Abstract
We developed a molecular-structure-based simulation to calculate the time dependence of damage caused to a single biomolecule by irradiation through short, high-intensity X-ray pulses. We consider the atomic processes of photoionization, Compton scattering, Auger decay, and electric-field ionization. The latter has yet to be included in simulations based on molecular structure. In the present study we use the small protein lysozyme as a target and calculate the average number of electrons bound to the atoms or ions of the protein molecule. The protein undergoes Coulomb explosion when exposed to a 5 fs pulse with photon energy of 12.4 keV. The atoms or ions of the protein are ionized by electric-field ionization when the incident X-ray-pulse intensity exceeds \(10^{20}\) photons/mm2, and Coulomb explosion of the protein at the peak intensity of the X-ray pulse is caused by strong generation of photoelectrons at incident X-ray intensities near \(10^{21}\) photons/mm2. We found that the upper limit of incide...
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