1. |
- Andreasson, Jakob, et al.
(författare)
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Automated identification and classification of single particle serial femtosecond X-ray diffraction data
- 2014
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Ingår i: Optics Express. - 1094-4087. ; 22:3, s. 2497-2510
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Tidskriftsartikel (refereegranskat)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. |
- Aquila, Andrew, et al.
(författare)
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Time-resolved protein nanocrystallography using an X-ray free-electron laser
- 2012
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Ingår i: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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3. |
- Awel, Salah, et al.
(författare)
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Optical bunching of particles in a liquid flow
- 2021
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Ingår i: Optics Express. - : Optical Society of America. - 1094-4087. ; 29:21, s. 34394-34410
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Tidskriftsartikel (refereegranskat)abstract
- High-speed liquid micro-jets are used to rapidly and repeatedly deliver protein microcrystals to focused and pulsed X-ray beams in the method of serial femtosecond crystallography. However, the current continuous flow of crystals is mismatched to the arrival of X-ray pulses, wasting vast amounts of an often rare and precious sample. Here, we introduce a method to address this problem by periodically trapping and releasing crystals in the liquid flow, creating locally concentrated crystal bunches, using an optical trap integrated in the microfluidic supply line. We experimentally demonstrate a 30-fold increase of particle concentration into 10 Hz bunches of 6.4 tm diameter polystyrene particles. Furthermore, using particle trajectory simulations, a comprehensive description of the optical bunching process and parameter space is presented. Adding this compact optofluidics device to existing injection systems would thereby dramatically reduce sample consumption and extend the application of serial crystallography to a greater range of protein crystal systems that cannot be produced in high abundance. Our approach is suitable for other microfluidic systems that require synchronous measurements of flowing objects. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
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4. |
- Caleman, Carl, et al.
(författare)
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Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
- 2015
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Ingår i: Optics Express. - 1094-4087. ; 23:2, s. 1213-1231
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Tidskriftsartikel (refereegranskat)abstract
- In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.
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5. |
- Chalupsky, J., et al.
(författare)
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Characteristics of focused soft X-ray free-electron laser beam determined by ablation of organic molecular solids
- 2007
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Ingår i: Optics Express. - 1094-4087. ; 15:10, s. 6036-6043
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Tidskriftsartikel (refereegranskat)abstract
- A linear accelerator based source of coherent radiation, FLASH (Free-electron LASer in Hamburg) provides ultra-intense femtosecond radiation pulses at wavelengths from the extreme ultraviolet (XUV; lambda< 100nm) to the soft X-ray (SXR; lambda<30nm) spectral regions. 25-fs pulses of 32-nm FLASH radiation were used to determine the ablation parameters of PMMA - poly ( methyl methacrylate). Under these irradiation conditions the attenuation length and ablation threshold were found to be (56.9 +/- 7.5) nm and similar to 2 mJ center dot cm(-2), respectively. For a second wavelength of 21.7 nm, the PMMA ablation was utilized to image the transverse intensity distribution within the focused beam at mu m resolution by a method developed here.
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6. |
- Chalupsky, J, et al.
(författare)
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Non-thermal desorption/ablation of molecular solids induced by ultra-short soft x-ray pulses
- 2009
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Ingår i: Optics Express. - 1094-4087. ; 17:1, s. 208-217
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Tidskriftsartikel (refereegranskat)abstract
- We report the first observation of single-shot soft x-ray laser induced desorption occurring below the ablation threshold in a thin layer of poly ( methyl methacrylate) - PMMA. Irradiated by the focused beam from the Free-electron LASer in Hamburg ( FLASH) at 21.7nm, the samples have been investigated by atomic-force microscope (AFM) enabling the visualization of mild surface modifications caused by the desorption. A model describing non-thermal desorption and ablation has been developed and used to analyze single-shot imprints in PMMA. An intermediate regime of materials removal has been found, confirming model predictions. We also report below-threshold multiple-shot desorption of PMMA induced by high-order harmonics (HOH) at 32nm. Short-time exposure imprints provide sufficient information about transverse beam profile in HOH's tight focus whereas long-time exposed PMMA exhibits radiation-initiated surface hardening making the beam profile measurement infeasible. (C) 2008 Optical Society of America
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7. |
- Chlouba, Tomas, et al.
