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Malin LE, Graves WS, Holl M, Spence JCH, Nanni EA, Li RK, Shen X, Weathersby S. Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers. Ultramicroscopy 2021; 223:113211. [PMID: 33582644 DOI: 10.1016/j.ultramic.2021.113211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/28/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022]
Abstract
Electron diffraction through a thin patterned silicon membrane can be used to create complex spatial modulations in electron distributions. By precisely varying parameters such as crystallographic orientation and wafer thickness, the intensity of reflections in the diffraction plane can be controlled and by placing an aperture to block all but one spot, we can form an image with different parts of the patterned membrane, as is done for bright-field imaging in microscopy. The patterned electron beams can then be used to control phase and amplitude of subsequent x-ray emission, enabling novel coherent x-ray methods. The electrons themselves can also be used for femtosecond time resolved diffraction and microscopy. As a first step toward patterned beams, we demonstrate experimentally and through simulation the ability to accurately predict and control diffraction spot intensities. We simulate MeV transmission electron diffraction patterns using the multislice method for various crystallographic orientations of a single crystal Si(001) membrane near beam normal. The resulting intensity maps of the Bragg reflections are compared to experimental results obtained at the Accelerator Structure Test Area Ultrafast Electron Diffraction (ASTA UED) facility at SLAC. Furthermore, the fraction of inelastic and elastic scattering of the initial charge is estimated along with the absorption of the membrane to determine the contrast that would be seen in a patterned version of the Si(001) membrane.
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Affiliation(s)
- L E Malin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
| | - W S Graves
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - M Holl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - J C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - E A Nanni
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - R K Li
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - X Shen
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - S Weathersby
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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2
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Candanedo J, Caleman C, Tîmneanu N, Beckstein O, Spence JCH. Dynamics of rare gas solids irradiated by electron beams. J Chem Phys 2020; 152:144303. [DOI: 10.1063/1.5134801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. Candanedo
- Department of Physics, Arizona State University, Tempe, Arizona 85282, USA
| | - C. Caleman
- Department of Physics and Astronomy, Uppsala University, Uppsala SE-75120, Sweden
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, Hamburg, Germany
| | - N. Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Uppsala SE-75120, Sweden
| | - O. Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85282, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona 85282, USA
| | - J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85282, USA
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3
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. Rep Prog Phys 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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Abstract
The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
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Affiliation(s)
- J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferré-D'Amaré AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JCH, Woodson SA, Wang YX. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317099081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P, Doniach S, Downing KH, Earnest T, Elmlund H, Elser V, Gühr M, Hajdu J, Hastings J, Hau-Riege SP, Huang Z, Lattman EE, Maia FRNC, Marchesini S, Ourmazd A, Pellegrini C, Santra R, Schlichting I, Schroer C, Spence JCH, Vartanyants IA, Wakatsuki S, Weis WI, Williams GJ. The linac coherent light source single particle imaging road map. Struct Dyn 2015; 2:041701. [PMID: 26798801 PMCID: PMC4711616 DOI: 10.1063/1.4918726] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/06/2015] [Indexed: 05/19/2023]
Abstract
Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.
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Affiliation(s)
| | - A Barty
- Center for Free-Electron Laser Science, DESY , Notkestr. 85, 22607 Hamburg, Germany
| | - C Bostedt
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S Boutet
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - G Carini
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - D dePonte
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - K H Downing
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | | | | | | | - M Gühr
- PULSE Institute , SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - J Hastings
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S P Hau-Riege
- Lawrence Livermore National Laboratory , Livermore, California 94550, USA
| | - Z Huang
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - S Marchesini
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - A Ourmazd
- Department of Physics, University of Wisconsin Milwaukee , 1900 E. Kenwood Blvd, Milwaukee, Wisconsin 53211, USA
| | | | | | - I Schlichting
- Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - C Schroer
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - J C H Spence
- Department of Physics, Arizona State University , Rural Rd, Tempe, Arizona 85287, USA
| | | | | | - W I Weis
- School of Medicine, Stanford University , 299 Campus Drive, Stanford, California 94305, USA
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Martin AV, Morgan AJ, Ekeberg T, Loh ND, Maia FRNC, Wang F, Spence JCH, Chapman HN. The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern. Opt Express 2013; 21:15102-15112. [PMID: 23842297 DOI: 10.1364/oe.21.015102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The structures of biological molecules may soon be determined with X-ray free-electron lasers without crystallization by recording the coherent diffraction patterns of many identical copies of a molecule. Most analysis methods require a measurement of each molecule individually. However, current injection methods deliver particles to the X-ray beam stochastically and the maximum yield of single particle measurements is 37% at optimal concentration. The remaining 63% of pulses intercept no particles or multiple particles. We demonstrate that in the latter case single particle diffraction patterns can be extracted provided the particles are sufficiently separated. The technique has the potential to greatly increase the amount of data available for three-dimensional imaging of identical particles with X-ray lasers.
