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Pietrini, Alberto
Publications (8 of 8) Show all publications
Bielecki, J., Hantke, M. F., Daurer, B. J., Reddy, H. K. N., Hasse, D., Larsson, D. S. D., . . . Maia, F. R. N. (2019). Electrospray sample injection for single-particle imaging with x-ray lasers. Science Advances, 5(5), Article ID eaav8801.
Open this publication in new window or tab >>Electrospray sample injection for single-particle imaging with x-ray lasers
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-387970 (URN)10.1126/sciadv.aav8801 (DOI)000470125000080 ()31058226 (PubMedID)
Available from: 2019-05-03 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Pietrini, A. (2019). Statistical processing of Flash X-ray Imaging of protein complexes. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Statistical processing of Flash X-ray Imaging of protein complexes
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 88
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1764
Keywords
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
National Category
Biological Sciences Physical Sciences
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-372987 (URN)978-91-513-0554-7 (ISBN)
Public defence
2019-03-06, C8:301, BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2019-02-08 Created: 2019-01-14 Last updated: 2019-02-18
Pietrini, A., Bielecki, J., Timneanu, N., Hantke, M. F., Andreasson, J., Loh, N. D., . . . Nettelblad, C. (2018). A statistical approach to detect protein complexes at X-ray free electron laser facilities. Communications Physics, 1, 92:1-11, Article ID 92.
Open this publication in new window or tab >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
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2018 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
Projects
eSSENCE
Available from: 2018-12-07 Created: 2018-12-17 Last updated: 2019-05-06Bibliographically approved
Lundholm, I. V., Sellberg, J. A., Ekeberg, T., Hantke, M. F., Okamoto, K., van der Schot, G., . . . Maia, F. R. N. (2018). Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ, 5, 531-541
Open this publication in new window or tab >>Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
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2018 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-360034 (URN)10.1107/S2052252518010047 (DOI)000444010100003 ()
Projects
eSSENCE
Available from: 2018-09-01 Created: 2018-09-09 Last updated: 2019-07-01Bibliographically approved
Gorkhover, T., Ulmer, A., Ferguson, K., Bucher, M., Maia, F. R. N., Bielecki, J., . . . Bostedt, C. (2018). Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles [Letter to the editor]. Nature Photonics, 12, 150-153
Open this publication in new window or tab >>Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
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2018 (English)In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal, Letter (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-345590 (URN)10.1038/s41566-018-0110-y (DOI)000426153800014 ()
Projects
eSSENCE
Available from: 2018-02-26 Created: 2018-03-09 Last updated: 2019-07-01Bibliographically approved
Pietrini, A. & Nettelblad, C. (2018). Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy. Optics Express, 26, 24422-24443
Open this publication in new window or tab >>Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
2018 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, p. 24422-24443Article in journal (Refereed) Published
National Category
Computational Mathematics Biophysics
Identifiers
urn:nbn:se:uu:diva-360037 (URN)10.1364/OE.26.024422 (DOI)000444705000012 ()30469561 (PubMedID)
Projects
eSSENCE
Available from: 2018-09-05 Created: 2018-09-09 Last updated: 2019-01-14Bibliographically approved
Pietrini, A. & Nettelblad, C. (2017). Artifact reduction in the CSPAD detectors used for LCLS experiments. Journal of Synchrotron Radiation, 24, 1092-1097
Open this publication in new window or tab >>Artifact reduction in the CSPAD detectors used for LCLS experiments
2017 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, p. 1092-1097Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-328543 (URN)10.1107/S160057751701058X (DOI)000408902800025 ()28862634 (PubMedID)
Projects
eSSENCE
Available from: 2017-07-18 Created: 2017-08-25 Last updated: 2019-01-14Bibliographically approved
Daurer, B. J., Okamoto, K., Bielecki, J., Maia, F. R. N., Mühlig, K., Seibert, M. M., . . . Larsson, D. S. D. (2017). Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ, 4, 251-262
Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
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2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-323439 (URN)10.1107/S2052252517003591 (DOI)000400460500008 ()28512572 (PubMedID)
Projects
eSSENCE
Available from: 2017-04-07 Created: 2017-11-14 Last updated: 2019-07-01Bibliographically approved
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