| 1. |
- Andreasson, Jakob, et al.
(author)
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Automated identification and classification of single particle serial femtosecond X-ray diffraction data
- 2014
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In: Optics Express. - 1094-4087. ; 22:3, s. 2497-2510
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Journal article (peer-reviewed)abstract
- The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of America
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| 2. |
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| 3. |
- Ayyer, Kartik, et al.
(author)
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3D diffractive imaging of nanoparticle ensembles using an x-ray laser
- 2021
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In: Optica. - : Optical Society of America. - 2334-2536. ; 8:1, s. 15-23
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Journal article (peer-reviewed)abstract
- 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.
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| 4. |
- Barty, A., et al.
(author)
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Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements
- 2012
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In: Nature Photonics. - 1749-4885 .- 1749-4893. ; 6:1, s. 35-40
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Journal article (peer-reviewed)abstract
- X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1, 2, 3, 4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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| 5. |
- Bellisario, Alfredo
(author)
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Deep learning assisted phase retrieval and computational methods in coherent diffractive imaging
- 2024
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Doctoral thesis (other academic/artistic)abstract
- In recent years, advances in Artificial Intelligence and experimental techniques have revolutionized the field of structural biology. X-ray crystallography and Cryo-EM have provided unprecedented insights into the structures of biomolecules, while the unexpected success of AlphaFold has opened up new avenues of investigation. However, studying the dynamics of proteins at high resolution remains a significant obstacle, especially for fast dynamics. Single-particle imaging (SPI) or Flash X-ray Imaging (FXI) is an emerging technique that may enable the mapping of the conformational landscape of biological molecules at high resolution and fast time scale. This thesis discusses the potential of SPI/FXI, its challenges, recent experimental successes, and the advancements driving its development. In particular, machine learning and neural networks could play a vital role in fostering data analysis and improving SPI/FXI data processing. In Paper I, we discuss the problem of noise and detector masks in collecting FXI data. I simulated a dataset of diffraction patterns and used it to train a Convolutional Neural Network (U-Net) to restore data by denoising and filling in detector masks. As a natural continuation of this work, I trained another machine learning model in Paper II to estimate 2D protein densities from diffraction intensities. In the final chapter, corresponding to Paper III, we discuss another experimental method, time-resolved Small Angle X-ray Scattering (SAXS), and a new algorithm recently developed for SAXS data, the DENsity from Solution Scattering (DENSS) algorithm. I discuss the potential of DENSS in time-resolved SAXS and its application for structural fitting of AsLOV2, a Light-Oxygen-Voltage (LOV) protein domain from Avena sativa.
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| 6. |
- Bellisario, Alfredo, et al.
(author)
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Deep learning phase retrieval in X-ray single-particle imaging and object support from autocorrelations
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Other publication (other academic/artistic)abstract
- Phase retrieval is an important optimization problem that occurs, for example, in the analysis of coherent diffraction patterns from isolated proteins. All iterative algorithms employed for phase retrieval in this context require some a priori knowledge of the object, usually in the form of a support that describes the extent of the particle. Phase retrieval is a time-consuming task that can often fail, particularly if the support is too loose or of bad quality. In this paper, we present a neural network that can produce low-resolution estimates of the phased object in a fraction of the time that it takes for a full phase retrieval and that can also successfully be used as support for further analysis. Our network is trained on simulated data from biological macromolecules and is thus tailored to the type of data seen in a typical CDI experiment. Other approaches to support finding either require very accurate data without missing regions or require the full phase-retrieval algorithm to be run for a long time. Our network could both speed up off-line analysis, and provide real-time feedback during data collection.
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| 7. |
- Bellisario, Alfredo, et al.
(author)
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Noise reduction and mask removal neural network for X-ray single-particle imaging
- 2022
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In: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55, s. 122-132
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Journal article (peer-reviewed)abstract
- 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.
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| 8. |
- Daurer, Benedikt J.
