Time constant Brillouin

Recently Maret et al. (JL) have observed the longitudinal acoustic mode in oriented DNA fibres and films in a Brillouin scattering experiment. They observed the largest acoustic velocity for the driest samples, smallest for wet samples and at all times the observed velocity was larger than that for water itself. We have assumed that the velocities for propagation parallel to the helix axis are characteristic of acoustic modes in the DNA double helix and have used these values along with previously refined valence force field parameters (2,3) to fit the non-bonded force constants for the double helix. 

The simulations follow the pattern described in previous sections. The CPMD program is used with Born-Oppenheimer MD and a time step of 3.0236 fs (125 a.u.). We employ an NVT ensemble with cubic simulation cell, periodic boundary conditions, and a single point (k = 0) in the Brillouin zone. Simulations have been performed on two samples of a-GST (Fig. 17.1), with 460 and 648 atoms, respectively. We embedded in both a crystalline seed of 4 x 4 x 4 sites (13 Ge, 13 Sb, and 32 Te atoms, 6 vacancies) in a rock salt structure with lattice constant of 3.0 A. The structure of the crystallite adopted the model of Yamada [7], which assumed that one sublattice of the rock salt structure comprises Te atoms, the other a random arrangement of Ge, Sb, and vacancies. We removed the atoms of the amorphous structure inside this volume, fixed the coordinates of the seed, and optimized the resulting structure. 

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