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Affiliation(s)
- A V Martin
- ARC Centre of Excellence for Coherent X-ray Science, School of Physics, The University of Melbourne, Victoria, 3010, Australia.
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8
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Starodub D, Aquila A, Bajt S, Barthelmess M, Barty A, Bostedt C, Bozek JD, Coppola N, Doak RB, Epp SW, Erk B, Foucar L, Gumprecht L, Hampton CY, Hartmann A, Hartmann R, Holl P, Kassemeyer S, Kimmel N, Laksmono H, Liang M, Loh ND, Lomb L, Martin AV, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Sierra RG, Soltau H, Steinbrener J, Stellato F, Stern S, Weidenspointner G, Frank M, Ullrich J, Strüder L, Schlichting I, Chapman HN, Spence JCH, Bogan MJ. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nat Commun 2013; 3:1276. [PMID: 23232406 DOI: 10.1038/ncomms2288] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 11/14/2012] [Indexed: 11/09/2022] Open
Abstract
Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.
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Affiliation(s)
- D Starodub
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
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Abstract
We trace the historical development of W. L. Bragg's `law' and the key experimental observation which made it possible using polychromatic radiation at a time when neither X-ray wavelengths nor cell constants were known. This led, through his phasing and solving large mineral structures (without use of a computer), to work on metals, proteins, bubble rafts and his X-ray microscope. The relationship of this to early X-ray microdiffraction is outlined, followed by a brief review of electron microdiffraction methods, where electron-probe sizes smaller than one unit cell can be formed with an interesting `failure' of Bragg's law. We end with a review of recent femtosecond X-ray `snapshot' diffraction from protein nanocrystals, using an X-ray laser which generates pulses so short that they terminate before radiation damage can commence, yet subsequently destroy the sample. In this way, using short pulses instead of freezing, the nexus between dose, resolution and crystal size has been broken, opening the way to time-resolved diffraction without damage for a stream of identical particles.
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Affiliation(s)
- J C H Spence
- Department of Physics, Arizona State University, Tempe, 85282, USA.
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10
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Abstract
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
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Affiliation(s)
- J C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
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11
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Fromme P, Chapman H, Kupitz C, Hunter MS, Kirian RA, Barty A, White TA, Aquilla A, Stellato F, Beyerlein K, DePonte DP, Frank M, Schlichting I, Shoeman R, Lomb L, Steinbrenner J, Nass K, Boutet S, Bogan MJ, Williams G, Zatsepin N, Basu S, Wang D, James D, Fromme R, Grotjohann I, Bottin H, Cherezov V, Stevens R, Cobbe D, Cramer W, Stroud R, Doak RB, Weierstall U, Schmidt K, Spence JCH. Femtosecond nanocrystallography of membrane proteins opens a new era for structural biology. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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12
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Abstract
We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.
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Affiliation(s)
- U Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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13
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Spence JCH. Time-resolved nanocrystallography with X-ray lasers. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311099922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Holton JM, Frankel KA, MacDowell AA, Spence JCH. Colliding beam anomalous measurements for S and P phasing. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311093482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Spence JCH, Jiang B. Real space charge density mapping by quantitative convergent beam electron diffraction (QCBED). Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311086867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Shah AB, Nelson-Cheeseman BB, May SJ, Zuo JM, Bhattacharya A, Spence JCH. Interfaces of lanthanum and strontium manganite superlattices. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311098576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P. X-ray diffraction from membrane protein nanocrystals. Biophys J 2011; 100:198-206. [PMID: 21190672 DOI: 10.1016/j.bpj.2010.10.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.
