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Publications (10 of 84) Show all publications
Ekeberg, T., Assalauova, D., Bielecki, J., Boll, R., Daurer, B. J., Eichacker, L. A., . . . Maia, F. R. N. (2024). Observation of a single protein by ultrafast X-ray diffraction. Light: Science & Applications, 13(1), Article ID 15.
Open this publication in new window or tab >>Observation of a single protein by ultrafast X-ray diffraction
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2024 (English)In: Light: Science & Applications, ISSN 2095-5545, E-ISSN 2047-7538, Vol. 13, no 1, article id 15Article in journal (Refereed) Published
Abstract [en]

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-520488 (URN)10.1038/s41377-023-01352-7 (DOI)001142025600001 ()38216563 (PubMedID)
Funder
German Research Foundation (DFG), 152/772-1German Research Foundation (DFG), 152/774-1German Research Foundation (DFG), 152/775-1German Research Foundation (DFG), 152/776-1German Research Foundation (DFG), 152/777-1German Research Foundation (DFG), 390715994EU, European Research Council, 614507European Regional Development Fund (ERDF), CZ.02.1.01/0.0/0.0/15_003/0000447Swedish Research Council, 2017-05336Swedish Research Council, 2018-00234Swedish Research Council, 2019-03935Swedish Foundation for Strategic Research, ITM17-0455
Available from: 2024-01-12 Created: 2024-01-12 Last updated: 2024-01-30Bibliographically approved
Konold, P. E., You, T., Bielecki, J., Valerio, J., Kloos, M., Westphal, D., . . . Maia, F. R. N. (2023). 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers. IUCrJ, 10(6), 662-670
Open this publication in new window or tab >>3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers
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2023 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 10, no 6, p. 662-670Article in journal (Refereed) Published
Abstract [en]

X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interaction point in such a way that produces data of the highest possible quality and with maximal efficiency. This is hampered by intrinsic constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves some form of high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines which causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the problems related to X-ray pointing. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. These are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although their use has increased for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, gas-accelerated liquid sheet jet sample injection is demonstrated at the European XFEL SPB/SFX nano focus beamline. Its performance relative to a conventional liquid jet is evaluated and superior performance across several key factors has been found. This includes a thickness profile ranging from hundreds of nanometres to 60 nm, a fourfold increase in background stability and favorable radiation-induced explosion dynamics at high repetition rates up to 1.13 MHz. Its minute thickness also suggests that ultrafast single-particle solution scattering is a possibility.

Place, publisher, year, edition, pages
International Union Of Crystallography, 2023
Keywords
free-electron lasers, injectors, single particles, fast SAX, time-resolved studies, fast WAX, sample delivery, XFELs
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-516986 (URN)10.1107/s2052252523007972 (DOI)001098137800005 ()37721770 (PubMedID)
Funder
Swedish Research Council, 2018-00234Swedish Research Council, 2019-00207Swedish Research Council, 2017-05336Swedish Foundation for Strategic Research, ITM17-0455Carl Tryggers foundation , CTS 19-227
Available from: 2023-12-01 Created: 2023-12-01 Last updated: 2023-12-14Bibliographically approved
Bellisario, A., Maia, F. & Ekeberg, T. (2022). Noise reduction and mask removal neural network for X-ray single-particle imaging. Journal of applied crystallography, 55, 122-132
Open this publication in new window or tab >>Noise reduction and mask removal neural network for X-ray single-particle imaging
2022 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 55, p. 122-132Article in journal (Refereed) Published
Abstract [en]

Free-electron lasers could enable X-ray imaging of single biological macro-molecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low signal-to-noise ratio and missing regions in the detectors, colloquially termed 'masks', affect data collection and hamper real-time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10-100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low-pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean-squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion-maximization-compression algorithm.

