Molecular-dynamics approach for studying the nonequilibrium behavior of x-ray-heated solid-density matter

Abstract

When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on sub-picosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte-Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate non-equilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and 3D spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an abinitio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven non-equilibrium dynamics in solids. In order to illustrate the potential of XMDYN for treating complex systems we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.2

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

“…We calculated the dynamics of the atoms and electrons within a smaller cubic volume of nm size (here called 'supercell') exposed to a pulse of a spatially uniform fluence and imposed periodic boundary conditions 55,56 . Ideally, one would choose the crystallographic unit cell of thaumatin as the supercell.…”

Electronic-structure calculations for nonisothermal warm dense matter

“…Over the years, various theoretical models and approaches have been developed to describe WDM and its properties. Among them are the Ecker-Kröll (EK) model [23], the Stewart-Pyatt (SP) model [24], the average-atom (AA) model [25][26][27][28] and its variation [29], finite-temperature density functional theory (DFT) [30][31][32], frequently in combination with ab-initio molecular dynamics (QMD) [33][34][35][36][37][38][39][40][41], timedependent DFT [42], Monte Carlo molecular dynamics [43], quantum kinetic theory [44,45], and quantum Monte Carlo simulations [46,47]. A recent review highlighting and analyzing the last two topics can be found in Ref.…”

Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description

“…XMDYN is a radiation-damage-simulation tool that takes into account the inner-shell processes, such as photoionization, Auger and fluorescent relaxation, as well as phenomena caused by the environment, such as collisional ionization, recombination and dynamics driven by Coulomb interaction between charged particles. This supercell approach of XMDYN has been applied before to bulk systems (Abdullah et al, 2016(Abdullah et al, , 2017. To construct a scattering pattern from the nanocrystal, we employ the code XSINC (Abdullah et al, 2016).…”

“…Numerous theoretical and numerical studies have been carried out in order to investigate the effects of radiation damage in single instances and nanocrystals of biological molecules (e.g. proteins) and also in non-biological systems (Murphy et al, 2014;Abdullah et al, 2016Abdullah et al, , 2017Neutze, 2014;Curwood et al, 2013;Chapman et al, 2014;Ziaja et al, 2015;Ho et al, 2016). X-ray irradiation causes electronic damage, which affects the atomic form factors (Quiney & Nugent, 2011;Son, Young & Santra, 2011) and may also result in atomic displacements on longer time-scales, leading to the annihilation of the Bragg diffraction spots (Barty et al, 2012).…”