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Affiliation(s)
- M S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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21
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Saldin DK, Poon HC, Bogan MJ, Marchesini S, Shapiro DA, Kirian RA, Weierstall U, Spence JCH. New light on disordered ensembles: ab initio structure determination of one particle from scattering fluctuations of many copies. Phys Rev Lett 2011; 106:115501. [PMID: 21469876 DOI: 10.1103/physrevlett.106.115501] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 05/25/2023]
Abstract
We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
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Deponte DP, McKeown JT, Weierstall U, Doak RB, Spence JCH. Towards ETEM serial crystallography: Electron diffraction from liquid jets. Ultramicroscopy 2010; 111:824-7. [PMID: 21146302 DOI: 10.1016/j.ultramic.2010.11.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/19/2010] [Accepted: 11/24/2010] [Indexed: 11/30/2022]
Abstract
A sufficiently thin column of liquid was produced to permit penetration with a 200 keV electron beam as evidenced by the observation of diffraction rings due to the intermolecular spacing of the liquid samples. For liquid thickness below 800 nm, the diffraction rings became visible above the inelastic background. Studies were carried out in the environmental chamber of a transmission electron microscope using water and isopropanol.
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Affiliation(s)
- D P Deponte
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287, USA.
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Jiang B, Zuo JM, Holec D, Humphreys CJ, Spackman M, Spence JCH. Combined structure-factor phase measurement and theoretical calculations for mapping of chemical bonds in GaN. Acta Crystallogr A 2010; 66:446-50. [PMID: 20555184 DOI: 10.1107/s0108767310008664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 03/06/2010] [Indexed: 11/11/2022] Open
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Saldin DK, Shneerson VL, Starodub D, Spence JCH. Reconstruction from a single diffraction pattern of azimuthally projected electron density of molecules aligned parallel to a single axis. Acta Crystallogr A 2009; 66:32-7. [PMID: 20029131 DOI: 10.1107/s0108767309041749] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/12/2009] [Indexed: 11/10/2022] Open
Abstract
Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. The limited size of the object results in continuous diffraction patterns characterized by neither Bragg spots nor layer lines. Equations relating the scattered amplitudes to the molecular electron density may be conveniently formulated in terms of cylindrical harmonics. For simulated diffraction patterns from short C nanotubes aligned along their axes, iterative solution of the equation for the zeroth-order cylindrical harmonic and its inverse with appropriate constraints in real and reciprocal space enables the phasing of the measured amplitudes, and hence a reconstruction of the azimuthal projection of the molecule.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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Affiliation(s)
- J. C. H. Spence
- a Arizona State University, Department of Physics and Astronomy , Tempe , Arizona , USA 85287-1504 , USA
| | - C. Koch
- a Arizona State University, Department of Physics and Astronomy , Tempe , Arizona , USA 85287-1504 , USA
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Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JCH, Starodub D. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J Electron Spectros Relat Phenomena 2009; 170:4-12. [PMID: 20463854 PMCID: PMC2867487 DOI: 10.1016/j.elspec.2008.10.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Nine years have elapsed since the technique was first introduced and it has made rapid progress in demonstrating high-resolution three-dimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a single life-science sample by XDM with a given resolution. We find that for simply-shaped objects the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered otherwise. The conclusion of this study is that, based on the natural contrast between protein and water and "Rose-criterion" image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.
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Affiliation(s)
- M. R. Howells
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - T. Beetz
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - H. N. Chapman
- Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA
| | - C. Cui
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. M. Holton
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA
| | - C. J. Jacobsen
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - J. Kirz
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - E. Lima
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - S. Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - H. Miao
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. Sayre
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. A. Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. C. H. Spence
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
| | - D. Starodub
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
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Spence JCH. Two-wavelength inversion of multiply scattered soft X-ray intensities to charge density. Acta Crystallogr A 2008; 65:28-38. [DOI: 10.1107/s0108767308032728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 10/10/2008] [Indexed: 11/10/2022] Open
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Schmidt KE, Spence JCH, Weierstall U, Kirian R, Wang X, Starodub D, Chapman HN, Howells MR, Doak RB. Tomographic femtosecond x-ray diffractive imaging. Phys Rev Lett 2008; 101:115507. [PMID: 18851299 DOI: 10.1103/physrevlett.101.115507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Indexed: 05/26/2023]
Abstract
A method is proposed for obtaining three simultaneous projections of a target from a single radiation pulse, which also allows the relative orientation of successive targets to be determined. The method has application to femtosecond x-ray diffraction, and does not require solution of the phase problem. We show that the principal axes of a compact charge-density distribution can be obtained from projections of its autocorrelation function, which is directly accessible in diffraction experiments. The results may have more general application to time resolved tomographic pump-probe experiments and time-series imaging.
