Comparison of Hartree–Fock and Hartree–Fock–Slater approximations for calculation of radiation damage dynamics of light and heavy atoms in the field of an x-ray free-electron laser

Abstract

Simulations of radiation damage in single molecule imaging using a X-ray free electron laser use atomic rates calculated in the lowest order. We investigate the difference in ion yield predictions using Hartree-Fock and Hartree-Fock-Slater approximations for light and heavy elements of biological significance. The results show that for the biologically abundant elements of the second and third rows of the periodic table both approximations agree to about 6%. For the heavier elements beyond the fourth row the discrepancy rices to 11% for the range of the pulse parameters covered in this work. Presented analysis can be used for an error estimation in a wide range of ab initio simulations of the X-ray pulse interaction with biological molecules. We also discuss other atomic structure effects and show that their account has considerably smaller effect on the ion yields of respective elements compared to the choice of the approximation.

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

“…The hybrid plasma-MD model consists of three stages: (i) atomic transition rate calculations, (ii) a rate-equations calculation to estimate mean plasma parameters, and (iii) ion dynamics calculation. The photoionization, Auger and fluorescence rates are calculated using a nonrelativistic quantum code 57 . These rates are sufficiently similar to those obtained by XATOM that differences in the values are not expected to significantly affect the results of the simulations.…”

“…A change in the crystal size weakly affects the predicted ion charges and resulting atomic motion between the pulses; these changes were captured by simulations over a distribution of particle sizes. Also, the changes in the rates of underlying atomic electronic processes on the scale of 10-30% translate into 2-5% changes in predicted charges 57 which has negligible effect on the observed motion of atoms.…”

Hybrid Plasma/Molecular-Dynamics Approach for Efficient XFEL Radiation Damage Simulations

“…The rate equation model utilizes precalculated rates for Auger decay, fluorescence and scattering cross-section [22]. Atomic rates and cross-sections are calculated using our computer code "Atomic code for damage calculation" (AC4DC).…”

“…Both MC/MD and plasma/MD simulations require detailed knowledge of the ionization rates for photoionization, radiative decay, Auger decay and electron-electron impact ionization. We use a detailed atomic model [22] to predict the ionization rates used in the REM part of our model, consistent with practices in state-of-art XFEL MC/MD simulations. We treat the ion motion using molecular dynamics and the ejected and trapped electrons using a continuum (plasma) model.…”

Effect of radiation damage and illumination variability on signal-to-noise ratio in X-ray free-electron laser single-particle imaging

“…The values of these two parameters were obtained as a best fit to a detailed atomic density model (Kozlov & Quiney, 2019) that includes all possible orbital occupancies. The time-dependent electron density was obtained by solving a system of rate equations (Hau-Riege et al, 2004) with atomic rates calculated in Hartree-Fock potential and averaged over all total spin and angular momentum terms of an electronic configuration (Kozlov & Quiney, 2019). We have included photoionization, fluorescence and Auger processes in our simulations.…”