Molecular dynamics relaxation correspondence

Hudock et al. [126] used the ab initio molecular dynamics multiple spawning method to go beyond the static picture based on PES and include the time dependent dynamical behavior and predict time-resolved photoelectron spectroscopy results. According to these results the first ultrafast component of the photoelectron spectra of uracil corresponds to relaxation on the S2 minimum rather than nonadiabatic transitions to the Si state. The authors suggest that the radiationless relaxation from... 

The ab initio molecular dynamics study by Hudock et al. discussed above for uracil included thymine as well [126], Similarly to uracil, it was found that the first ultrafast component of the photoelectron spectra corresponds to relaxation on the S2 minimum. Subsequently a barrier exists on the S2 surface leading to the conical intersection between S2 and Si. The barrier involves out-of-plane motion of the methyl group attached to C5 in thymine or out-of-plane motion of H5 in uracil. Because of the difference of masses between these two molecules, kinematic factors will lead to a slower rate (longer lifetime) in thymine compared to uracil. Experimentally there are three components for the lifetimes of these systems, a subpicosecond, a picosecond and a nanosecond component. The picosecond component, which is suggested to correspond to the nonadiabatic S2/S1 transition, is 2.4 ps in uracil and 6.4 ps in thymine. This difference in the lifetimes could be explained by the barrier described above. 

Consider a molecular dynamics simulation of a polymer system consisting of 20 chains, each with 100 Lennard-Jones monomers. Let us assume that the molecular dynamics step 5t = 0.01iLj takes 10 ms of CPU time, where tlj is the Lennard-Jones time (corresponding to the monomeric relaxation time) ... 

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