ab(0). 

MD simulations have been employed in a wide variety of simulations. In the simplest applications, trajectories are generated for biomolecular systems and analyzed for a variety of structural, dynamic, and thermodynamic properties. The average motions of atoms over time may be observed, as well as time correlations for atomic positions and velocities. This type of information can often provide insight regarding structure-function relations and mechanistic details for biomacromolecules. Root mean square position fluctuations and other rms geometric fluctuations can be computed and compared with experimental observations. For example, in the limit of harmonic and isotropic atomic motion, mean square position fluctuations... 

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