The effect of inhomogenities on single molecule imaging by hard XFEL pulses

We study the local distortion of the atomic structure in small biological samples illuminated by x-ray free electron laser (XFEL) pulses. We concentrate on the effect of inhomogenities: heavy atoms in a light matrix and non-homogeneous spatial distribution of atoms. In biological systems we find both. Using molecular-dynamics type modeling it is shown that the local distortions about heavy atoms are larger than the average distortion in the light matrix. Further it is also shown that the large spatial density fluctuations also significantly alter the time evolution of atomic displacements as compared to samples with uniform density. This fact has serious consequences on single particle imaging. This is discussed and the possibility of a correction is envisaged.Comment: Movies: http://www.szfki.hu/~jurek/art2009_1/index.htm

Dynamics in a cluster under the influence of intense femtosecond hard x-ray pulses

In this paper we examine the behavior of small cluster of atoms in a short (10-50 fs) very intense hard x-ray (10 keV) pulse. We use numerical modeling based on the non-relativistic classical equation of motion. Quantum processes are taken into account by the respective cross sections. We show that there is a Coulomb explosion, which has a different dynamics than one finds in classical laser driven cluster explosions. We discuss the consequences of our results to single molecule imaging by the free electron laser pulses.Comment: 14 pages, 13 figure

Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

The interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., $>1$ ps. To have a better understanding of ion and electron data from experiments derived from laser-irradiated clusters, one needs to simulate cluster dynamics on such long timescales for which the molecular dynamics approach becomes inefficient. We therefore propose a two-step Molecular Dynamics-Hydrodynamic scheme. In the first step we use molecular dynamics code to follow the dynamics of an irradiated cluster until all the photo-excitation and corresponding relaxation processes are finished and a nanoplasma, consisting of ground-state ions and thermalized electrons, is formed. In the second step we perform long-timescale propagation of this nanoplasma with a computationally efficient hydrodynamic approach. In the present paper we examine the feasibility of a hydrodynamic two-fluid approach to follow the expansion of spherically symmetric nanoplasma, without accounting for the impact ionization and three-body recombination processes at this stage. We compare our results with the corresponding molecular dynamics simulations. We show that all relevant information about the nanoplasma propagation can be extracted from hydrodynamic simulations at a significantly lower computational cost when compared to a molecular dynamics approach. Finally, we comment on the accuracy and limitations of our present model and discuss possible future developments of the two-step strategy.Comment: 14 pages, 6 figure

The effect of tamper layer on the explosion dynamics of atom clusters

The behavior of small samples in very short and intense hard x-ray pulses is studied by molecular dynamics type calculations. The main emphasis is put on the effect of various tamper layers about the sample. This is discussed from the point of view of structural imaging of single particles, including not only the distortion of the structure but also the background conditions. A detailed picture is given about the Coulomb explosion, with explanation of the tampering mechanism. It is shown that a thin water layer is efficient in slowing down the distortion of the atomic structure, but it gives a significant contribution to the background

A molecular-dynamics approach for studying the non-equilibrium behavior of x-ray-heated solid-density matter

When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on sub-picosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte-Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate non-equilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and 3D spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab-initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven non-equilibrium dynamics in solids. In order to illustrate the potential of XMDYN for treating complex systems we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species

Quantum-mechanical calculation of ionization potential lowering in dense plasmas

The charged environment within a dense plasma leads to the phenomenon of ionization potential depression (IPD) for ions embedded in the plasma. Accurate predictions of the IPD effect are of crucial importance for modeling atomic processes occurring within dense plasmas. Several theoretical models have been developed to describe the IPD effect, with frequently discrepant predictions. Only recently, first experiments on IPD in Al plasma have been performed with an x-ray free-electron laser (XFEL), where their results were found to be in disagreement with the widely-used IPD model by Stewart and Pyatt. Another experiment on Al, at the Orion laser, showed disagreement with the model by Ecker and Kr\"oll. This controversy shows a strong need for a rigorous and consistent theoretical approach to calculate the IPD effect. Here we propose such an approach: a two-step Hartree-Fock-Slater model. With this parameter-free model we can accurately and efficiently describe the experimental Al data and validate the accuracy of standard IPD models. Our model can be a useful tool for calculating atomic properties within dense plasmas with wide-ranging applications to studies on warm dense matter, shock experiments, planetary science, inertial confinement fusion and studies of non-equilibrium plasmas created with XFELs.Comment: 13 pages, 9 figures, to be published in Phys. Rev. X; added references [46,47

Incoherent x-ray scattering in single molecule imaging

Imaging of the structure of single proteins or other biomolecules with atomic resolution would be enormously beneficial to structural biology. X-ray free-electron lasers generate highly intense and ultrashort x-ray pulses, providing a route towards imaging of single molecules with atomic resolution. The information on molecular structure is encoded in the coherent x-ray scattering signal. In contrast to crystallography there are no Bragg reflections in single molecule imaging, which means the coherent scattering is not enhanced. Consequently, a background signal from incoherent scattering deteriorates the quality of the coherent scattering signal. This background signal cannot be easily eliminated because the spectrum of incoherently scattered photons cannot be resolved by usual scattering detectors. We present an ab initio study of incoherent x-ray scattering from individual carbon atoms, including the electronic radiation damage caused by a highly intense x-ray pulse. We find that the coherent scattering pattern suffers from a significant incoherent background signal at high resolution. For high x-ray fluence the background signal becomes even dominating. Finally, based on the atomic scattering patterns, we present an estimation for the average photon count in single molecule imaging at high resolution. By varying the photon energy from 3.5 keV to 15 keV, we find that imaging at higher photon energies may improve the coherent scattering signal quality

Effect of two-particle correlations on x-ray coherent diffractive imaging studies performed with continuum models

Coherent diffraction imaging (CDI) of single molecules at atomic resolution is a major goal for the x-ray free electron lasers (XFELs). However, during an imaging pulse, the fast laser-induced ionization may strongly affect the recorded diffraction pattern of the irradiated sample. The radiation tolerance of the imaged molecule should then be investigated 'a priori' with a dedicated simulation tool. The continuum approach is a powerful tool for modeling the evolution of irradiated large systems consisting of more than a few hundred thousand atoms. However, this method follows the evolution of average single-particle densities, and the experimentally recorded intensities reflect the spatial two-particle correlations. The information on these correlations is then inherently not accessible within the continuum approach. In this paper we analyze this limitation of continuum models and discuss the applicability of continuum models for imaging studies. We propose a formula to calculate scattered intensities (including both elastic and inelastic scattering) from the estimates obtained with a single-particle continuum model. We derive this formula for systems under conditions typical for CDI studies with XFELs

XCALIB: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms

We develop the XCALIB toolkit to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Accurate characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. To obtain theoretical CSDs, we use XATOM, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. We have implemented an optimization procedure employing the reinforcement learning technique. The technique can automatize and organize calibration procedures which, before, had been performed manually. XCALIB has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with XATOM, XCALIB serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.Comment: 28 pages, 7 figure