(author)
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Algorithms for Coherent Diffractive Imaging with X-ray Lasers
- 2017
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Doctoral thesis (other academic/artistic)abstract
- Coherent diffractive imaging (CDI) has become a very popular technique over the past two decades. CDI is a "lensless" imaging method which replaces the objective lens of a conventional microscope by a computational image reconstruction procedure. Its increase in popularity came together with the development of X-ray free-electron lasers (XFELs) which produce extremely bright and coherent X-rays. By facilitating these unique properties, CDI enables structure determination of non-crystalline samples at nanometre resolution and has many applications in structural biology, material science and X-ray optics among others. This work focuses on two specific CDI techniques, flash X-ray diffractive imaging (FXI) on biological samples and X-ray ptychography.While the first FXI demonstrations using soft X-rays have been quite promising, they also revealed remaining technical challenges. FXI becomes even more demanding when approaching shorter wavelengths to allow subnanometre resolution imaging. We described one of the first FXI experiments using hard X-rays and characterized the most critical components of such an experiment, namely the properties of X-ray focus, sample delivery and detectors. Based on our findings, we discussed experimental and computational strategies for FXI to overcome its current difficulties and reach its full potential. We deposited the data in the Coherent X-ray Database (CXIDB) and made our data analysis code available in a public repository. We developed algorithms targeted towards the needs of FXI experiments and implemented a software package which enables the analysis of diffraction data in real time.X-ray ptychography has developed into a very useful tool for quantitative imaging of complex materials and has found applications in many areas. However, it involves a computational reconstruction step which can be slow. Therefore, we developed a fast GPU-based ptychographic solver and combined it with a framework for real-time data processing which already starts the ptychographic reconstruction process while data is still being collected. This provides immediate feedback to the user and allows high-throughput ptychographic imaging.Finally, we have used ptychographic imaging as a method to study the wavefront of a focused XFEL beam under typical FXI conditions. We are convinced that this work on developing strategies and algorithms for FXI and ptychography is a valuable contribution to the development of coherent diffractive imaging.
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| 9. |
- Daurer, Benedikt J., et al.
(author)
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Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
- 2017
-
In: IUCrJ. - : INT UNION CRYSTALLOGRAPHY. - 2052-2525. ; 4, s. 251-262
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Journal article (peer-reviewed)abstract
- This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of similar to 40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from similar to 35 to similar to 300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 * 10(12) photons per mu m(2) per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
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| 10. |
- Daurer, Benedikt J., et al.
(author)
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Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
- 2021
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In: Optica. - : Optical Society of America. - 2334-2536. ; 8:4, s. 551-562
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Journal article (peer-reviewed)abstract
- 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.
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| 11. |
- Daurer, Benedikt J, et al.
(author)
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Wavefront sensing of individual XFEL pulses using ptychography
-
Other publication (other academic/artistic)abstract
- The characterization of the wavefront dynamics is important for many X-ray free-electron laser (XFEL) experiments, in particular for coherent diffractive imaging (CDI), as the reconstructed image is always the product of the incoming wavefront with the object. An accurate understanding of the wavefront is also important for any experiment wishing to achieve peak power densities, making use of the tightest possible focal spots. With the use of ptychography we demonstrate high-resolution imaging of the Linac Coherent Light Source (LCLS) beam focused at the endstation for Atomic, Molecular and Optical (AMO) experiments, including its phase and intensity at every plane along its propagation axis, for each individual pulse. Using a mixed-state approach, we have reconstructed the most dominant beam components that constitute an ensemble of pulses, and from the reconstructed components determined their respective contribution in each of the individual pulses. This enabled us to obtain complete wavefront information about each individual pulse. We hope that our findings aid interpretation of data from past and future LCLS experiments and we propose this method to be used routinely for XFEL beam diagnostics.
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| 12. |
- Ekeberg, Tomas, 1983-, et al.
(author)
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Data requirements for single-particle diffractive imaging
-
Other publication (other academic/artistic)abstract
- Single-shot diffractive imaging with ultra-short and very intense coherent X-ray pulses has become a routine experimental technique at new free-electron-laser facilities. Extension to three-dimensional imaging requires many diffraction pat- terns from identical objects captured in different orientations. These can then be combined into a full three-dimensional Fourier transform of the object. The ori- entation of the particle intercepted by the pulsed X-ray beam is usually unknown. This makes it hard to predict the number of patterns required to fully cover the Fourier space. In this paper we provide formulae to estimate the number of expo- sures required to achieve a given coverage of Fourier space as a function of parti- cle size, resolution and shot noise.
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| 13. |
- Ekeberg, Tomas, 1983-
(author)
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Flash Diffractive Imaging in Three Dimensions
- 2012
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Doctoral thesis (other academic/artistic)abstract
- During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers.These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus.We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient.Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.
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| 14. |
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| 15. |
- Ekeberg, Tomas, et al.
(author)
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Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters
- 2015
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In: The international journal of high performance computing applications. - : SAGE Publications. - 1094-3420 .- 1741-2846. ; 29, s. 233-243
-
Journal article (peer-reviewed)abstract
- The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a beam of streaming particles to be intercepted and hit by an ultrashort high-energy X-ray beam. Through machine learning methods the data thus collected can be transformed into a three-dimensional volumetric intensity map of the particle itself. The computational complexity associated with this problem is very high such that clusters of data parallel accelerators are required. We have implemented a distributed and highly efficient algorithm for the inversion of large collections of diffraction patterns targeting clusters of hundreds of GPUs. With the expected enormous amount of diffraction data to be produced in the foreseeable future, this is the required scale to approach real-time processing of data at the beam site. Using both real and synthetic data we look at the scaling properties of the application and discuss the overall computational viability of this exciting and novel imaging technique.
