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John D. Bozek

Bio: John D. Bozek is an academic researcher from SLAC National Accelerator Laboratory. The author has contributed to research in topics: Photoionization & Ionization. The author has an hindex of 55, co-authored 282 publications receiving 14804 citations. Previous affiliations of John D. Bozek include Université Paris-Saclay & Lawrence Berkeley National Laboratory.


Papers
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Journal ArticleDOI
TL;DR: The Linac Coherent Light Source free-electron laser has achieved coherent X-ray generation down to a wavelength of 1.2 A and at a brightness that is nearly ten orders of magnitude higher than conventional synchrotrons.
Abstract: The Linac Coherent Light Source free-electron laser has now achieved coherent X-ray generation down to a wavelength of 1.2 A and at a brightness that is nearly ten orders of magnitude higher than conventional synchrotrons. Researchers detail the first operation and beam characteristics of the system, which give hope for imaging at atomic spatial and temporal scales.

2,648 citations

Journal ArticleDOI
Henry N. Chapman1, Petra Fromme2, Anton Barty, Thomas A. White, Richard A. Kirian2, Andrew Aquila, Mark S. Hunter2, Joachim Schulz, Daniel P. DePonte, Uwe Weierstall2, R. Bruce Doak2, Filipe R. N. C. Maia3, Andrew V. Martin, Ilme Schlichting4, Lukas Lomb4, Nicola Coppola5, Robert L. Shoeman4, Sascha W. Epp4, Robert Hartmann, Daniel Rolles4, Artem Rudenko4, Lutz Foucar4, Nils Kimmel4, Georg Weidenspointner4, Peter Holl, Mengning Liang, Miriam Barthelmess, Carl Caleman, Sébastien Boutet6, Michael J. Bogan6, Jacek Krzywinski6, Christoph Bostedt6, Saša Bajt, Lars Gumprecht, Benedikt Rudek4, Benjamin Erk4, Carlo Schmidt4, André Hömke4, Christian Reich, Daniel Pietschner4, Lothar Strüder4, Günter Hauser4, H. Gorke7, Joachim Ullrich4, Sven Herrmann4, Gerhard Schaller4, Florian Schopper4, Heike Soltau, Kai-Uwe Kühnel4, Marc Messerschmidt6, John D. Bozek6, Stefan P. Hau-Riege8, Matthias Frank8, Christina Y. Hampton6, Raymond G. Sierra6, Dmitri Starodub6, Garth J. Williams6, Janos Hajdu3, Nicusor Timneanu3, M. Marvin Seibert6, M. Marvin Seibert3, Jakob Andreasson3, Andrea Rocker3, Olof Jönsson3, Martin Svenda3, Stephan Stern, Karol Nass1, Robert Andritschke4, Claus Dieter Schröter4, Faton Krasniqi4, Mario Bott4, Kevin Schmidt2, Xiaoyu Wang2, Ingo Grotjohann2, James M. Holton9, Thomas R. M. Barends4, Richard Neutze10, Stefano Marchesini9, Raimund Fromme2, Sebastian Schorb11, Daniela Rupp11, M. Adolph11, Tais Gorkhover11, Inger Andersson12, Helmut Hirsemann, Guillaume Potdevin, Heinz Graafsma, Björn Nilsson, John C. H. Spence2 
03 Feb 2011-Nature
TL;DR: This work offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage, by using pulses briefer than the timescale of most damage processes.
Abstract: X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

