Zoltan Jurek

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

Abstract.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.

Femtosecond X-ray-induced explosion of C 60 at extreme intensity

Understanding molecular femtosecond dynamics under intense X-ray exposure is critical to progress in biomolecular imaging and matter under extreme conditions. Imaging viruses and proteins at an atomic spatial scale and on the time scale of atomic motion requires rigorous, quantitative understanding of dynamical effects of intense X-ray exposure. Here we present an experimental and theoretical study of C60 molecules interacting with intense X-ray pulses from a free-electron laser, revealing the influence of processes not previously reported. Our work illustrates the successful use of classical mechanics to describe all moving particles in C60, an approach that scales well to larger systems, for example, biomolecules. Comparisons of the model with experimental data on C60 ion fragmentation show excellent agreement under a variety of laser conditions. The results indicate that this modelling is applicable for X-ray interactions with any extended system, even at higher X-ray dose rates expected with future light sources.

Imaging atom clusters by hard X-ray free-electron lasers

The ingenious idea of single-molecule imaging by hard X-ray Free Electron Laser (X-FEL) pulses was recently proposed by Neutze et al. (Nature 406 (2000) 752). However, in their numerical modelling of the Coulomb explosion, several interactions were neglected and no reconstruction of the atomic structure was given. In this work we carried out improved molecular-dynamics calculations including all quantum processes which affect the explosion. Based on this time evolution, we generated composite elastic-scattering patterns, and by using Fienups algorithm successfully reconstructed the original atomic structure. The critical evaluation of these results gives guidelines and sets important conditions for future experiments aiming at single-molecule structure solution.

XMDYN and XATOM: versatile simulation tools for quantitative modeling of X‐ray free‐electron laser induced dynamics of matter

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.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

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

AbstractThe 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.

Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser

Biological samples are highly radiation sensitive. The rapid progress of their radiation damage prevents accurate structure determination of single macromolecular assemblies in standard diffraction experiments. However, computer simulations of the damage formation have shown that the radiation tolerance might be extended at very high intensities with ultrafast imaging such as is possible with the presently developed and operating x-ray free-electron lasers. Recent experiments with free-electron lasers on nanocrystals have demonstrated proof of the imaging principle at resolutions down to 1:6 Angstroms. However, there are still many physical and technical problems to be clarified on the way to imaging of single biomolecules at atomic resolution. In particular, theoretical simulations try to address an important question: How does the radiation damage progressing within an imaged single object limit the structural information about this object recorded in its diffraction image during a 3D imaging experiment? This information is crucial for adjusting pulse parameters during imaging so that high-resolution diffraction patterns can be obtained. Further, dynamics simulations should be used to verify the accuracy of the structure reconstruction performed from the experimental data. This is an important issue as the experimentally recorded diffraction signal is recorded from radiation-damaged samples. It also contains various kinds of background. In contrast, the currently used reconstruction algorithms assume perfectly coherent scattering patterns with shot noise only. In this review paper, we discuss the most important processes and effects relevant for imaging-related simulations that are not yet fully understood, or omitted in the irradiation description. We give estimates for their contribution to the overall radiation damage. In this way we can identify unsolved issues and challenges for simulations of x-ray irradiated single molecules relevant for imaging studies. They should be addressed during further development of these simulation tools.

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.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

The optimal XFEL pulse duration for single-particle imaging of small proteins is narrowed down to the 3–9 fs range, using start-to-end simulations of a single-particle imaging experiment at the European XFEL.

Orienting single-molecule diffraction patterns from XFELs using heavy-metal explosion fragments

Single-molecule imaging is one of the main target areas of X-ray free-electron lasers. It relies on the possibility of orienting the large number of low-counting-statistics 2D diffraction patterns taken at random orientations of identical replicas of the sample. This is a difficult process and the low statistics limits the usability of orientation methods and ultimately it could prevent single-molecule imaging. We suggest a new approach, which avoids the orientation process from the diffraction patterns. We propose to determine sample orientation through identifying the direction of ejection fragments. The orientation of the sample is measured together with the diffraction pattern by detecting some fragments of the Coulomb explosion. We show by molecular-dynamics simulations that from the angular distribution of the fragments one can obtain the orientation of the samples.