Vibrational energy funneling in viruses-simulations of impulsive stimulated Raman scattering in M13 bacteriophage

The vibrational excitation of a tubular M13 bacteriophage capsid is simulated using classical molecular dynamics. The excitation occurs through impulsive stimulated Raman scattering by ultra-short laser pulses which ping the vibrational modes of the capsid. Tuning the laser pulse temporal width determines the frequency region of the capsid that is excited. The simulations reveal that electromagnetic energy transferred to the high frequency modes by ultra-short pulses is funneled via anharmonicity to just five low frequency modes which receive approximately 80% of the funneled energy. A single mode receives most of the funneled energy (3-4% of the total energy delivered) involves swelling and is effective in damaging the capsid. However, the laser intensity necessary to produce damage to the capsid from a single laser pulse is found to be extremely high for this mechanism to be effective.