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

Abstract

X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes.

Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides

“…53 For a crystal in a plasma phase, Coulomb interactions will be dominated by small lengths scales, due to Debye screening from the trapped free electron gas. 17,18 Future studies using this model could therefore investigate the effects of the free electrons on the fragmentation dynamics, which will be applicable to larger systems.…”

“…This will affect the long range interactions in the system through Debye screening, resulting in local interactions driving the dynamics in the system. 17,18 Studying molecules containing heavier atoms is of importance, since the rates at which these atoms will be ionized is different compared to the more common atoms (C, N, O) available in biomolecules. 15 They also provide more complicated damage dynamics in the local area of the heavy atoms, which might require one to account for molecular effects in the modeling.…”

Theoretical Studies of Anisotropic Melting of Ice Induced by Ultrafast Nonthermal Heating

“…In a second step we use molecular dynamics (MD) simulations to model structural changes, by providing the time-resolved charge states and free electron temperature/density as input. This hybrid CR/MD approach, called MolDStruct, has been able to reproduce experimental findings. ,, To relate our simulations to relevant parameters in coherent diffraction imaging with XFELs, we use 8 keV photon energy, pulse duration of 50 fs with a flat temporal pulse profile, and intensities of range 10 18 to 10 19 Wcm –2 . We simulate the interaction of the photon beam with the ice using a CR code Cretin, which has in earlier studies proven to be able to simulate these processes with a good agreement to experimental data, specifically in the case of XFEL experiments .…”

A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography

“…A recent development in XFEL damage simulation proposes to overcome the computational limitations of MD by combining it with the rate-equations approach. The details of this model are described in an another article in this issue [53] and in Reference [13]. The so-called hybrid plasma/MD model treats the ions as classical particles, but the electrons a continuum.…”