MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics

Abstract

We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelisation through domain decomposition, large-scale molecular dynamics and ionisation induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.

arXiv comment12 pages, 11 figures, 50 references

References in corpus (5)

• A Molecular Dynamics Study of Laser-Excited Gold
• Hydrodynamic model for expansion and collisional relaxation of x-ray laser-excited multi-component nanoplasma
• Fluorescence intensity correlation imaging with high resolution and elemental contrast using intense x-ray pulses
• Decreasing ultrafast X-ray pulse durations with saturable absorption and resonant transitions
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Cited by in corpus (2)

• Protein structure classification based on X-ray laser induced Coulomb explosion
• Partial Orientation Retrieval of Proteins From Coulomb Explosions