Daniel Westphal
Uppsala University
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Publication
Featured researches published by Daniel Westphal.
Nature | 2011
M. Marvin Seibert; Tomas Ekeberg; Filipe R. N. C. Maia; Martin Svenda; Jakob Andreasson; O Jonsson; Duško Odić; Bianca Iwan; Andrea Rocker; Daniel Westphal; Max F. Hantke; Daniel P. DePonte; Anton Barty; Joachim Schulz; Lars Gumprecht; Nicola Coppola; Andrew Aquila; Mengning Liang; Thomas A. White; Andrew V. Martin; Carl Caleman; Stephan Stern; Chantal Abergel; Virginie Seltzer; Jean-Michel Claverie; Christoph Bostedt; John D. Bozek; Sébastien Boutet; A. Miahnahri; Marc Messerschmidt
X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
Nature Communications | 2015
Gijs van der Schot; Martin Svenda; Filipe R. N. C. Maia; Max F. Hantke; Daniel P. DePonte; M. Marvin Seibert; Andrew Aquila; Joachim Schulz; Richard A. Kirian; Mengning Liang; Francesco Stellato; Bianca Iwan; Jakob Andreasson; Nicusor Timneanu; Daniel Westphal; F. Nunes Almeida; Duško Odić; Dirk Hasse; Gunilla H. Carlsson; Daniel S. D. Larsson; Anton Barty; Andrew V. Martin; S. Schorb; Christoph Bostedt; John D. Bozek; Daniel Rolles; Artem Rudenko; Sascha W. Epp; Lutz Foucar; Benedikt Rudek
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.
Scientific Data | 2016
Anna Munke; Jakob Andreasson; Andrew Aquila; Salah Awel; Kartik Ayyer; Anton Barty; Richard Bean; Peter Berntsen; Johan Bielecki; Sébastien Boutet; Maximilian Bucher; Henry N. Chapman; Benedikt J. Daurer; Hasan Demirci; Veit Elser; Petra Fromme; Janos Hajdu; Max F. Hantke; Akifumi Higashiura; Brenda G. Hogue; Ahmad Hosseinizadeh; Yoonhee Kim; Richard A. Kirian; Hemanth K. N. Reddy; Ti Yen Lan; Daniel S. D. Larsson; Haiguang Liu; N. Duane Loh; Filipe R. N. C. Maia; Adrian P. Mancuso
Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
Proceedings of SPIE | 2011
Andrew V. Martin; Jakob Andreasson; Andrew Aquila; Sasa Bajt; Thomas R. M. Barends; Miriam Barthelmess; Anton Barty; W. Henry Benner; Christoph Bostedt; John D. Bozek; Phillip Bucksbaum; Carl Caleman; Nicola Coppola; Daniel P. DePonte; Tomas Ekeberg; Sascha W. Epp; Benjamin Erk; George R. Farquar; Holger Fleckenstein; Lutz Foucar; Matthias Frank; Lars Gumprecht; Christina Y. Hampton; Max F. Hantke; Andreas Hartmann; Elisabeth Hartmann; Robert Hartmann; Stephan P. Hau-Riege; G. Hauser; Peter Holl
Results of coherent diffractive imaging experiments performed with soft X-rays (1-2 keV) at the Linac Coherent Light Source are presented. Both organic and inorganic nano-sized objects were injected into the XFEL beam as an aerosol focused with an aerodynamic lens. The high intensity and femtosecond duration of X-ray pulses produced by the Linac Coherent Light Source allow structural information to be recorded by X-ray diffraction before the particle is destroyed. Images were formed by using iterative methods to phase single shot diffraction patterns. Strategies for improving the reconstruction methods have been developed. This technique opens up exciting opportunities for biological imaging, allowing structure determination without freezing, staining or crystallization.
IUCrJ | 2017
Benedikt J. Daurer; Kenta Okamoto; Johan Bielecki; Filipe R. N. C. Maia; Kerstin Mühlig; M. Marvin Seibert; Max F. Hantke; Carl Nettelblad; W. Henry Benner; Martin Svenda; Nicusor Timneanu; Tomas Ekeberg; N. Duane Loh; Alberto Pietrini; Alessandro Zani; Asawari D. Rath; Daniel Westphal; Richard A. Kirian; Salah Awel; Max O. Wiedorn; Gijs van der Schot; Gunilla H. Carlsson; Dirk Hasse; Jonas A. Sellberg; Anton Barty; Jakob Andreasson; Sebastian Boutet; Garth J. Williams; Jason E. Koglin; Inger Andersson
Facilitating the very short and intense pulses from an X-ray laser for the purpose of imaging small bioparticles carries the potential for structure determination at atomic resolution without the need for crystallization. In this study, experimental strategies for this idea are explored based on data collected at the Linac Coherent Light Source from 40 nm virus particles injected into a hard X-ray beam.
