scholarly journals Three-dimensional double helical DNA structure directly revealed from its X-ray fiber diffraction pattern by iterative phase retrieval

2018 ◽  
Vol 26 (23) ◽  
pp. 30991 ◽  
Author(s):  
Tatiana Latychevskaia ◽  
Hans-Werner Fink
IUCrJ ◽  
2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Hiroyuki Iwamoto

X-ray fiber diffraction is potentially a powerful technique to study the structure of fibrous materials, such as DNA and synthetic polymers. However, only rotationally averaged diffraction patterns can be recorded and it is difficult to correctly interpret them without the knowledge of esoteric diffraction theories. Here we demonstrate that, in principle, the non-rotationally averaged 3D structure of a fibrous material can be restored from its fiber diffraction pattern. The method is a simple puzzle-solving process and in ideal cases it does not require any prior knowledge about the structure, such as helical symmetry. We believe that the proposed method has a potential to transform the fiber diffraction to a 3D imaging technique, and will be useful for a wide field of life and materials sciences.


2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.


2017 ◽  
Vol 4 ◽  
Author(s):  
Emely L. Bortel ◽  
Max Langer ◽  
Alexander Rack ◽  
Jean-Baptiste Forien ◽  
Georg N. Duda ◽  
...  

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Longlong Wu ◽  
Shinjae Yoo ◽  
Ana F. Suzana ◽  
Tadesse A. Assefa ◽  
Jiecheng Diao ◽  
...  

AbstractAs a critical component of coherent X-ray diffraction imaging (CDI), phase retrieval has been extensively applied in X-ray structural science to recover the 3D morphological information inside measured particles. Despite meeting all the oversampling requirements of Sayre and Shannon, current phase retrieval approaches still have trouble achieving a unique inversion of experimental data in the presence of noise. Here, we propose to overcome this limitation by incorporating a 3D Machine Learning (ML) model combining (optional) supervised learning with transfer learning. The trained ML model can rapidly provide an immediate result with high accuracy which could benefit real-time experiments, and the predicted result can be further refined with transfer learning. More significantly, the proposed ML model can be used without any prior training to learn the missing phases of an image based on minimization of an appropriate ‘loss function’ alone. We demonstrate significantly improved performance with experimental Bragg CDI data over traditional iterative phase retrieval algorithms.


2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Shengkun Yao ◽  
Yunbing Zong ◽  
Jiadong Fan ◽  
Zhibin Sun ◽  
Huaidong Jiang

X-ray imaging techniques significantly advanced our understanding of materials and biology, among which phase contrast X-ray microscopy has obvious advantages in imaging biological specimens which have low contrast by conventional absorption contrast microscopy. In this paper, three-dimensional microstructure of arthropod with high contrast has been demonstrated by synchrotron X-ray in-line phase contrast tomography. The external morphology and internal structures of an earthworm were analyzed based upon tomographic reconstructions with and without phase retrieval. We also identified and characterized various fine structural details such as the musculature system, the digestive system, the nervous system, and the circulatory system. This work exhibited the high efficiency, high precision, and wide potential applications of synchrotron X-ray phase contrast tomography in nondestructive investigation of low-density materials and biology.


2020 ◽  
Author(s):  
M. Reichardt ◽  
C. Neuhaus ◽  
J-D. Nicolas ◽  
M. Bernhardt ◽  
K. Toischer ◽  
...  

ABSTRACTWe present a multi-scale imaging approach to characterize the structure of isolated adult murine cardiomyocytes based on a combination of full-field three-dimensional (3d) coherent x-ray imaging and scanning x-ray diffraction. Using these modalities, we probe the structure from the molecular to the cellular scale. Holographic projection images on freeze-dried cells have been recorded using highly coherent and divergent x-ray waveguide radiation. Phase retrieval and tomographic reconstruction then yield the 3d electron density distribution with a voxel size below 50 nm. In the reconstruction volume, myofibrils, sarcomeric organisation and mitochondria can be visualized and quantified within a single cell without sectioning. Next, we use micro-focusing optics by compound refractive lenses to probe the diffraction signal of the acto-myosin lattice. Comparison between recordings of chemically fixed and untreated, living cells indicate that the characteristic lattice distances shrink by approximately 10% upon fixation.SIGNIFICANCEDiffraction with synchrotron radiation has played an important role to decipher the molecular structure underlying force generation in muscle. In this work, the diffraction signal of the actomyosin contractile unit has for the first time been recorded from living cardiomyocytes, bringing muscle diffraction to the scale of single cells. In addition to scanning diffraction, we use coherent optics at the same synchrotron endstation to perform holographic imaging and tomography on a single cardiomyocyte. By this hard x-ray microscopy modality, we extend the length scales covered by scanning diffraction and reconstruct the electron density of an entire freeze-dried cardiomyocyte, visualizing the 3d architecture of myofibrils, sarcomers, and mitochondria with a voxel size below 50 nm.


A crystal consisting, as it does, of some molecular combination repeated as a unit at regular intervals in three directions in space can act as a three- dimensional diffraction grating. When monochromatic rays fall upon it, the scattered rays form a diffraction pattern, which can be derived by calculation from the diffraction formula. The pattern of ‘diffuse spots’ now under discussion agrees very closely, in fact within the errors of experiment so far made, with this calculated result. Either the conditions in the crystal which give rise to the diffuse spots are those which allow the diffraction pattern to be observed or they simulate them. This diffraction pattern differs from the diffraction effects so widely used in recent years in the examination of crystal structure. The Laue pattern of spots is not a true diffraction pattern because every spot in it is due to a different wave-length. In the examination of a crystal by an ionization spectrometer or in the oscillation photograph, the different spots are not observed simultaneously. In a true diffraction pattern all the spots or lines are due to monochromatic rays and are observed at one and the same time.


2008 ◽  
Vol 93 (15) ◽  
pp. 153901 ◽  
Author(s):  
S. C. Irvine ◽  
D. M. Paganin ◽  
S. Dubsky ◽  
R. A. Lewis ◽  
A. Fouras

2014 ◽  
Vol 21 (4) ◽  
pp. 774-783 ◽  
Author(s):  
A. A. Minkevich ◽  
M. Köhl ◽  
S. Escoubas ◽  
O. Thomas ◽  
T. Baumbach

The retrieval of spatially resolved atomic displacements is investigatedviathe phases of the direct(real)-space image reconstructed from the strained crystal's coherent X-ray diffraction pattern. It is demonstrated that limiting the spatial variation of the first- and second-order spatial displacement derivatives improves convergence of the iterative phase-retrieval algorithm for displacements reconstructions to the true solution. This approach is exploited to retrieve the displacement in a periodic array of silicon lines isolated by silicon dioxide filled trenches.


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