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In this perspective article we propose and discuss a possible technique of in-depth material processing based on undersurface focusing of intense x-ray pulses. Currently, x-ray free-electron lasers can produce such intense x-ray pulses with femtosecond pulse durations, reaching intensities sufficiently high to cause ultrafast melting of a material after a single laser shot. Here, on the example of silicon crystal we will demonstrate that with a proper choice of pulse parameters and focusing parameters, the already existing nanofocusing setup has a capability to focus hard x rays down to several hundreds micrometers below the material surface. This can trigger the required structural modification in the focal point, without damaging the material above. Potential applications of the new technique are discussed. [ABSTRACT FROM AUTHOR]

Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation. [ABSTRACT FROM AUTHOR]

In this communication, we describe the application of Boltzmann kinetic equations for modeling massive electronic excitation in a silicon nanocrystal film after its irradiation with intense femtosecond hard X-ray pulses. This analysis was inspired by an experiment recently performed at the X-ray free-electron laser facility SACLA, which measured a significant reduction in atomic scattering factors triggered by an X-ray pulse of the intensity ∼ 10 19 W/cm 2 , occurring on a timescale comparable with the X-ray pulse duration (6 fs full width at half maximum). We show that a Boltzmann kinetic equation solver can accurately follow the details of the electronic excitation in silicon atoms caused by such a hard X-ray pulse, yielding predictions in very good agreement with the experimental data. [ABSTRACT FROM AUTHOR]

Modern X-ray free-electron lasers (XFELs) produce intense femtosecond X-ray pulses able to cause significant damage to irradiated targets. Energetic photoelectrons created upon X-ray absorption, and Auger electrons emitted after relaxation of core-hole states trigger secondary electron cascades, which contribute to the increasing transient free electron density on femtosecond timescales. Further evolution may involve energy and particle diffusion, creation of point defects, and lattice heating. This long-timescale (up to a microsecond) X-ray-induced dynamics is discussed on the example of silicon in two-dimensional geometry. For modeling, we apply an extended Two-Temperature model with electron density dynamics, nTTM, which describes relaxation of an irradiated sample between two successive X-ray pulses, emitted from XFEL at MHz pulse repetition rate. It takes into account ambipolar carrier diffusion, electronic and atomic heat conduction, as well as electron-ion coupling. To solve the nTTM system of equations in two dimensions, we developed a dedicated finite-difference integration algorithm based on Alternating Direction Implicit method with an additional predictor-corrector scheme. We show first results obtained with the model and discuss its possible applications for XFEL optics, detectors, and for diagnostics tools. In particular, the model can estimate the timescale of material relaxation relevant for beam diagnostic applications during MHz operation of contemporary and future XFELs. [ABSTRACT FROM AUTHOR]

The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a "disconcurrence" metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments. [ABSTRACT FROM AUTHOR]

In this review, we describe the application of Boltzmann kinetic equations for modelling warm dense matter and plasma formed after irradiation of solid materials with intense femtosecond X-ray pulses. Classical Boltzmann kinetic equations are derived from the reduced N-particle Liouville equations. They include only single-particle densities of ions and free electrons present in the sample. The first version of the Boltzmann kinetic equation solver was completed in 2006. It could model non-equilibrium evolution of X-ray-irradiated finite-size atomic systems. In 2016, the code was adapted to study plasma created from X-ray-irradiated materials. Additional extension of the code was then also performed, enabling simulations in the hard X-ray irradiation regime. In order to avoid treatment of a very high number of active atomic configurations involved in the excitation and relaxation of X-ray-irradiated materials, an approach called 'predominant excitation and relaxation path' (PERP) was introduced. It limited the number of active atomic configurations by following the sample evolution only along most PERPs. The performance of the Boltzmann code is illustrated in the examples of X-ray-heated solid carbon and gold. Actual model limitations and further model developments are discussed. This article is part of the theme issue 'Dynamic and transient processes in warm dense matter'. [ABSTRACT FROM AUTHOR]

We present a comparative theoretical study of silicon crystals irradiated with X-ray free-electron laser pulses, using hard X-ray photons of various energies. Simulations are performed with our in-house hybrid code XTANT based on Monte Carlo, Tight Binding and Molecular Dynamics simulation techniques. By comparing the strength of the coherently scattered signal and the corresponding electronic radiation damage for three X-ray photon energies available at the SACLA free-electron laser facility, we conclude that it would be beneficial to use higher photon energies for "diffraction-before-destruction" experiments. [ABSTRACT FROM AUTHOR]

Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments. XMDYN is a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by the ab initio XATOM toolkit. Here these tools are discussed in detail. [ABSTRACT FROM AUTHOR]

The irradiation of an atomic cluster with a femtosecond x-ray free-electron laser pulse results in a nanoplasma formation. This typically occurs within a few hundred femtoseconds. By this time the x-ray pulse is over, and the direct photoinduced processes no longer contributing. All created electrons within the nanoplasma are thermalized. The nanoplasma thus formed is a mixture of atoms, electrons, and ions of various charges. While expanding, it is undergoing electron impact ionization and three-body recombination. Below we present a hydrodynamic model to describe the dynamics of such multi-component nanoplasmas. The model equations are derived by taking the moments of the corresponding Boltzmann kinetic equations. We include the equations obtained, together with the source terms due to electron impact ionization and three-body recombination, in our hydrodynamic solver. Model predictions for a test case, expanding spherical Ar nanoplasma, are obtained. With this model, we complete the two-step approach to simulate x-ray created nanoplasmas, enabling computationally efficient simulations of their picosecond dynamics. Moreover, the hydrodynamic framework including collisional processes can be easily extended for other source terms and then applied to follow relaxation of any finite non-isothermal multi-component nanoplasma with its components relaxed into local thermodynamic equilibrium. [ABSTRACT FROM AUTHOR]