Scientific Data | 2016
Max F. Hantke; Dirk Hasse; Tomas Ekeberg; Katja John; Martin Svenda; Duane Loh; Andrew V. Martin; Nicusor Timneanu; Daniel S. D. Larsson; Gijs van der Schot; Gunilla H. Carlsson; Margareta Ingelman; Jakob Andreasson; Daniel Westphal; Bianca Iwan; Charlotte Uetrecht; Johan Bielecki; Mengning Liang; Francesco Stellato; Daniel P. DePonte; Sadia Bari; Robert Hartmann; Nils Kimmel; Richard A. Kirian; M. Marvin Seibert; Kerstin Mühlig; Sebastian Schorb; Ken R. Ferguson; Christoph Bostedt; Sebastian Carron
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.
Scientific Data | 2016
Gijs van der Schot; Martin Svenda; Filipe R. N. C. Maia; Max F. Hantke; Daniel P. DePonte; M. Marvin Seibert; Andrew Aquila; Joachim Schulz; Richard A. Kirian; Mengning Liang; Francesco Stellato; Sadia Bari; Bianca Iwan; Jakob Andreasson; Nicusor Timneanu; Johan Bielecki; Daniel Westphal; Francisca Nunes de Almeida; Duško Odić; Dirk Hasse; Gunilla H. Carlsson; Daniel S. D. Larsson; Anton Barty; Andrew V. Martin; Sebastian Schorb; Christoph Bostedt; John D. Bozek; Sebastian Carron; Ken R. Ferguson; Daniel Rolles
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.
Scientific Data | 2016
Tomas Ekeberg; Martin Svenda; M. Marvin Seibert; Chantal Abergel; Filipe R. N. C. Maia; Virginie Seltzer; Daniel P. DePonte; Andrew Aquila; Jakob Andreasson; Bianca Iwan; O Jonsson; Daniel Westphal; Duško Odić; Inger Andersson; Anton Barty; Meng Liang; Andrew V. Martin; Lars Gumprecht; Holger Fleckenstein; Sasa Bajt; Miriam Barthelmess; Nicola Coppola; Jean-Michel Claverie; N. Duane Loh; Christoph Bostedt; John D. Bozek; J. Krzywinski; Marc Messerschmidt; Michael J. Bogan; Christina Y. Hampton
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.
Optics Express | 2014
Asawari D. Rath; Nicusor Timneanu; Filipe R. N. C. Maia; Johan Bielecki; Holger Fleckenstein; Bianca Iwan; Martin Svenda; Dirk Hasse; Gunilla H. Carlsson; Daniel Westphal; Kerstin Mühlig; Max F. Hantke; Tomas Ekeberg; M. Marvin Seibert; Alessandro Zani; Mengning Liang; Francesco Stellato; Richard A. Kirian; Richard Bean; Anton Barty; Lorenzo Galli; Karol Nass; Miriam Barthelmess; Andrew Aquila; S. Toleikis; Rolf Treusch; Sebastian Roling; Michael Wöstmann; H. Zacharias; Henry N. Chapman
We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 10¹⁶W/cm² with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.
Nature Photonics | 2018
Tais Gorkhover; Anatoli Ulmer; Ken R. Ferguson; Max Bucher; Filipe R. N. C. Maia; Johan Bielecki; Tomas Ekeberg; Max F. Hantke; Benedikt J. Daurer; Carl Nettelblad; Jakob Andreasson; Anton Barty; Petr Bruza; Sebastian Carron; Dirk Hasse; J. Krzywinski; Daniel S. D. Larsson; Andrew J. Morgan; Kerstin Mühlig; Maria Müller; Kenta Okamoto; Alberto Pietrini; Daniela Rupp; Mario Sauppe; Gijs van der Schot; M. Marvin Seibert; Jonas A. Sellberg; Martin Svenda; M. Swiggers; Nicusor Timneanu
Ultrafast X-ray imaging on individual fragile specimens such as aerosols1, metastable particles2, superfluid quantum systems3 and live biospecimens4 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.Femtosecond X-ray Fourier holography imaging with record-high lateral resolution below 20 nm is demonstrated. Phase information is encoded into the interference of the diffraction patterns of a reference particle with a measurement sample.