Literature DB >> 24914155

A minimal view of single-particle imaging with X-ray lasers.

N Duane Loh1.   

Abstract

The ability to serially interrogate single biomolecules with femtosecond X-ray pulses from free-electron lasers has ushered in the possibility of determining the three-dimensional structure of biomolecules without crystallization. However, the complexity of imaging a sample's structure from very many of its noisy and incomplete diffraction data can be daunting. In this review, we introduce a simple analogue of this imaging workflow, use it to describe a structure reconstruction algorithm based on the expectation maximization principle, and consider the effects of extraneous noise. Such a minimal model can aid experiment and algorithm design in future studies.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.

Keywords:  X-ray free-electron laser; bioimaging; coherent diffraction; single particle imaging

Mesh:

Year:  2014        PMID: 24914155      PMCID: PMC4052864          DOI: 10.1098/rstb.2013.0328

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  19 in total

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Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

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Journal:  Nature       Date:  2012-06-27       Impact factor: 49.962

4.  High-resolution ab initio three-dimensional x-ray diffraction microscopy.

Authors:  Henry N Chapman; Anton Barty; Stefano Marchesini; Aleksandr Noy; Stefan P Hau-Riege; Congwu Cui; Malcolm R Howells; Rachel Rosen; Haifeng He; John C H Spence; Uwe Weierstall; Tobias Beetz; Chris Jacobsen; David Shapiro
Journal:  J Opt Soc Am A Opt Image Sci Vis       Date:  2006-05       Impact factor: 2.129

5.  Classification of continuous diffraction patterns: a numerical study.

Authors:  G Bortel; G Faigel
Journal:  J Struct Biol       Date:  2006-10-26       Impact factor: 2.867

6.  Reconstruction algorithm for single-particle diffraction imaging experiments.

Authors:  Ne-Te Duane Loh; Veit Elser
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-08-24

7.  Single mimivirus particles intercepted and imaged with an X-ray laser.

Authors:  M Marvin Seibert; Tomas Ekeberg; Filipe R N C Maia; Martin Svenda; Jakob Andreasson; Olof Jönsson; Duško Odić; Bianca Iwan; Andrea Rocker; Daniel Westphal; Max Hantke; Daniel P DePonte; Anton Barty; Joachim Schulz; Lars Gumprecht; Nicola Coppola; Andrew Aquila; Mengning Liang; Thomas A White; Andrew Martin; Carl Caleman; Stephan Stern; Chantal Abergel; Virginie Seltzer; Jean-Michel Claverie; Christoph Bostedt; John D Bozek; Sébastien Boutet; A Alan Miahnahri; Marc Messerschmidt; Jacek Krzywinski; Garth Williams; Keith O Hodgson; Michael J Bogan; Christina Y Hampton; Raymond G Sierra; Dmitri Starodub; Inger Andersson; Saša Bajt; Miriam Barthelmess; John C H Spence; Petra Fromme; Uwe Weierstall; Richard Kirian; Mark Hunter; R Bruce Doak; Stefano Marchesini; Stefan P Hau-Riege; Matthias Frank; Robert L Shoeman; Lukas Lomb; Sascha W Epp; Robert Hartmann; Daniel Rolles; Artem Rudenko; Carlo Schmidt; Lutz Foucar; Nils Kimmel; Peter Holl; Benedikt Rudek; Benjamin Erk; André Hömke; Christian Reich; Daniel Pietschner; Georg Weidenspointner; Lothar Strüder; Günter Hauser; Hubert Gorke; Joachim Ullrich; Ilme Schlichting; Sven Herrmann; Gerhard Schaller; Florian Schopper; Heike Soltau; Kai-Uwe Kühnel; Robert Andritschke; Claus-Dieter Schröter; Faton Krasniqi; Mario Bott; Sebastian Schorb; Daniela Rupp; Marcus Adolph; Tais Gorkhover; Helmut Hirsemann; Guillaume Potdevin; Heinz Graafsma; Björn Nilsson; Henry N Chapman; Janos Hajdu
Journal:  Nature       Date:  2011-02-03       Impact factor: 49.962

8.  Recovering magnetization distributions from their noisy diffraction data.

Authors:  Ne-Te Duane Loh; Stefan Eisebitt; Samuel Flewett; Veit Elser
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-12-22

9.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements.

