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Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2025年第4期81卷 196-206页

作者： Iwamoto, Hiroyuki Japan Synchrotron Radiat Res Inst Scattering & Imaging Div I-1-1 Kouto Sayo Hyogo 6795198 Japan

The contractile machinery of muscle, especially that of skeletal muscle, has a very regular array of contractile protein filaments, and gives rise to a complex and informative diffraction pattern when irradiated with X-rays. However, analyzing these diffraction patterns is often challenging because (i) only rotationally averaged diffraction patterns can be obtained, resulting in a substantial loss of information, and (ii) the contractile machinery contains two different sets of protein filaments (actin and myosin) with different helical symmetries. The reflections originating from them often overlap. These problems may be solved if the real-space 3D structure of the contractile machinery is directly calculated from the diffraction pattern. Here, we demonstrate that by using the conventional phase-retrieval algorithm (hybrid input-output), the real-space 3D structure of the contractile machinery can be effectively restored from a single rotationally averaged 2D diffraction pattern. In this calculation, we used an in silico model of insect flight muscle, which is known for its highly regular structure. We also extended this technique to an experimentally recorded muscle diffraction pattern.

关键词： X-ray fiber diffraction coherent diffractive imaging hybrid input-output algorithm insect flight muscle

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Ciphertext-only attack on optical scanning cryptography

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OPTICS AND LASERS IN ENGINEERING 2020年 126卷 105901-000页

作者： Chang, Xiangyu Yan, Aimin Zhang, Hongbo Shanghai Normal Univ Coll Math & Sci Shanghai 200234 Peoples R China Virginia Mil Inst Dept Comp & Informat Sci Lexington VA 24450 USA

The optical scanning cryptography (OSC) is one of the most utilized optical encryption systems. Our research is inspired from the observation that there is a linear system property within the ciphertext expression equation of OSC. Given the linear system property, it is feasible to recover the plaintext with cipher-only attack (COA). Our proposed COA method converts the problem of COA into a phase retrieval problem with a single intensity measurement. With the frequency domain constraint and the object domain support obtained from the ciphertext of OSC, the hybrid input-output (HIO) algorithm can be used to recover plaintext. Simulation results demonstrate the feasibility and robustness of the attack. This shows for the first time that the OSC scheme is vulnerable to COA attack.

关键词： Ciphertext-only attack Optical scanning cryptography (OSC) hybrid input-output algorithm

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Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

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ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016年第5期72卷 539-547页

作者： He, Hongxing Fang, Hengrui Miller, Mitchell D. Phillips, George N., Jr. Su, Wu-Pei Univ Houston Dept Phys Houston TX 77204 USA Univ Houston Texas Ctr Superconduct Houston TX 77204 USA Rice Univ Dept Biosci Houston TX 77005 USA Rice Univ Dept Chem POB 1892 Houston TX 77005 USA Univ Wisconsin Dept Biochem Madison WI 53706 USA

An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.

关键词： molecular replacement hybrid input-output algorithm ab initio phasing protein crystallography

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Direct phasing of protein crystals with high solvent content

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ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2015年第1期71卷 92-98页

作者： He, Hongxing Su, Wu-Pei Univ Houston Dept Phys Houston TX 77204 USA Univ Houston Texas Ctr Superconduct Houston TX 77204 USA

An iterative transform method is proposed for solving the phase problem in protein crystallography. In each iteration, a weighted average electron-density map is constructed to define an estimated protein mask. Solvent flattening is then imposed through the hybrid input-output algorithm [Fienup (1982). Appl. Opt. 21, 2758-2769]. Starting from random initial phases, after thousands of iterations the mask evolves into the correct shape and the phases converge to the correct values with an average error of 30-40 degrees for high-resolution data for several protein crystals with high solvent content. With the use of non-crystallographic symmetry, the method could potentially be extended to phase protein crystals with less than 50% solvent fraction. The new phasing algorithm can supplement and enhance the traditional refinement tools. (C) 2015 International Union of Crystallography

关键词： ab initio phasing protein crystallography hybrid input-output algorithm solvent flattening

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Effects of Aberrations on Image Reconstruction of Data from hybrid Intensity Interferometers

Effects of Aberrations on Image Reconstruction of Data from ...