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Affiliation(s)
- K E Schmidt
- Department of Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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Barty A, Marchesini S, Chapman HN, Cui C, Howells MR, Shapiro DA, Minor AM, Spence JCH, Weierstall U, Ilavsky J, Noy A, Hau-Riege SP, Artyukhin AB, Baumann T, Willey T, Stolken J, van Buuren T, Kinney JH. Three-dimensional coherent x-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms. Phys Rev Lett 2008; 101:055501. [PMID: 18764404 DOI: 10.1103/physrevlett.101.055501] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 04/29/2008] [Indexed: 05/26/2023]
Abstract
Ultralow density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area, and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by x-ray diffractive imaging. Finite-element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion-limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.
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Affiliation(s)
- A Barty
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
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30
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Starodub D, Rez P, Hembree G, Howells M, Shapiro D, Chapman HN, Fromme P, Schmidt K, Weierstall U, Doak RB, Spence JCH. Dose, exposure time and resolution in serial X-ray crystallography. J Synchrotron Radiat 2008; 15:62-73. [PMID: 18097080 DOI: 10.1107/s0909049507048893] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 10/05/2007] [Indexed: 05/25/2023]
Abstract
The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed serial crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. The incident X-ray fluence (energy/area) is evaluated that is required to obtain a given resolution from (i) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (ii) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (iii) the spatial frequency cut-off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. An inverse fourth-power dependence of exposure time on resolution is confirmed, with important implications for all coherent X-ray imaging. It is found that multiple single-file protein beams will be needed for sub-nanometer resolution on current third-generation synchrotrons, but not on fourth-generation designs, where reconstruction of secondary protein structure at a resolution of 7 A should be possible with relatively short exposures.
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Affiliation(s)
- D Starodub
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA.
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Affiliation(s)
- J. C. H. Spence
- a Department of Physics , Arizona State University , Tempe, Arizona 85287, U.S.A
| | - G. Reese
- a Department of Physics , Arizona State University , Tempe, Arizona 85287, U.S.A
| | - N. Yamamoto
- a Department of Physics , Arizona State University , Tempe, Arizona 85287, U.S.A
| | - G. Kurizki
- b Department of Physics and Astronomy , University of New Mexico, Albuquerque , New Mexico 87131, U.S.A
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Holmestad R, Zuo JM, Spence JCH, Hoiert R, Horita Z. Effect of Mn doping on charge density in γ-TiAl by quantitative convergent beam electron diffraction. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/01418619508243787] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Affiliation(s)
- N. Yamamoto
- a Department of Physics , Arizona State University , Tempe , Arizona , 85287 , U.S.A
| | - J. C. H. Spence
- a Department of Physics , Arizona State University , Tempe , Arizona , 85287 , U.S.A
- b Department of Metallurgy , University of Oxford , Parks Road, Oxford , England
| | - D. Fathy
- a Department of Physics , Arizona State University , Tempe , Arizona , 85287 , U.S.A
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Starodub D, Doak RB, Schmidt K, Weierstall U, Wu JS, Spence JCH, Howells M, Marcus M, Shapiro D, Barty A, Chapman HN. Damped and thermal motion of laser-aligned hydrated macromolecule beams for diffraction. J Chem Phys 2005; 123:244304. [PMID: 16396534 DOI: 10.1063/1.2137313] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We consider a monodispersed Rayleigh droplet beam of water droplets doped with proteins. An intense infrared laser is used to align these droplets. The arrangement has been proposed for electron- and x-ray-diffraction studies of proteins which are difficult to crystallize. This paper considers the effect of thermal fluctuations on the angular spread of alignment in thermal equilibrium, and relaxation phenomena, particularly the damping of oscillations excited as the molecules enter the field. The possibility of adiabatic alignment is also considered. We find that damping times in a high-pressure gas cell as used in x-ray-diffraction experiments are short compared with the time taken for molecules to traverse the beam and that a suitably shaped field might be used for electron-diffraction experiments in vacuum to provide adiabatic alignment, thus obviating the need for a damping gas cell.
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Affiliation(s)
- D Starodub
- Department of Physics and Astronomy, Arizona State University, P.O. Box 871504 Tempe, Arizona 85287-1504, USA.
