Velocity Reassignment Echoes
A new echo phenomenon in proteins, a generalization of so-called temperature quench echoes, is introduced and shown to reveal, through molecular dynamics simulations, periodic motions (normal modes) in proteins with phase coherence times of about a picosecond.
The echoes are induced through reassignments of Cartesian velocities to protein atoms at times 0 and t (with t around or less than 1ps) and appear as two sharp (widths about 5 fs) features in the kinetic and potential energy at 3t/2 and 2t. The velocities, assigned at 0 and t, need to be correlated, but can otherwise be random.
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