(författare)
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Diamond-based dielectric laser acceleration
- 2022
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Ingår i: Optics Express. - 1094-4087. ; 30:1, s. 505-510
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Tidskriftsartikel (refereegranskat)abstract
- The field of dielectric laser accelerators (DLA) garnered a considerable interest in the past six years as it offers novel opportunities in accelerator science and potentially transformative applications. Currently, the most widespread approach considers silicon-based structures due to their low absorption and high refractive index in the infrared spectral region and the well-developed silicon processing technology. In this paper we investigate a diamond as an alternative to silicon, mainly due to its considerably higher damage threshold. In particular, we find that our diamond grating allows a three times higher acceleration gradient (60 MeV/m) compared to silicon gratings designed for a similar electron energy. Using more complex geometries, GeV/m acceleration gradients are within reach for subrelativistic electrons.
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8. |
- Forsberg, Pontus, 1981-, et al.
(författare)
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Inclined surfaces in diamond : broadband antireflective structures and coupling light through waveguides
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:3, s. 2693-2700
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Tidskriftsartikel (refereegranskat)abstract
- Control of the sidewall angle of diamond microstructures was achieved by varying the gas mixture, bias power and mask shape during inductively coupled plasma etching. Different etch mechanisms were responsible for the angle of the lower and upper part of the sidewall formed during diamond etching. These angles could to some extent be controlled separately. The developed etch process was used to fabricate wideband antireflective structures with an average transmission of 96.4% for wavelengths between 10 and 50 mu m. Smooth facetted edges for coupling light through waveguides from above were also demonstrated.
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9. |
- Fredenberg, Erik, PhD, 1979-, et al.
(författare)
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A low-absorption x-ray energy filter for small-scale applications
- 2009
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Ingår i: Optics Express. - : The Optical Society. - 1094-4087. ; 17:14, s. 11388-11398
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Tidskriftsartikel (refereegranskat)abstract
- We present an experimental and theoretical evaluation of an x-ray energy filter based on the chromatic properties of a prism-array lens (PAL). It is intended for small-scale applications such as medical imaging. The PAL approximates a Fresnel lens and allows for high efficiency compared to filters based on ordinary refractive lenses, however at the cost of a lower energy resolution. Geometrical optics was found to provide a good approximation for the performance of a flawless lens, but a field-propagation model was used for quantitative predictions. The model predicted a 0.29 ΔE/E energy resolution and an intensity gain of 6.5 for a silicon PAL at 23.5 keV. Measurements with an x-ray tube showed good agreement with the model in energy resolution and peak energy, but a blurred focal line contributed to a 29% gain reduction. We believe the blurring to be caused mainly by lens imperfections, in particular at the periphery of the lens.
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10. |
- Ge, X., et al.
(författare)
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Impact of wave front and coherence optimization in coherent diffractive imaging
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:9, s. 11441-11447
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Tidskriftsartikel (refereegranskat)abstract
- We present single shot nanoscale imaging using a table-top femtosecond soft X-ray laser harmonic source at a wavelength of 32 nm. We show that the phase retrieval process in coherent diffractive imaging critically depends on beam quality. Coherence and image fidelity are measured from single-shot coherent diffraction patterns of isolated nano-patterned slits. Impact of flux, wave front and coherence of the soft X-ray beam on the phase retrieval process and the image quality are discussed. After beam improvements, a final image reconstruction is presented with a spatial resolution of 78 nm (half period) in a single 20 fs laser harmonic shot.
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