Place, publisher, year, edition, pages
International Union of Crystallography (IUCr), 2022
Keywords
coherent X-ray diffractive imaging (CXDI), free-electron lasers, diffract-then-destroy, protein structures, single particles, XFELs, imaging
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-467393 (URN)10.1107/S1600576721012371 (DOI)000749998900013 ()35145358 (PubMedID)
Funder
Swedish Foundation for Strategic Research , ITM17-0455Swedish Foundation for Strategic Research , 2017-05336Swedish Foundation for Strategic Research , 2018-00234
Available from: 2022-02-14 Created: 2022-02-14 Last updated: 2022-02-14Bibliographically approved
Zhuang, Y., Awel, S., Barty, A., Bean, R., Bielecki, J., Bergemann, M., . . . Ayyer, K. (2022). Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging. IUCrJ, 9, 204-214
Open this publication in new window or tab >>Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging
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2022 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 9, p. 204-214Article in journal (Refereed) Published
Abstract [en]

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximizecompress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

Place, publisher, year, edition, pages
International Union of Crystallography (IUCr), 2022
Keywords
coherent X-ray diffractive imaging (CXDI), single particles, XFELs
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-475200 (URN)10.1107/S2052252521012707 (DOI)000795673400007 ()35371510 (PubMedID)
Funder
EU, FP7, Seventh Framework Programme, ERC-614507Swedish Research CouncilCarl Tryggers foundation
Available from: 2022-06-07 Created: 2022-06-07 Last updated: 2022-09-28Bibliographically approved
Ayyer, K., Xavier, P. L., Bielecki, J., Shen, Z., Daurer, B. J., Samanta, A. K., . . . Chapman, H. N. (2021). 3D diffractive imaging of nanoparticle ensembles using an x-ray laser. Optica, 8(1), 15-23
Open this publication in new window or tab >>3D diffractive imaging of nanoparticle ensembles using an x-ray laser
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2021 (English)In: Optica, E-ISSN 2334-2536, Vol. 8, no 1, p. 15-23Article in journal (Refereed) Published
Abstract [en]

Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely, the collection of sufficient high-quality diffraction patterns and robust computational purification to overcome structural heterogeneity. We report the breaking of both of these barriers using gold nanoparticle test samples, recording around 10 million diffraction patterns at the European XFEL and structurally and orientationally sorting the patterns to obtain better than 3-nm-resolution 3D reconstructions for each of four samples. With these new developments, integrating advancements in x-ray sources, fast-framing detectors, efficient sample delivery, and data analysis algorithms, we illuminate the path towards sub-nano meter biomolecular imaging. The methods developed here can also be extended to characterize ensembles that are inherently diverse to obtain their full structural landscape. Published by The Optical Society under the terms of the Creative Commons Attribution 4.0 License.

Place, publisher, year, edition, pages
Optical Society of AmericaOPTICAL SOC AMER, 2021
National Category
Condensed Matter Physics Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-435983 (URN)10.1364/OPTICA.410851 (DOI)000610085000003 ()
Funder
EU, European Research Council, ERC-614507Swedish Research Council
Available from: 2021-06-30 Created: 2021-06-30 Last updated: 2024-01-15Bibliographically approved
Marchesini, S., Shapiro, D. & Maia, F. (2021). Introduction to the special issue on Ptychography: software and technical developments. Journal of applied crystallography, 54, 384-385
Open this publication in new window or tab >>Introduction to the special issue on Ptychography: software and technical developments
2021 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 54, p. 384-385Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
International Union Of CrystallographyInternational Union of Crystallography (IUCr), 2021
Keywords
editorial, ptychography, imaging
National Category
Condensed Matter Physics Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-442246 (URN)10.1107/S1600576721002983 (DOI)000637331900001 ()
Available from: 2021-05-17 Created: 2021-05-17 Last updated: 2024-01-15Bibliographically approved
Daurer, B. J., Sala, S., Hantke, M., Reddy, H. K. .., Bielecki, J., Shen, Z., . . . Thibault, P. (2021). Ptychographic wavefront characterization for single-particle imaging at x-ray lasers. Optica, 8(4), 551-562
Open this publication in new window or tab >>Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
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2021 (English)In: Optica, ISSN 2334-2536, Vol. 8, no 4, p. 551-562Article in journal (Refereed) Published
Abstract [en]

