Jönsson H Olof, Tîmneanu Nicuşor, Östlin Christofer, Scott Howard A, Caleman Carl
Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA.
J Synchrotron Radiat. 2015 Mar;22(2):256-66. doi: 10.1107/S1600577515002878. Epub 2015 Feb 25.
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
利用来自X射线自由电子激光的超短强脉冲对蛋白质纳米晶体进行系列飞秒X射线晶体学分析已被证明是一种成功的结构测定方法。然而，由于脉冲间衍射图样质量存在显著差异，所收集的帧中只有一小部分能够被使用。在实验中，X射线的时间脉冲轮廓未知且每次照射都会变化。本模拟研究描述了脉冲形状如何影响损伤动力学，而损伤动力学最终会影响电子密度的生物学解释。由于脉冲特性以及样品中的结构和电子变化，在脉冲照射期间瞬时检测到的信号会发生变化。在此，使用辐射传输等离子体代码对电离和原子运动进行模拟。考虑了具有X射线自由电子激光典型参数的脉冲：脉冲能量范围为10⁴至10⁷ J cm⁻²，光子能量为2至12 keV，脉冲长度可达100 fs。这里考虑了以样品加热形式出现的辐射损伤，这种损伤会导致晶体周期性丧失以及由于电离原子的电子重新配置而引起散射因子变化。模拟结果显示了不同时间脉冲轮廓和强度下辐射损伤过程动力学的差异，其中电离或原子运动可能占主导。不同的动力学在任何给定分辨率下都会影响记录的衍射信号，并将影响后续的结构测定。