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Conference on Multisensor, Multisource Information Fusion - Architectures, algorithms, and Applications

作者： Murray-Krezan, Jeremy Crabtree, Peter N. USAF Res Lab Kirtland AFB NM 87117 USA

ISBN: (纸本)9780819490858

Intensity interferometery (II) holds tremendous potential for remote sensing of space objects. We investigate the properties of a hybrid intensity interferometer concept where information from an II is fused with information from a traditional imaging telescope. Although not an imager, hybrid intensity interferometery measurements can be used to reconstruct an image. In previous work we investigated the effects of poor SNR on this image formation process. In this work, we go beyond the obviously deleterious effects of SNR, to investigate reconstructed image quality as a function of the chosen support constraint, and the resultant image quality issues. The benefits to fusion of assumed perfect-yet-partial a priori information with traditional intensity interferometery measurements are explored and shown to result in increased sensitivity and improved reconstructed-image quality.

关键词： Phase retrieval hybrid input-output algorithm intensity interferometry computational imaging

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A study of image quality for imagery generated by standard and hybrid intensity interferometers

A study of image quality for imagery generated by standard a...

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Conference on Sensors and Systems for Space Applications IV

作者： Murray-Krezan, Jeremy Crabtree, Peter N. Picard, Richard H. USAF Res Lab 3550 Aberdeen Ave SE Kirtland AFB NM 87117 USA US Air Force Hanscom AFB MA 01731 USA

ISBN: (纸本)9780819486189

关键词： Phase retrieval hybrid input-output algorithm intensity interferometry computational imaging

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A Study of Image Reconstruction algorithms for hybrid Intensity Interferometers

A Study of Image Reconstruction Algorithms for Hybrid Intens...

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Conference on Unconventional Imaging, Wavefront Sensing, and Adaptive Coded Aperture Imaging and Non-Imaging Sensor Systems

作者： Crabtree, Peter N. Murray-Krezan, Jeremy Picard, Richard H. USAF Res Lab 3550 Aberdeen Ave SE Kirtland AFB NM 87117 USA US Air Force AF Res Lab Bedford MA 01731 USA

ISBN: (纸本)9780819487759

Phase retrieval is explored for image reconstruction using outputs from both a simulated intensity interferometer (II) and a hybrid system that combines the II outputs with partially resolved imagery from a traditional imaging telescope. Partially resolved imagery provides an additional constraint for the iterative phase retrieval process, as well as an improved starting point. The benefits of this additional a priori information are explored and include lower residual phase error for SNR values above 0.01, increased sensitivity, and improved image quality. Results are also presented for image reconstruction from II measurements alone, via current state-of-the-art phase retrieval techniques. These results are based on the standard hybrid input-output (HIO) algorithm, as well as a recent enhancement to HIO that optimizes step lengths in addition to step directions. The additional step length optimization yields a reduction in residual phase error, but only for SNR values greater than about 10. Image quality for all algorithms studied is quite good for SNR >= 10, but it should be noted that the studied phase-recovery techniques yield useful information even for SNRs that are much lower.

关键词： Phase retrieval hybrid input-output algorithm saddle-point optimization intensity interferometry computational imaging data fusion

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3D Reconstruction of 2D Crystals 11

3D Reconstruction of 2D Crystals

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49th Annual Association-for-Computing-Machinery (ACM) Southeast Conference (ACMSE)

作者： Zeng, Xiangyan Glover, James Ervin Hughes, Owen Stahlberg, Henning Ft Valley State Univ 1005 State Univ Dr Ft Valley GA 31030 USA Eon Corp Davis CA 95616 USA Univ Basel CH-4058 Basel Switzerland

