Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest. X-ray lasers, such as the recently bui
lt LINAC Coherent Light Source (LCLS), offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters or nanoparticles, but coherent flash imaging will also open up new avenues for structural studies on nano- and micro-crystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate primary and secondary ionization dynamics in the crystalline sample. Our results establish conditions for ultrafast nanocrystallography diffraction experiments as a function of fluence and pulse duration.
Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-ray sources. In crystallography this process can be limited through damage distribution in a crystal, while for single molecular
imaging it can be outrun by employing short intense pulses. Secondary electron generation is crucial during damage formation and we present a study in urea, as model for biomaterial. From first principles we calculate the band structure and energy loss function, and subsequently the inelastic electron cross section in urea. Using Molecular Dynamics simulations, we quantify the damage and study the magnitude and spatial extent of the electron cloud coming from an incident electron, as well as the dependence with initial energy.