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Weierstall U, Starodub D, Spence JCH, Doak B. Electron diffraction from a beam of laser-aligned proteins: progress report. Acta Crystallogr A 2005. [DOI: 10.1107/s010876730509625x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Spackman MA, Jiang B, Groy TL, He H, Whitten AE, Spence JCH. Phase measurement for accurate mapping of chemical bonds in acentric space groups. Phys Rev Lett 2005; 95:085502. [PMID: 16196869 DOI: 10.1103/physrevlett.95.085502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Indexed: 05/04/2023]
Abstract
Although the electron density is fundamental to the study of chemical bonding and density-functional theory, it cannot be accurately mapped experimentally for the important class of crystals lacking inversion symmetry, since structure factor phase information is normally inaccessible. We report the combination of x-ray and electron diffraction experiments for the determination of the electron density in acentric AlN, using multiple-scattering effects in convergent-beam electron diffraction to obtain sensitivity to structure factor phases, and describe a new error metric and weighting scheme for multipole refinement using combined measurements of structure factor magnitudes and phases.
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Wu JS, Spence JCH. Reconstruction of complex single-particle images using charge-flipping algorithm. Acta Crystallogr A 2005; 61:194-200. [PMID: 15724069 DOI: 10.1107/s0108767304033525] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 12/16/2004] [Indexed: 11/10/2022] Open
Abstract
An iterative algorithm is developed to retrieve the complex exit-face wavefunction for a two-dimensional projection of a nanoparticle from a measurement of the oversampled modulus of its Fourier transform in reciprocal space. The algorithm does not require the support (boundary) of the object to be known. A loose support for the complex object is gradually found using the Oszlanyi-Suto charge-flipping algorithm, and a compact support is then iteratively developed using a dynamic Gerchberg-Saxton-Fienup algorithm. At the same time, the complex object is reconstructed using this compact support. The algorithm applies to the reconstruction of complex images with any distribution of phase values from 0 to 2pi. Modification of the algorithm by using real-value constraints for a complex object in the charge-flipping algorithm leads to faster reconstruction of the object whose phase value is smaller than pi/2.
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Affiliation(s)
- J S Wu
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA.
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Spence JCH, Schmidt K, Wu JS, Hembree G, Weierstall U, Doak B, Fromme P. Diffraction and imaging from a beam of laser-aligned proteins: resolution limits. Acta Crystallogr A 2005; 61:237-45. [PMID: 15724074 DOI: 10.1107/s0108767305002710] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2004] [Accepted: 01/24/2005] [Indexed: 11/10/2022] Open
Abstract
The effect of the limited alignment of hydrated molecules is considered in a laser-aligned molecular beam, on diffraction patterns taken from the beam. Simulated patterns for a protein beam are inverted using the Fienup-Gerchberg-Saxton phasing algorithm, and the effect of limited alignment on the resolution of the resulting potential maps is studied. For a typical protein molecule (lysozyme) with anisotropic polarizability, it is found that up to 1 kW of continuous-wave near-infrared laser power (depending on dielectric constant), together with cooling to liquid-nitrogen temperatures, may be needed to produce sufficiently accurate alignment for direct observation of the secondary structure of proteins in the reconstructed potential or charge-density map. For a typical virus (TMV), a 50 W continuous-wave laser is adequate for subnanometre resolution at room temperature. The dependence of resolution on laser power, temperature, molecular size, shape and dielectric constant is analyzed.
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Affiliation(s)
- J C H Spence
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA.
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Spence JCH, Weierstall U, Howells M. Coherence and sampling requirements for diffractive imaging. Ultramicroscopy 2004; 101:149-52. [PMID: 15450660 DOI: 10.1016/j.ultramic.2004.05.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Revised: 05/10/2004] [Accepted: 05/11/2004] [Indexed: 11/28/2022]
Abstract
Coherent Diffractive Imaging (CDI) allows images to be reconstructed from diffraction patterns by solving the non-crystallographic phase problem for isolated nanostructures. We show that the Shannon sampling of diffraction intensities needed in CDI requires a coherence width about twice the lateral dimensions of the object, and that the linear number of detector pixels fixes the energy spread needed in the beam. The Shannon sampling, defined by the transform of the periodically repeated autocorrelation of the object, is related to Bragg scattering from an equivalent crystal, and shown to be consistent with the sampling of Young's fringes established by scattering from extreme points in the object. The results are relevant to the design of diffraction cameras for CDI and plans for femotosecond X-ray diffraction from individual proteins.
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Affiliation(s)
- J C H Spence
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1505, USA.
