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BETA
Seibert, Marvin
Alternative names
Publications (10 of 63) Show all publications
Gorkhover, T., Ulmer, A., Ferguson, K., Bucher, M., Maia, F. R. .., Bielecki, J., . . . Bostedt, C. (2018). Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles. Nature Photonics, 12(3), 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, no 3, p. 150-153Article in journal (Refereed) Published
Abstract [en]

Ultrafast X-ray imaging on individual fragile specimens such as aerosols 1 , metastable particles 2 , superfluid quantum systems 3 and live biospecimens 4 provides high-resolution information that is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely defined4,5. Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lateral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond timescale.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-345590 (URN)10.1038/s41566-018-0110-y (DOI)000426153800014 ()
Funder
German Research Foundation (DFG), BO3169/2-2European Regional Development Fund (ERDF), CZ.02.1.01/0.0/0.0/15European Regional Development Fund (ERDF), 003/0000447
Available from: 2018-03-09 Created: 2018-03-09 Last updated: 2018-05-04Bibliographically approved
Reddy, H. K. N., Yoon, C. H., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Xavier Paulraj, L. (2017). Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source. Scientific Data, 4, Article ID 170079.
Open this publication in new window or tab >>Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
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2017 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-328536 (URN)10.1038/sdata.2017.79 (DOI)000404232100001 ()28654088 (PubMedID)
Projects
eSSENCE
Available from: 2017-06-27 Created: 2017-08-25 Last updated: 2018-04-26Bibliographically 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: 2018-04-26Bibliographically approved
Popp, D., Loh, N. D., Zorgati, H., Ghoshdastider, U., Liow, L. T., Ivanova, M. I., . . . Robinson, R. C. (2017). Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Paper presented at International Symposium on Now in Actin, DEC, 2016, Nagoya Univ, Nagoya, JAPAN. CYTOSKELETON, 74(12), 472-481
Open this publication in new window or tab >>Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser
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2017 (English)In: CYTOSKELETON, ISSN 1949-3584, Vol. 74, no 12, p. 472-481Article in journal (Refereed) Published
Abstract [en]

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.

Place, publisher, year, edition, pages
WILEY, 2017
Keywords
fiber diffraction, filament systems, XFEL
National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-340293 (URN)10.1002/cm.21378 (DOI)000417746200005 ()28574190 (PubMedID)
Conference
International Symposium on Now in Actin, DEC, 2016, Nagoya Univ, Nagoya, JAPAN
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2018-01-29 Created: 2018-01-29 Last updated: 2018-01-29Bibliographically approved
Ryan, R. A., Williams, S., Martin, A. V., Dilanian, R. A., Darmanin, C., Putkunz, C. T., . . . Abbey, B. (2017). Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene. Journal of Visualized Experiments (126), Article ID e56296.
Open this publication in new window or tab >>Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
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2017 (English)In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 126, article id e56296Article in journal (Refereed) Published
Abstract [en]

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

Keywords
Chemistry, Issue 126, Nanocrystallography, Femtosecond X-ray Diffraction, Correlated Electron Dynamics, X-ray Free Electron Lasers, Linac Coherent Light Source, Buckminsterfullerene
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-343144 (URN)10.3791/56296 (DOI)000415369500095 ()
Available from: 2018-02-26 Created: 2018-02-26 Last updated: 2018-02-26Bibliographically approved
Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. .. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, Article ID 160061.
Open this publication in new window or tab >>A data set from flash X-ray imaging of carboxysomes
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed) Published
Abstract [en]

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300202 (URN)10.1038/sdata.2016.61 (DOI)000390225400006 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Munke, A., Andreasson, J., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Zook, J. (2016). Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific Data, 3, 160064:1-12, Article ID 160064.
Open this publication in new window or tab >>Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300203 (URN)10.1038/sdata.2016.64 (DOI)000390225700001 ()
Projects
eSSENCE
Available from: 2016-08-01 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. .., Hantke, M. F., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2016). Open data set of live cyanobacterial cells imaged using an X-ray laser. Scientific Data, 3, Article ID 160058.
Open this publication in new window or tab >>Open data set of live cyanobacterial cells imaged using an X-ray laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed) Published
Abstract [en]

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300201 (URN)10.1038/sdata.2016.58 (DOI)000390225400003 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Ekeberg, T., Svenda, M., Seibert, M. M., Abergel, C., Maia, F. R. .., Seltzer, V., . . . Hajdu, J. (2016). Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. Scientific Data, 3, Article ID UNSP 160060.
Open this publication in new window or tab >>Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed) Published
Abstract [en]

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-314814 (URN)10.1038/sdata.2016.60 (DOI)000390225400005 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilStiftelsen Olle Engkvist Byggmästare
Available from: 2017-02-07 Created: 2017-02-06 Last updated: 2017-11-29Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. N., Hantke, M., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2015). Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communications, 6, Article ID 5704.
Open this publication in new window or tab >>Imaging single cells in a beam of live cyanobacteria with an X-ray laser
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 5704Article in journal (Refereed) Published
Abstract [en]

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245040 (URN)10.1038/ncomms6704 (DOI)000350034400002 ()25669616 (PubMedID)
Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2017-12-04Bibliographically approved
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