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6. Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution

Author

Yang, Hao, MacLaren, Ian, Jones, Lewys, Martinez, Gerardo T, Simson, Martin, Huth, Martin, Ryll, Henning, Soltau, Heike, Sagawa, Ryusuke, Kondo, Yukihito, Ophus, Colin, Ercius, Peter, Jin, Lei, Kovács, András, and Nellist, Peter D

Subjects
Quantum Physics, Physical Sciences, Bioengineering, 4D-STEM, Pixelated detectors, Ptychography, Phase retrieval, Wigner distribution deconvolution, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Optical Physics, Other Physical Sciences, Microscopy, Biochemistry and cell biology, Physical chemistry, Condensed matter physics
Abstract

Recent development in fast pixelated detector technology has allowed a two dimensional diffraction pattern to be recorded at every probe position of a two dimensional raster scan in a scanning transmission electron microscope (STEM), forming an information-rich four dimensional (4D) dataset. Electron ptychography has been shown to enable efficient coherent phase imaging of weakly scattering objects from a 4D dataset recorded using a focused electron probe, which is optimised for simultaneous incoherent Z-contrast imaging and spectroscopy in STEM. Therefore coherent phase contrast and incoherent Z-contrast imaging modes can be efficiently combined to provide a good sensitivity of both light and heavy elements at atomic resolution. In this work, we explore the application of electron ptychography for atomic resolution imaging of strongly scattering crystalline specimens, and present experiments on imaging crystalline specimens including samples containing defects, under dynamical channelling conditions using an aberration corrected microscope. A ptychographic reconstruction method called Wigner distribution deconvolution (WDD) was implemented. Experimental results and simulation results suggest that ptychography provides a readily interpretable phase image and great sensitivity for imaging light elements at atomic resolution in relatively thin crystalline materials.

Published
2017

7. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Author

Ekeberg, Tomas, Svenda, Martin, Seibert, M Marvin, Abergel, Chantal, Maia, Filipe RNC, Seltzer, Virginie, DePonte, Daniel P, Aquila, Andrew, Andreasson, Jakob, Iwan, Bianca, Jönsson, Olof, Westphal, Daniel, Odić, Duško, Andersson, Inger, Barty, Anton, Liang, Meng, Martin, Andrew V, Gumprecht, Lars, Fleckenstein, Holger, Bajt, Saša, Barthelmess, Miriam, Coppola, Nicola, Claverie, Jean-Michel, Loh, N Duane, Bostedt, Christoph, Bozek, John D, Krzywinski, Jacek, Messerschmidt, Marc, Bogan, Michael J, Hampton, Christina Y, Sierra, Raymond G, Frank, Matthias, Shoeman, Robert L, Lomb, Lukas, Foucar, Lutz, Epp, Sascha W, Rolles, Daniel, Rudenko, Artem, Hartmann, Robert, Hartmann, Andreas, Kimmel, Nils, Holl, Peter, Weidenspointner, Georg, Rudek, Benedikt, Erk, Benjamin, Kassemeyer, Stephan, Schlichting, Ilme, Strüder, Lothar, Ullrich, Joachim, Schmidt, Carlo, Krasniqi, Faton, Hauser, Günter, Reich, Christian, Soltau, Heike, Schorb, Sebastian, Hirsemann, Helmut, Wunderer, Cornelia, Graafsma, Heinz, Chapman, Henry, and Hajdu, Janos

Subjects
Biochemistry and Cell Biology, Physical Sciences, Biological Sciences, Biomedical Imaging, Algorithms, Computer Simulation, Crystallography, X-Ray, Data Collection, Electrons, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Lasers, Mimiviridae, Models, Theoretical, Particle Size, Scattering, Radiation, X-Ray Diffraction, X-Rays
Abstract

