Phase retrieval from single biomolecule diffraction pattern

Ikeda, Shiro; Kono, Hidetoshi

doi:10.1364/oe.20.003375

Cited by 14 publications

(8 citation statements)

References 20 publications

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“…In this study, we used the gradient search method (Fienup & Wackerman, 1986) and accounted for the missing region of the detector and the small number of photons, as described in previous work (Ikeda & Kono, 2012), and combined this method with an initial estimate of the structure.…”

Section: Refinement Methodsmentioning

confidence: 99%

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Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

Nishiyama

Niozu

Bostedt

et al. 2020

IUCrJ

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With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power.

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Section: Refinement Methodsmentioning

confidence: 99%

“…We carried out optimization of the Poisson likelihood with a conventional gradient descent method. The gradient of the Poisson likelihood function is expressed as follows (Ikeda & Kono, 2012),…”

Section: Refinement Methodsmentioning

confidence: 99%

Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

Nishiyama

Niozu

Bostedt

et al. 2020

IUCrJ

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“…When diffraction patterns in smaller angle are available, we would expect substantial increase in the reliability of phase-retrieved images. In addition to X-ray optics, phase-retrieval algorithm such as the darkfield phase-retrieval method 54 and the sparse phase retrieval method based on the Bayesian statistics 55 will contribute to determine the support shape for HIO-SW calculation. In our experience, the appropriate support shape leads to fast and efficient convergence of electron density map in HIO-SW calculation.…”

Section: A On the Performance Of Kotobuki-1 In Synchrotron Cxdimentioning

confidence: 99%

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

Nakasako,

Takayama,

Oroguchi

et al. 2013

Review of Scientific Instruments

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We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.

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“…Next, the relative orientations of the 2329-7778/2015/2(4)/041702/11 V C Author(s) 2015 2, 041702-1 different images is determined, so that the 3D intensity distribution of the particle can be obtained. 5,6 The 3D electron density of the molecule is obtained from the 3D diffraction pattern with the help of a phase retrieval method. An important parameter of the problem is the number of scattered photons per effective Shannon pixel.…”

Section: Introduction and Requirementsmentioning

confidence: 99%

Advanced source apportionment of size-resolved trace elements at multiple sites in London during winter

Visser¹,

Slowik²,

Furger³

et al. 2015

Preprint

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Abstract. Trace element measurements in PM10–2.5, PM2.5–1.0 and PM1.0–0.3 aerosol were performed with 2 h time resolution at kerbside, urban background and rural sites during the ClearfLo winter 2012 campaign in London. The environment-dependent variability of emissions was characterized using the Multilinear Engine implementation of the Positive Matrix Factorization model, conducted on datasets comprising all three sites but segregated by size. Combining the sites enabled separation of sources with high temporal covariance but significant spatial variability. Separation of sizes improved source resolution by preventing sources occurring in only a single size fraction from having too small a contribution for the model to resolve. Anchor profiles were retrieved internally by analysing data subsets, and these profiles were used in the analyses of the complete datasets of all sites for enhanced source apportionment. A total of nine different factors was resolved (notable elements in brackets): in PM10–2.5 brake wear (Cu, Zr, Sb, Ba), other traffic-related (Fe), resuspended dust (Si, Ca), sea/road salt (Cl), aged sea salt (Na, Mg) and industrial (Cr, Ni); in PM2.5–1.0 brake wear, other traffic-related, resuspended dust, sea/road salt, aged sea salt and S-rich (S); and in PM1.0–0.3 traffic-related (Fe, Cu, Zr, Sb, Ba), resuspended dust, sea/road salt, aged sea salt, reacted Cl (Cl), S-rich and solid fuel (K, Pb). Human activities enhance the kerb-to-rural concentration gradients of coarse aged sea salt, typically considered to have a natural source, by 1.7–2.2. These site-dependent concentration differences reflect the effect of local resuspension processes in London. The anthropogenically-influenced factors traffic (brake wear and other traffic-related processes), dust and sea/road salt provide further kerb-to-rural concentration enhancements by direct source emissions by a factor of 3.5–12.7. The traffic and dust factors are mainly emitted in PM10–2.5 and show strong diurnal variations with concentrations up to four times higher during rush hour than during night-time. Regionally-influenced S-rich and solid fuel factors, occurring primarily in PM1.0–0.3, have negligible resuspension influences, and concentrations are similar throughout the day and across the regions.

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Phase retrieval from single biomolecule diffraction pattern

Cited by 14 publications

References 20 publications

Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

Advanced source apportionment of size-resolved trace elements at multiple sites in London during winter

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