1,708 citations

Journal ArticleDOI
M. Marvin Seibert1, Tomas Ekeberg1, Filipe R. N. C. Maia1, Martin Svenda1, Jakob Andreasson1, Olof Jönsson1, Dusko Odic1, Bianca Iwan1, Andrea Rocker1, Daniel Westphal1, Max F. Hantke1, Daniel P. DePonte, Anton Barty, Joachim Schulz, Lars Gumprecht, Nicola Coppola, Andrew Aquila, Mengning Liang, Thomas A. White, Andrew V. Martin, Carl Caleman1, Stephan Stern2, Chantal Abergel3, Virginie Seltzer3, Jean-Michel Claverie3, Christoph Bostedt4, John D. Bozek4, Sébastien Boutet4, A. Miahnahri4, Marc Messerschmidt4, Jacek Krzywinski4, Garth J. Williams4, Keith O. Hodgson4, Michael J. Bogan4, Christina Y. Hampton4, Raymond G. Sierra4, D. Starodub4, Inger Andersson5, Sǎa Bajt, Miriam Barthelmess, John C. H. Spence6, Petra Fromme6, Uwe Weierstall6, Richard A. Kirian6, Mark S. Hunter6, R. Bruce Doak6, Stefano Marchesini7, Stefan P. Hau-Riege8, Matthias Frank8, Robert L. Shoeman9, Lukas Lomb9, Sascha W. Epp9, Robert Hartmann, Daniel Rolles9, Artem Rudenko9, Carlo Schmidt9, Lutz Foucar9, Nils Kimmel9, Peter Holl, Benedikt Rudek9, Benjamin Erk9, André Hömke9, Christian Reich, Daniel Pietschner9, Georg Weidenspointner9, Lothar Strüder9, Günter Hauser9, H. Gorke, Joachim Ullrich9, Ilme Schlichting9, Sven Herrmann9, Gerhard Schaller9, Florian Schopper9, Heike Soltau, Kai Uwe Kuhnel9, Robert Andritschke9, Claus Dieter Schröter9, Faton Krasniqi9, Mario Bott9, Sebastian Schorb10, Daniela Rupp10, M. Adolph10, Tais Gorkhover10, Helmut Hirsemann, Guillaume Potdevin, Heinz Graafsma, Björn Nilsson, Henry N. Chapman2, Janos Hajdu1 
03 Feb 2011-Nature
TL;DR: This work shows that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source.
Abstract: The start-up of the Linac Coherent Light Source (LCLS), the new femtosecond hard X-ray laser facility in Stanford, California, has brought high expectations of a new era for biological imaging. The intense, ultrashort X-ray pulses allow diffraction imaging of small structures before radiation damage occurs. Two papers in this issue of Nature present proof-of-concept experiments showing the LCLS in action. Chapman et al. tackle structure determination from nanocrystals of macromolecules that cannot be grown in large crystals. They obtain more than three million diffraction patterns from a stream of nanocrystals of the membrane protein photosystem I, and assemble a three-dimensional data set for this protein. Seibert et al. obtain images of a non-crystalline biological sample, mimivirus, by injecting a beam of cooled mimivirus particles into the X-ray beam. The start-up of the new femtosecond hard X-ray laser facility in Stanford, the Linac Coherent Light Source, has brought high expectations for a new era for biological imaging. The intense, ultrashort X-ray pulses allow diffraction imaging of small structures before radiation damage occurs. This new capability is tested for the problem of imaging a non-crystalline biological sample. Images of mimivirus are obtained, the largest known virus with a total diameter of about 0.75 micrometres, by injecting a beam of cooled mimivirus particles into the X-ray beam. The measurements indicate no damage during imaging and prove the concept of this imaging technique. X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1,2,3,4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

838 citations

Journal ArticleDOI
01 Jul 2010-Nature
TL;DR: The nature of the electronic response in a free atom to unprecedented high-intensity, short-wavelength, high-fluence radiation is revealed and successful modelling of X-ray/atom interactions using a straightforward rate equation approach augurs favourably for extension to complex systems.
Abstract: An era of exploring the interactions of high-intensity, hard X-rays with matter has begun with the start-up of a hard-X-ray free-electron laser, the Linac Coherent Light Source (LCLS). Understanding how electrons in matter respond to ultra-intense X-ray radiation is essential for all applications. Here we reveal the nature of the electronic response in a free atom to unprecedented high-intensity, short-wavelength, high-fluence radiation (respectively 10(18) W cm(-2), 1.5-0.6 nm, approximately 10(5) X-ray photons per A(2)). At this fluence, the neon target inevitably changes during the course of a single femtosecond-duration X-ray pulse-by sequentially ejecting electrons-to produce fully-stripped neon through absorption of six photons. Rapid photoejection of inner-shell electrons produces 'hollow' atoms and an intensity-induced X-ray transparency. Such transparency, due to the presence of inner-shell vacancies, can be induced in all atomic, molecular and condensed matter systems at high intensity. Quantitative comparison with theory allows us to extract LCLS fluence and pulse duration. Our successful modelling of X-ray/atom interactions using a straightforward rate equation approach augurs favourably for extension to complex systems.