ISBN: (纸本)9781450306867

High Resolution three-dimensional (3D) reconstruction of several proteins has been achieved from two-dimensional (2D) crystals by electron crystallography structure determination. However, for badly ordered 2D crystals, especially non-flat crystals, Fourierfiltering based methods fail, while single particle processing approaches can produce reconstructions of superior resolution by aligning particles in 3D space. We have investigated a single particle processing approach combined with the crystallographic method to generate images centered on the unit cells of 2D crystal images. The implemented software uses the predictive lattice node tracking in 2dx/ MRC software to extract particles from the microscope images. These particles are then subjected to a local contrast transfer function (CTF) correction. The tilt geometry obtained in the 2dx software is used to initialize the Euler angles, which along with translations are then refined by a single particle processing approach. Finally, iterative transform algorithms, namely the error reduction algorithm and the hybrid input-output algorithm, are applied to retrieve missing information in the previously obtained 3D reconstruction. Compared with conventional single particle processing for randomly oriented particles, the required computational costs are greatly reduced as the 2D crystals restrict the parameter search space. Preliminary results from a 3D reconstruction of the membrane protein GlpF suggest that the iterative transform process improves 3D resolution.

关键词： 3D reconstruction electron crystallography single particle processing error reduction algorithm hybrid input-output algorithm

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Determination of polymer morphology from the intensity measurement in the reciprocal space

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EUROPEAN POLYMER JOURNAL 2010年第9期46卷 1891-1895页

作者： Situ, Guohai Yan, Li-Tang Univ Stuttgart Inst Tech Opt D-70569 Stuttgart Germany Univ Bayreuth D-95440 Bayreuth Germany Univ Pittsburgh Dept Chem Engn Pittsburgh PA 15261 USA

Reciprocal space techniques based on scattering have been widely used for structure analysis of polymer materials. It would be more useful if the reciprocal methods can determine simultaneously the morphology of the polymer as those in the real space. However, the inverse problem, i.e., determining polymer morphology from the available scattering pattern, is very difficult because of the absence of the relative phase spectrum in the experimental measurements. Therefore, the retrieval of the missing phase spectrum plays a crucial role in this problem. Herein we theoretically propose that this can be accomplished by using phase-spectrum retrieval technique. We combined the Gerchberg-Saxton and hybrid input-output algorithms to determine the morphology of block copolymers from the corresponding scattering patterns in the reciprocal space. Numerical computations have been carried out to demonstrate the concept. It has also been shown that the algorithm is immune to noise. The demonstrated method could provide an extensive methodology for the investigation of polymer behaviors in the micro- and nano-scales by interconnecting real and reciprocal spaces. (C) 2010 Elsevier Ltd. All rights reserved.

关键词： Phase-spectrum retrieval technique Polymer morphology hybrid input-output algorithm Reciprocal space

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Preliminary Studies on Iterative Transform algorithms for 3D Reconstruction of 2D Crystals

Preliminary Studies on Iterative Transform Algorithms for 3D...

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The 2nd International Conference on Software Engineering and Data Mining(IEEE 第二届国际软件工程和数据挖掘学术大会 SEDM 2010)

作者： Xiangyan Zeng Yen-Wei Chen Owen Hughes Henning Stahlberg Department of Mathematics and Computer Science Fort Valley State University Fort Valley GA 31030. U College of Information Science and Engineering Ritsumeikan University Shiga 525-8577Japan Eon Corporation Davis CA 95616USA Center for Cellular Imaging and Nanoanalytics University Basel CH-4058 Basel Switzerland

ISBN: (纸本)9781424473243;9788988678220;9788988678213

In this paper, we apply iterative transform algorithms,namely the error reduction algorithm and the hybrid input-output algorithm, to retrieve missing data in 3D reconstruction from 2D crystal images. 3D protein structures are determined using cryo-electron microscopy (cryo-EM). Extremely strong noise in cryo-EM brings in unreliable artifacts and a limited number of projections leave missing components in 3D Fourier space. We consider all these cases as missing data problems. The iterative transform algorithms aim at improving 3D resolution through applying constraints in Fourier space and real space. In Fourier space, the “true” signal components, which are either physically measured or assumed, are retained while the delusive components are updated iteratively. In real space, the protein has spatial limitation or “finite support” and possesses non-negativity values. Preliminary results of 3D reconstruction of membrane protein GlpF suggest that the iterative transform process improves 3D resolution.

关键词： 3D reconstruction cryo-electron microscopy error reduction algorithm hybrid input-output algorithm

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