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Ultrafast Structura...
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Jönsson, Olof,1985-Uppsala universitet,Molekyl- och kondenserade materiens fysik,Molekylär biofysik,Molecular dynamics and structure
(author)
Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
Publisher, publication year, extent ...
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Uppsala :Acta Universitatis Upsaliensis,2017
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78 s.
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-331936
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ISBN:9789151301341
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-331936URI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:vet swepub-contenttype
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Subject category:dok swepub-publicationtype
Notes
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Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins. We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.
Subject headings and genre
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NATURVETENSKAP Biologi Biofysik hsv//swe
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NATURAL SCIENCES Biological Sciences Biophysics hsv//eng
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X-ray free-electron laser; Serial Femtosecond Crystallography; Radiation Damage; Plasma Simulations; Ultrafast Lasers; X-ray Imaging; Diffraction Theory; Ultrafast Phenomena; Hit Detection; Plasma Emission Spectra; Serial Femtosecond Crystallography; Protein Structure; Protein Crystallography; Metalloprotein; Non-thermal Heating; Water; Ferredoxin; NLTE Simulation; XFEL; FEL; SFX
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Physics with specialization in Biophysics
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Fysik med inriktning mot biofysik
Added entries (persons, corporate bodies, meetings, titles ...)
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Caleman, Carl,DocentUppsala universitet,Molekyl- och kondenserade materiens fysik,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron
(thesis advisor)
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Timneanu, Nicusor,DocentUppsala universitet,Molekyl- och kondenserade materiens fysik,Molekylär biofysik
(thesis advisor)
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Björneholm, Olle,ProfessorUppsala universitet,Molekyl- och kondenserade materiens fysik
(thesis advisor)
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Larsson, Jörgen,ProfessorLunds universitet
(opponent)
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Uppsala universitetMolekyl- och kondenserade materiens fysik
(creator_code:org_t)
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