Literature DB >> 22714310

The symmetries of image formation by scattering. II. Applications.

Peter Schwander1, Dimitrios Giannakis, Chun Hong Yoon, Abbas Ourmazd.   

Abstract

We show that the symmetries of image formation by scattering enable graph-theoretic manifold-embedding techniques to extract structural and timing information from simulated and experimental snapshots at extremely low signal. The approach constitutes a physically-based, computationally efficient, and noise-robust route to analyzing the large and varied datasets generated by existing and emerging methods for studying structure and dynamics by scattering. We demonstrate three-dimensional structure recovery from X-ray diffraction and cryo-electron microscope image snapshots of unknown orientation, the latter at 12 times lower dose than currently in use. We also show that ultra-low-signal, random sightings of dynamically evolving systems can be sequenced into high quality movies to reveal their evolution. Our approach offers a route to recovering timing information in time-resolved experiments, and extracting 3D movies from two-dimensional random sightings of dynamic systems.

Year:  2012        PMID: 22714310     DOI: 10.1364/OE.20.012827

Source DB:  PubMed          Journal:  Opt Express        ISSN: 1094-4087            Impact factor:   3.894


  17 in total

1.  Trajectories of the ribosome as a Brownian nanomachine.

Authors:  Ali Dashti; Peter Schwander; Robert Langlois; Russell Fung; Wen Li; Ahmad Hosseinizadeh; Hstau Y Liao; Jesper Pallesen; Gyanesh Sharma; Vera A Stupina; Anne E Simon; Jonathan D Dinman; Joachim Frank; Abbas Ourmazd
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-24       Impact factor: 11.205

2.  Conformational landscape of a virus by single-particle X-ray scattering.

Authors:  Ahmad Hosseinizadeh; Ghoncheh Mashayekhi; Jeremy Copperman; Peter Schwander; Ali Dashti; Reyhaneh Sepehr; Russell Fung; Marius Schmidt; Chun Hong Yoon; Brenda G Hogue; Garth J Williams; Andrew Aquila; Abbas Ourmazd
Journal:  Nat Methods       Date:  2017-08-14       Impact factor: 28.547

3.  The correlation of single-particle diffraction patterns as a continuous function of particle orientation.

Authors:  Andrew V Martin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

Review 4.  Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Authors:  Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Chem Rev       Date:  2022-07-04       Impact factor: 72.087

Review 5.  Conformations of macromolecules and their complexes from heterogeneous datasets.

Authors:  P Schwander; R Fung; A Ourmazd
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

6.  Atomic structure from large-area, low-dose exposures of materials: a new route to circumvent radiation damage.

Authors:  J C Meyer; J Kotakoski; C Mangler
Journal:  Ultramicroscopy       Date:  2013-12-01       Impact factor: 2.689

7.  A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser.

Authors:  Chun Hong Yoon; Mikhail V Yurkov; Evgeny A Schneidmiller; Liubov Samoylova; Alexey Buzmakov; Zoltan Jurek; Beata Ziaja; Robin Santra; N Duane Loh; Thomas Tschentscher; Adrian P Mancuso
Journal:  Sci Rep       Date:  2016-04-25       Impact factor: 4.379

8.  Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.

Authors:  Anna Munke; Jakob Andreasson; Andrew Aquila; Salah Awel; Kartik Ayyer; Anton Barty; Richard J Bean; Peter Berntsen; Johan Bielecki; Sébastien Boutet; Maximilian Bucher; Henry N Chapman; Benedikt J Daurer; Hasan DeMirci; Veit Elser; Petra Fromme; Janos Hajdu; Max F Hantke; Akifumi Higashiura; Brenda G Hogue; Ahmad Hosseinizadeh; Yoonhee Kim; Richard A Kirian; Hemanth K N Reddy; Ti-Yen Lan; Daniel S D Larsson; Haiguang Liu; N Duane Loh; Filipe R N C Maia; Adrian P Mancuso; Kerstin Mühlig; Atsushi Nakagawa; Daewoong Nam; Garrett Nelson; Carl Nettelblad; Kenta Okamoto; Abbas Ourmazd; Max Rose; Gijs van der Schot; Peter Schwander; M Marvin Seibert; Jonas A Sellberg; Raymond G Sierra; Changyong Song; Martin Svenda; Nicusor Timneanu; Ivan A Vartanyants; Daniel Westphal; Max O Wiedorn; Garth J Williams; Paulraj Lourdu Xavier; Chun Hong Yoon; James Zook
Journal:  Sci Data       Date:  2016-08-01       Impact factor: 6.444

9.  Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses.

Authors:  Ruslan P Kurta; Jeffrey J Donatelli; Chun Hong Yoon; Peter Berntsen; Johan Bielecki; Benedikt J Daurer; Hasan DeMirci; Petra Fromme; Max Felix Hantke; Filipe R N C Maia; Anna Munke; Carl Nettelblad; Kanupriya Pande; Hemanth K N Reddy; Jonas A Sellberg; Raymond G Sierra; Martin Svenda; Gijs van der Schot; Ivan A Vartanyants; Garth J Williams; P Lourdu Xavier; Andrew Aquila; Peter H Zwart; Adrian P Mancuso
Journal:  Phys Rev Lett       Date:  2017-10-12       Impact factor: 9.161

10.  High-resolution structure of viruses from random diffraction snapshots.

Authors:  A Hosseinizadeh; P Schwander; A Dashti; R Fung; R M D'Souza; A Ourmazd
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

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