Authors:  Anton Barty; Carl Caleman; Andrew Aquila; Nicusor Timneanu; Lukas Lomb; Thomas A White; Jakob Andreasson; David Arnlund; Saša Bajt; Thomas R M Barends; Miriam Barthelmess; Michael J Bogan; Christoph Bostedt; John D Bozek; Ryan Coffee; Nicola Coppola; Jan Davidsson; Daniel P Deponte; R Bruce Doak; Tomas Ekeberg; Veit Elser; Sascha W Epp; Benjamin Erk; Holger Fleckenstein; Lutz Foucar; Petra Fromme; Heinz Graafsma; Lars Gumprecht; Janos Hajdu; Christina Y Hampton; Robert Hartmann; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; Mark S Hunter; Linda Johansson; Stephan Kassemeyer; Nils Kimmel; Richard A Kirian; Mengning Liang; Filipe R N C Maia; Erik Malmerberg; Stefano Marchesini; Andrew V Martin; Karol Nass; Richard Neutze; Christian Reich; Daniel Rolles; Benedikt Rudek; Artem Rudenko; Howard Scott; Ilme Schlichting; Joachim Schulz; M Marvin Seibert; Robert L Shoeman; Raymond G Sierra; Heike Soltau; John C H Spence; Francesco Stellato; Stephan Stern; Lothar Strüder; Joachim Ullrich; X Wang; Georg Weidenspointner; Uwe Weierstall; Cornelia B Wunderer; Henry N Chapman
Journal:  Nat Photonics       Date:  2012       Impact factor: 38.771

10.  Solving structure with sparse, randomly-oriented x-ray data.

Authors:  Hugh T Philipp; Kartik Ayyer; Mark W Tate; Veit Elser; Sol M Gruner
Journal:  Opt Express       Date:  2012-06-04       Impact factor: 3.894

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  5 in total

1.  The birth of a new field.

Authors:  John C H Spence; Henry N Chapman
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

2.  An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser.

Authors:  Dameli Assalauova; Young Yong Kim; Sergey Bobkov; Ruslan Khubbutdinov; Max Rose; Roberto Alvarez; Jakob Andreasson; Eugeniu Balaur; Alice Contreras; Hasan DeMirci; Luca Gelisio; Janos Hajdu; Mark S Hunter; Ruslan P Kurta; Haoyuan Li; Matthew McFadden; Reza Nazari; Peter Schwander; Anton Teslyuk; Peter Walter; P Lourdu Xavier; Chun Hong Yoon; Sahba Zaare; Viacheslav A Ilyin; Richard A Kirian; Brenda G Hogue; Andrew Aquila; Ivan A Vartanyants
Journal:  IUCrJ       Date:  2020-10-15       Impact factor: 4.769

3.  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

4.  Dragonfly: an implementation of the expand-maximize-compress algorithm for single-particle imaging.

Authors:  Kartik Ayyer; Ti-Yen Lan; Veit Elser; N Duane Loh
Journal:  J Appl Crystallogr       Date:  2016-06-20       Impact factor: 3.304

5.  Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses.

Authors:  Benedikt J Daurer; Kenta Okamoto; Johan Bielecki; Filipe R N C Maia; Kerstin Mühlig; M Marvin Seibert; Max F Hantke; Carl Nettelblad; W Henry Benner; Martin Svenda; Nicuşor Tîmneanu; Tomas Ekeberg; N Duane Loh; Alberto Pietrini; Alessandro Zani; Asawari D Rath; Daniel Westphal; Richard A Kirian; Salah Awel; Max O Wiedorn; Gijs van der Schot; Gunilla H Carlsson; Dirk Hasse; Jonas A Sellberg; Anton Barty; Jakob Andreasson; Sébastien Boutet; Garth Williams; Jason Koglin; Inger Andersson; Janos Hajdu; Daniel S D Larsson
Journal:  IUCrJ       Date:  2017-04-07       Impact factor: 4.769

  5 in total

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