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We simulated Coulomb explosion dynamics due to fast ionization induced by high-intensity x-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual detector, providing a unique explosion footprint. After collecting 500 explosion footprints for each protein, we utilized principal component analysis and 𝑡-distributed stochastic neighbor embedding to classify these. Results show that the classification algorithms were able to separate proteins on the basis of explosion footprints from structurally similar proteins into distinct groups. The explosion footprints, therefore, provide a unique identifier for each protein. We envision that method could be used concurrently with single-particle coherent imaging experiments to provide additional information on shape, mass, or conformation.

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.

Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular-dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.

- Single particle imaging using X-ray lasers is a technique aiming to capture atomic resolution structures of biomolecules in their native state. Knowing the particle's orientation during exposure is crucial for method enhancement. It has been shown that the trajectories of sulfur atoms in a Coulomb exploding lysozyme are reproducible, providing orientation information. This study explores if sulfur atom depth influences explosion trajectory. Employing a hybrid collisional-radiative/molecular dynamics model, we analyze the X-ray laser-induced dynamics of a single sulfur ion at varying depths in water. Our findings indicate that the ion spread-depth relationship depends on pulse parameters. At a photon energy of 2 keV, high-charge states are obtained, resulting in an increase of the spread with depth. However, at 8 keV photon energy, where lower charge states are obtained, the spread is essentially independent with depth. Finally, lower ion mass results in less reproducible trajectories, opening a promising route for determining protein orientation through the introduction of heavy atoms.