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Statistical processing of Flash X-ray Imaging of protein complexes
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.ORCID-id: 0000-0002-1171-6683
2019 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Flash X-ray Imaging (FXI) at X-ray Free Electron Lasers (XFELs) is a promising technique that permits the investigation of the 3D structure of molecules without the need for crystallization, by diffracting on single individual sample particles.

In the past few years, some success has been achieved by using FXI on quite large biological complexes (40 nm-1 μm in diameter size). Still, the desired dream-goal of imaging a single individual of a molecule or a protein complex (<15 nm in diameter size) has not been reached yet. The main issue that prevented us from a complete success has been the low signal strength, almost comparable to background noise. That is particularly true for experiments performed at the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS).

In this thesis, we provide a brief review of the CXI instrument (focusing on experiments there performed) and present a statistical method to deal with low signal-to-noise ratios. We take into account a variety of biological particles, showing the benefits of estimating a background model from sample data and using that for processing said data. Moreover, we present the results of some computer simulations in order to explore the limits and potentials of the proposed approach.

Last, we show another method (named COACS) that, being fed with the previous findings from the background model, helps obtaining clearer results in the phase retrieval problem.

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2019. , s. 88
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1764
Emneord [en]
X-ray, XFEL, single particle, hit-finder, statistical hit-finder, single protein, protein complex, RNA polymerase II, FEL, free-electron laser, FXI, Flash X-ray Imaging, CXI, CSPAD, x-ray imaging, COACS
HSV kategori
Forskningsprogram
Fysik med inriktning mot biofysik
Identifikatorer
URN: urn:nbn:se:uu:diva-372987ISBN: 978-91-513-0554-7 (tryckt)OAI: oai:DiVA.org:uu-372987DiVA, id: diva2:1278413
Disputas
2019-03-06, C8:301, BMC, Husargatan 3, Uppsala, 09:15 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2019-02-08 Laget: 2019-01-14 Sist oppdatert: 2019-02-18
Delarbeid
1. Artifact reduction in the CSPAD detectors used for LCLS experiments
Åpne denne publikasjonen i ny fane eller vindu >>Artifact reduction in the CSPAD detectors used for LCLS experiments
2017 (engelsk)Inngår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, s. 1092-1097Artikkel i tidsskrift (Fagfellevurdert) Published
HSV kategori
Identifikatorer
urn:nbn:se:uu:diva-328543 (URN)10.1107/S160057751701058X (DOI)000408902800025 ()28862634 (PubMedID)
Prosjekter
eSSENCE
Tilgjengelig fra: 2017-07-18 Laget: 2017-08-25 Sist oppdatert: 2019-01-14bibliografisk kontrollert
2. A statistical approach to detect protein complexes at X-ray free electron laser facilities
Åpne denne publikasjonen i ny fane eller vindu >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
Vise andre…
2018 (engelsk)Inngår i: Communications Physics, E-ISSN 2399-3650, Vol. 1, s. 92:1-11, artikkel-id 92Artikkel i tidsskrift (Fagfellevurdert) Published
HSV kategori
Identifikatorer
urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
Prosjekter
eSSENCE
Tilgjengelig fra: 2018-12-07 Laget: 2018-12-17 Sist oppdatert: 2019-05-06bibliografisk kontrollert
3. Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
Åpne denne publikasjonen i ny fane eller vindu >>Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
2018 (engelsk)Inngår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, s. 24422-24443Artikkel i tidsskrift (Fagfellevurdert) Published
HSV kategori
Identifikatorer
urn:nbn:se:uu:diva-360037 (URN)10.1364/OE.26.024422 (DOI)000444705000012 ()30469561 (PubMedID)
Prosjekter
eSSENCE
Tilgjengelig fra: 2018-09-05 Laget: 2018-09-09 Sist oppdatert: 2019-01-14bibliografisk kontrollert

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