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Nanocrystal imaging using intense and ultrashort X-ray pulses
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters or nanoparticles, but coherent flash imaging will also open up new avenues for structural studies on nano- and micro-crystalline substances. This paper addresses the potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances, and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals.

National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-102116OAI: oai:DiVA.org:uu-102116DiVA, id: diva2:214366
Available from: 2009-06-25 Created: 2009-05-05 Last updated: 2013-02-26Bibliographically approved
In thesis
1. First Principles Calculations of Electron Transport and Structural Damage by Intense Irradiation
Open this publication in new window or tab >>First Principles Calculations of Electron Transport and Structural Damage by Intense Irradiation
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

First principle electronic structure theory is used to describe the effect of crystal binding on radiation detectors, electron transport properties, and structural damage induced by intense irradiation. A large database containing general electronic structure results to which data mining algorithms can be applied in the search for new functional materials, a case study is presented for scintillator detector materials. Inelastic cross sections for the generation of secondary electron cascades through impact ionization are derived from the dielectric response of an electron gas and evolved in time with Molecular Dynamics (MD). Qualitative and quantitive estimates are presented for the excitation and relaxation of a sample irradiated with Free Electron Laser pulses. A study is presented in where the structural damage on covalent bonded crystals following intense irradiation is derived from a Tight Binding approach and evolved in time with MD in where the evolution of the sample is derived from GW theory for the quasiparticle spectra and a dedicated Boltzmann transport equation for the impact ionization.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. p. 61
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 652
Keywords
Condense matter theory, electronic structure, quasiparticles, GW theory, molecular dynamics, Boltzmann transport, electron transport, impact ionization, structural damage, dielectric response, structural biology, radiation detectors, scintillators, positron emission tommography
National Category
Other Materials Engineering Condensed Matter Physics
Research subject
Physics of Matter
Identifiers
urn:nbn:se:uu:diva-102376 (URN)978-91-554-7547-5 (ISBN)
Public defence
2009-06-12, Polhemsalen, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2009-05-20 Created: 2009-05-06 Last updated: 2013-02-26Bibliographically approved

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Caleman, CarlOrtiz, CarlosMaia, Filipe R. N. C.Marklund, Erik G.van der Spool, DavidTimneanu, Nicusor

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