649 citations

Journal ArticleDOI
TL;DR: Measurements indicate that current X-ray free-electron laser technology should enable structural determination from submicrometre protein crystals with atomic resolution, and the shortest apparent pulse lengths occur at the highest resolution.
Abstract: Researchers describe a mechanism capable of compressing fast and intense X-ray pulses through the rapid loss of crystalline periodicity. It is hoped that this concept, combined with X-ray free-electron laser technology, will allow scientists to obtain structural information at atomic resolutions.

309 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: The authors show the double-slit interference effect in the strong-field ionization of neon dimers by employing COLTRIMS method to record the momentum distribution of the photoelectrons in the molecular frame.
Abstract: Wave-particle duality is an inherent peculiarity of the quantum world. The double-slit experiment has been frequently used for understanding different aspects of this fundamental concept. The occurrence of interference rests on the lack of which-way information and on the absence of decoherence mechanisms, which could scramble the wave fronts. Here, we report on the observation of two-center interference in the molecular-frame photoelectron momentum distribution upon ionization of the neon dimer by a strong laser field. Postselection of ions, which are measured in coincidence with electrons, allows choosing the symmetry of the residual ion, leading to observation of both, gerade and ungerade, types of interference.

7,160 citations

Journal ArticleDOI
01 Oct 2019
TL;DR: Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

3,268 citations

Journal ArticleDOI
TL;DR: In this article, the authors present the landmarks of the 30-odd-year evolution of ultrashort-pulse laser physics and technology culminating in the generation of intense few-cycle light pulses and discuss the impact of these pulses on high-field physics.
Abstract: The rise time of intense radiation determines the maximum field strength atoms can be exposed to before their polarizability dramatically drops due to the detachment of an outer electron. Recent progress in ultrafast optics has allowed the generation of ultraintense light pulses comprising merely a few field oscillation cycles. The arising intensity gradient allows electrons to survive in their bound atomic state up to external field strengths many times higher than the binding Coulomb field and gives rise to ionization rates comparable to the light frequency, resulting in a significant extension of the frontiers of nonlinear optics and (nonrelativistic) high-field physics. Implications include the generation of coherent harmonic radiation up to kiloelectronvolt photon energies and control of the atomic dipole moment on a subfemtosecond $(1{\mathrm{f}\mathrm{s}=10}^{\mathrm{\ensuremath{-}}15}\mathrm{}\mathrm{s})$ time scale. This review presents the landmarks of the 30-odd-year evolution of ultrashort-pulse laser physics and technology culminating in the generation of intense few-cycle light pulses and discusses the impact of these pulses on high-field physics. Particular emphasis is placed on high-order harmonic emission and single subfemtosecond extreme ultraviolet/x-ray pulse generation. These as well as other strong-field processes are governed directly by the electric-field evolution, and hence their full control requires access to the (absolute) phase of the light carrier. We shall discuss routes to its determination and control, which will, for the first time, allow access to the electromagnetic fields in light waves and control of high-field interactions with never-before-achieved precision.

2,547 citations

Journal ArticleDOI
01 Oct 1971-Nature
TL;DR: Lipson and Steeple as mentioned in this paper interpreted X-ray powder diffraction patterns and found that powder-diffraction patterns can be represented by a set of 3-dimensional planes.
Abstract: Interpretation of X-ray Powder Diffraction Patterns . By H. Lipson and H. Steeple. Pp. viii + 335 + 3 plates. (Mac-millan: London; St Martins Press: New York, May 1970.) £4.

1,867 citations