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Abstract
An iterative phase retrieval method for nonperiodic objects has been developed from the charge-flipping algorithm proposed in crystallography. A combination of the hybrid input-output (HIO) algorithm and the flipping algorithm has greatly improved performance. In this combined algorithm the flipping algorithm serves to find the support (object boundary) dynamically, and the HIO part improves convergence and moves the algorithm out of local minima. It starts with a single intensity measurement in the Fourier domain and does not require a priori knowledge of the support in the image domain. This method is suitable for general image recovery from oversampled diffuse elastic x-ray and electron-diffraction intensities. The relationship between this algorithm and the output-output algorithm is elucidated.
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Affiliation(s)
- J S Wu
- Department of Physics and Astronomy, Arizona State University, Tempe, Arizona 85287-1504, USA.
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Pogrebnyakov AV, Redwing JM, Raghavan S, Vaithyanathan V, Schlom DG, Xu SY, Li Q, Tenne DA, Soukiassian A, Xi XX, Johannes MD, Kasinathan D, Pickett WE, Wu JS, Spence JCH. Enhancement of the superconducting transition temperature of MgB2 by a strain-induced bond-stretching mode softening. Phys Rev Lett 2004; 93:147006. [PMID: 15524834 DOI: 10.1103/physrevlett.93.147006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2004] [Indexed: 05/24/2023]
Abstract
We report a systematic increase of the superconducting transition temperature T(c) with a biaxial tensile strain in MgB2 films to well beyond the bulk value. The tensile strain increases with the MgB2 film thickness, caused primarily by the coalescence of initially nucleated discrete islands (the Volmer-Weber growth mode.) The T(c) increase was observed in epitaxial films on SiC and sapphire substrates, although the T(c) values were different for the two substrates due to different lattice parameters and thermal expansion coefficients. We identified, by first-principles calculations, the underlying mechanism for the T(c) increase to be the softening of the bond-stretching E(2g) phonon mode, and we confirmed this conclusion by Raman scattering measurements. The result suggests that the E(2g) phonon softening is a possible avenue to achieve even higher T(c) in MgB2-related material systems.
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Affiliation(s)
- A V Pogrebnyakov
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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48
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Carrozzini B, Cascarano GL, De Caro L, Giacovazzo C, Marchesini S, Chapman H, He H, Howells M, Wu JS, Weierstall U, Spence JCH. Phasing diffuse scattering. Application of the SIR2002 algorithm to the non-crystallographic phase problem. Acta Crystallogr A 2004; 60:331-8. [PMID: 15218213 DOI: 10.1107/s0108767304012395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 05/20/2004] [Indexed: 11/10/2022] Open
Abstract
A new phasing algorithm has been used to determine the phases of diffuse elastic X-ray scattering from a non-periodic array of gold balls of 50 nm diameter. Two-dimensional real-space images, showing the charge-density distribution of the balls, have been reconstructed at 50 nm resolution from transmission diffraction patterns recorded at 550 eV energy. The reconstructed image fits well with a scanning-electron-microscope (SEM) image of the same sample. The algorithm, which uses only the density modification portion of the SIR2002 program, is compared with the results obtained via the Gerchberg-Saxton-Fienup HiO algorithm. The new algorithm requires no knowledge of the object's boundary and proceeds from low to high resolution. In this way, the relationship between density modification in crystallography and the HiO algorithm used in signal and image processing is elucidated.
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Affiliation(s)
- B Carrozzini
- Istituto di Cristallografia, CNR, Via G. Amendola 122/o, 70126 Bari, Italy
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Wu JS, Spence JCH, O'Keeffe M, Groy TL. Application of a modified Oszlányi and Sütoab initiocharge-flipping algorithm to experimental data. Acta Crystallogr A 2004; 60:326-30. [PMID: 15218212 DOI: 10.1107/s0108767304012231] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 05/19/2004] [Indexed: 11/10/2022] Open
Abstract
The structures of two crystals have been solved using a new iterative phasing method. The iterative phasing algorithm is developed from the 'charge-flipping' method proposed by Oszlányi & Süto [Acta Cryst. (2004), A60, 134-141]. Positivity and point-atom constraints are incorporated within this extremely simple and effective algorithm by flipping (sign reversal) of less-positive density values during the iterations. Convergence is reliably achieved and the two structures were solved. This structure solution method does not require information on atomic scattering factors or symmetry. Heavy atoms can be distinguished from light ones by their charge-density values.
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Affiliation(s)
- J S Wu
- Department of Physics and Astronomy, Arizona State University, Tempe 85287-1504, USA.
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Abstract
For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.
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Affiliation(s)
- J C H Spence
- Department of Physics and Astronomy, Arizona State University, Tempe, Arizona 85287-1504, USA
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