Clusters in the XFEL beam

Faigel, G.; Jurek, Zoltán; Oszlányi, G.; Tegze, M.

doi:10.1016/j.jallcom.2005.01.061

Cited by 14 publications

(13 citation statements)

References 17 publications

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“…the size of the atomic cloud is much larger than the original size of the sample, and the expansion continues as time goes on. This behavior agrees with our earlier findings [3,11,12]. Now we concentrate on the motion of Fe atoms, since we would like to use them to fix the orientation of the molecule.…”

Section: -P2supporting

confidence: 90%

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

Jurek¹,

Faigel²

2013

EPL

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PACS 61.05.-a -Techniques for structure determination PACS 61.46.-w -Structure of nanoscale materials PACS 87.15.A--Theory, modeling, and computer simulation Abstract -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.

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Section: -P2supporting

confidence: 90%

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

Jurek¹,

Faigel²

2013

EPL

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“…Following this idea, several theoretical approaches were used to simulate the radiation damage processes including the movement of the atoms: References [27][28][29][30][31][32][33] employed molecular dynamics, Refs. [34][35][36][37][38] based their description on a hydrodynamic model, and Refs.…”

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confidence: 99%

Impact of hollow-atom formation on coherent x-ray scattering at high intensity

2011

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X-ray free-electron lasers (FELs) are promising tools for structural determination of macromolecules via coherent x-ray scattering. During ultrashort and ultraintense x-ray pulses with an atomic scale wavelength, samples are subject to radiation damage and possibly become highly ionized, which may influence the quality of x-ray scattering patterns. We develop a toolkit to treat detailed ionization, relaxation, and scattering dynamics for an atom within a consistent theoretical framework. The coherent x-ray scattering problem including radiation damage is investigated as a function of x-ray FEL parameters such as pulse length, fluence, and photon energy. We find that the x-ray scattering intensity saturates at a fluence of ∼ 10 7 photons/Å 2 per pulse, but can be maximized by using a pulse duration much shorter than the time scales involved in the relaxation of the inner-shell vacancy states created. Under these conditions, both inner-shell electrons in a carbon atom are removed, and the resulting hollow atom gives rise to a scattering pattern with little loss of quality for a spatial resolution > 1Å. Our numerical results predict that in order to scatter from a carbon atom 0.1 photons per x-ray pulse, within a spatial resolution of 1.7Å, a fluence of 1 × 10 7 photons/Å 2 per pulse is required at a pulse length of 1 fs and a photon energy of 12 keV. By using a pulse length of a few hundred attoseconds, one can suppress even secondary ionization processes in extended systems. The present results suggest that high-brightness attosecond x-ray FELs would be ideal for single-shot imaging of individual macromolecules.

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“…However, the CPU requirement of these calculations increase very fast with the number of particles, therefore it is difficult to model large enough systems. We have developed a special MD algorithm for the description of the dynamics of a small atom-cluster (or a molecule) in the intense x-ray pulse [6,10]. Lately, we improved this code to a highly parallelized form.…”

Section: Introductionmentioning

confidence: 99%

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

Jurek

Faigel

2008

Eur. Phys. J. D

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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.

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Clusters in the XFEL beam

Cited by 14 publications

References 17 publications

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

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

Impact of hollow-atom formation on coherent x-ray scattering at high intensity

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

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