A well-characterized wavefront is important for many x-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual biomolecules randomly sample a nanometer region of highly focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick–Baez mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase tilts likely has no impact. Our detailed characterization will aid interpretation of data from past and future SPI experiments and provides a basis for further improvements to experimental design and reconstruction algorithms.

Place, publisher, year, edition, pages
Optical Society of America, 2021
Keywords
Femtosecond pulses, Imaging techniques, Reconstruction algorithms, Synchrotron radiation, Wave front sensing, X ray lasers
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-441839 (URN)10.1364/OPTICA.416655 (DOI)000642200300017 ()
Funder
eSSENCE - An eScience CollaborationSwedish Research Council
Available from: 2021-05-05 Created: 2021-05-05 Last updated: 2023-10-30Bibliographically approved
Okamoto, K., Ferreira, R. J., Larsson, D. S., Maia, F. R. .., Isawa, H., Sawabe, K., . . . Miyazaki, N. (2020). Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus. Structure, 28(8), 888-+
Open this publication in new window or tab >>Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus
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2020 (English)In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 28, no 8, p. 888-+Article in journal (Refereed) Published
Abstract [en]

Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).

Place, publisher, year, edition, pages
Elsevier BV, 2020
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-420813 (URN)10.1016/j.str.2020.04.016 (DOI)000557639900004 ()32413288 (PubMedID)
Funder
Swedish Research Council, 628-20081109Swedish Research Council, 822-20106157Swedish Research Council, 822-2012-5260Swedish Research Council, 828-2012-108Swedish Research Council, 2018-03387Knut and Alice Wallenberg Foundation, KAW2011.081EU, European Research Council, ERC-291602Swedish Research Council Formas, 2018-00421
Available from: 2020-10-14 Created: 2020-10-14 Last updated: 2023-10-30Bibliographically approved
Li, H., Nazari, R., Abbey, B., Alvarez, R., Aquila, A., Ayyer, K., . . . Zaare, S. (2020). Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Scientific Data, 7(1), Article ID 404.
Open this publication in new window or tab >>Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source
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2020 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 7, no 1, article id 404Article in journal (Refereed) Published
Abstract [en]

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 mu m x 1.7 mu m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

Place, publisher, year, edition, pages
NATURE RESEARCH, 2020
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-429064 (URN)10.1038/s41597-020-00745-2 (DOI)000594590300003 ()33214568 (PubMedID)
Available from: 2020-12-21 Created: 2020-12-21 Last updated: 2021-01-18Bibliographically approved
Sobolev, E., Zolotarev, S., Giewekemeyer, K., Bielecki, J., Okamoto, K., Reddy, H. K. .., . . . Maia, F. R. .. (2020). Megahertz single-particle imaging at the European XFEL. Communications Physics, 3(1), Article ID 97.
Open this publication in new window or tab >>Megahertz single-particle imaging at the European XFEL
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2020 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 3, no 1, article id 97Article in journal (Refereed) Published
Abstract [en]

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-420501 (URN)10.1038/s42005-020-0362-y (DOI)000553489000001 ()
Funder
EU, European Research Council, 609920Swedish Research Council, 2018-03387Swedish Research Council Formas, 2018-00421Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2020-09-28 Created: 2020-09-28 Last updated: 2023-10-30Bibliographically approved
Projects
Software Infrastructure for Imaging with X-ray Lasers [2012-03404_VR]; Uppsala UniversityLaserbird [2018-01720_ VINNOVA]; Uppsala UniversityThe Torrent Ahead: Algorithms for X-ray Lasers to Study Structure, Function and Dynamics [2018-00234_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-2141-438x

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