1. MolDStruct: Modeling the dynamics and structure of matter exposed to ultrafast x-ray lasers with hybrid collisional-radiative/molecular dynamics.
- Author
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Dawod, Ibrahim, Cardoch, Sebastian, André, Tomas, De Santis, Emiliano, E, Juncheng, Mancuso, Adrian P., Caleman, Carl, and Timneanu, Nicusor
- Subjects
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ATOMIC clusters , *X-ray spectra , *ATOMIC interactions , *FEMTOSECOND lasers , *CRYSTALLOIDS (Botany) , *X-ray lasers , *X-ray imaging , *MICROCLUSTERS , *FREE electron lasers - 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 determined based on changes to their electronic occupations and the formation of a free electron cloud created from 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, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. 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 present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the 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–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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