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| 16. |
- Ekeberg, Tomas, 1983-, et al.
(author)
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Observation of a single protein by ultrafast X-ray diffraction
- 2024
-
In: Light. - : Springer Nature. - 2095-5545 .- 2047-7538. ; 13:1
-
Journal article (peer-reviewed)abstract
- 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.
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| 17. |
- Ekeberg, Tomas, et al.
(author)
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Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
- 2016
-
In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
-
Journal article (peer-reviewed)abstract
- 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.
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| 18. |
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| 19. |
- Ekeberg, Tomas, 1983-, et al.
(author)
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Three-dimensional structure determination with an X-ray laser
-
Other publication (other academic/artistic)abstract
- Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus.
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| 20. |
- Gorkhover, Tais, et al.
(author)
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Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
- 2018
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In: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 12:3, s. 150-153
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Journal article (peer-reviewed)abstract
- 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 defined 4,5 . 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.
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| 21. |
- Hantke, Max F., et al.
(author)
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A data set from flash X-ray imaging of carboxysomes
- 2016
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
-
Journal article (peer-reviewed)abstract
- 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.
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| 22. |
- Hantke, Max F., et al.
(author)
-
Condor : a simulation tool for flash X-ray imaging
- 2016
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In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 1356-1362
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Research review (peer-reviewed)abstract
- Flash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.
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| 23. |
- Hantke, Max F., et al.
(author)
-
High-throughput imaging of heterogeneous cell organelles with an X-ray laser
- 2014
-
In: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 8:12, s. 943-949
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Journal article (peer-reviewed)abstract
- We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.
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| 24. |
- Johansson, Linda C, 1983, et al.
(author)
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Lipidic phase membrane protein serial femtosecond crystallography.
- 2012
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In: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265
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Journal article (peer-reviewed)abstract
- X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
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| 25. |
- Kamae, Tuneyoshi, et al.
(author)
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PoGOLite - A high sensitivity balloon-borne soft gamma-ray polarimeter
- 2008
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In: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 30:2, s. 72-84
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Journal article (peer-reviewed)abstract
- We describe a new balloon-borne instrument (PoGOLite) capable of detecting 10% polarisation from 200 mCrab point-like sources between 25 and 80 keV in one 6-h flight. Polarisation measurements in the soft gamma-ray band are expected to provide a powerful probe into high energy emission mechanisms as well as the distribution of magnetic fields, radiation fields and interstellar matter. Synchrotron radiation, inverse Compton scattering and propagation through high magnetic fields are likely to produce high degrees of polarisation in the energy band of the instrument. We demonstrate, through tests at accelerators, with radioactive sources and through computer simulations, that PoGOLite will be able to detect degrees of polarisation as predicted by models for several classes of high energy sources. At present, only exploratory polarisation measurements have been carried out in the soft gamma-ray band. Reduction of the large background produced by cosmic-ray particles while securing a large effective area has been the greatest challenge. PoGOLite uses Compton scattering and photo-absorption in an array of 217 well-type phoswich detector cells made of plastic and BGO scintillators surrounded by a BGO anticoincidence shield and a thick polyethylene neutron shield. The narrow Held of view (FWHM = 1.25 msr, 2.0 deg x 2.0 deg) obtained with detector cells and the use of thick background shields warrant a large effective area for polarisation measurements (similar to 228 cm(2) at E = 40 keV) without sacrificing the signal-to-noise ratio. Simulation studies for an atmospheric overburden of 3-4 g/cm(2) indicate that neutrons and gamma-rays entering the PDC assembly through the shields are dominant backgrounds. Off-line event selection based on recorded phototube waveforms and Compton kinematics reduce the background to that expected for a similar to 100 mCrab source between 25 and 50 keV. A 6-h observation of the Crab pulsar will differentiate between the Polar Cap/Slot Gap, Outer Gap, and Caustic models with greater than 5 sigma significance; and also cleanly identify the Compton reflection component in the Cygnus X-1 hard state. Long-duration flights will measure the dependence of the polarisation across the cyclotron absorption line in Hercules X-1. A scaled-down instrument will be flown as a pathfinder mission from the north of Sweden in 2010. The first science flight is planned to take place shortly thereafter.
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