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

Published
2016

8. X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser

Author

Küpper, Jochen, Stern, Stephan, Holmegaard, Lotte, Filsinger, Frank, Rouzée, Arnaud, Rudenko, Artem, Johnsson, Per, Martin, Andrew V., Adolph, Marcus, Aquila, Andrew, Bajt, Saša, Barty, Anton, Bostedt, Christoph, Bozek, John, Caleman, Carl, Coffee, Ryan, Coppola, Nicola, Delmas, Tjark, Epp, Sascha, Erk, Benjamin, Foucar, Lutz, Gorkhover, Tais, Gumprecht, Lars, Hartmann, Andreas, Hartmann, Robert, Hauser, Günter, Holl, Peter, Hömke, Andre, Kimmel, Nils, Krasniqi, Faton, Kühnel, Kai-Uwe, Maurer, Jochen, Messerschmidt, Marc, Mosshammer, Robert, Reich, Christian, Rudek, Benedikt, Santra, Robin, Schlichting, Ilme, Schmidt, Carlo, Schorb, Sebastian, Schulz, Joachim, Soltau, Heike, Spence, John C. H., Starodub, Dmitri, Strüder, Lothar, Thøgersen, Jan, Vrakking, Marc J. J., Weidenspointner, Georg, White, Thomas A., Wunderer, Cornelia, Meijer, Gerard, Ullrich, Joachim, Stapelfeldt, Henrik, Rolles, Daniel, and Chapman, Henry N.

Subjects
Physics - Atomic Physics
Abstract

We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules., Comment: submitted to PRL

Published
2013
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11. Time-resolved protein nanocrystallography using an X-ray free-electron laser

Author

Aquila, Andrew, Hunter, Mark S, Doak, R Bruce, Kirian, Richard A, Fromme, Petra, White, Thomas A, Andreasson, Jakob, Arnlund, David, Bajt, Saša, Barends, Thomas RM, Barthelmess, Miriam, Bogan, Michael J, Bostedt, Christoph, Bottin, Hervé, Bozek, John D, Caleman, Carl, Coppola, Nicola, Davidsson, Jan, DePonte, Daniel P, Elser, Veit, Epp, Sascha W, Erk, Benjamin, Fleckenstein, Holger, Foucar, Lutz, Frank, Matthias, Fromme, Raimund, Graafsma, Heinz, Grotjohann, Ingo, Gumprecht, Lars, Hajdu, Janos, Hampton, Christina Y, Hartmann, Andreas, Hartmann, Robert, Hau-Riege, Stefan, Hauser, Günter, Hirsemann, Helmut, Holl, Peter, Holton, James M, Hömke, André, Johansson, Linda, Kimmel, Nils, Kassemeyer, Stephan, Krasniqi, Faton, Kühnel, Kai-Uwe, Liang, Mengning, Lomb, Lukas, Malmerberg, Erik, Marchesini, Stefano, Martin, Andrew V, Maia, Filipe RNC, Messerschmidt, Marc, Nass, Karol, Reich, Christian, Neutze, Richard, Rolles, Daniel, Rudek, Benedikt, Rudenko, Artem, Schlichting, Ilme, Schmidt, Carlo, Schmidt, Kevin E, Schulz, Joachim, Seibert, M Marvin, Shoeman, Robert L, Sierra, Raymond, Soltau, Heike, Starodub, Dmitri, Stellato, Francesco, Stern, Stephan, Strüder, Lothar, Timneanu, Nicusor, Ullrich, Joachim, Wang, Xiaoyu, Williams, Garth J, Weidenspointner, Georg, Weierstall, Uwe, Wunderer, Cornelia, Barty, Anton, Spence, John CH, and Chapman, Henry N

Subjects
Crystallography, X-Ray, Electrons, Ferredoxins, Lasers, Nanostructures, Protein Conformation, X-Ray Diffraction, X-Rays, Optical Physics, Electrical and Electronic Engineering, Communications Technologies, Optics
Abstract

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

Published
2012

18. Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources

Author

Strüder, Lothar, Epp, Sascha, Rolles, Daniel, Hartmann, Robert, Holl, Peter, Lutz, Gerhard, Soltau, Heike, Eckart, Rouven, Reich, Christian, Heinzinger, Klaus, Thamm, Christian, Rudenko, Artem, Krasniqi, Faton, Kühnel, Kai-Uwe, Bauer, Christian, Schröter, Claus-Dieter, Moshammer, Robert, Techert, Simone, Miessner, Danilo, Porro, Matteo, Hälker, Olaf, Meidinger, Norbert, Kimmel, Nils, Andritschke, Robert, Schopper, Florian, Weidenspointner, Georg, Ziegler, Alexander, Pietschner, Daniel, Herrmann, Sven, Pietsch, Ullrich, Walenta, Albert, Leitenberger, Wolfram, Bostedt, Christoph, Möller, Thomas, Rupp, Daniela, Adolph, Marcus, Graafsma, Heinz, Hirsemann, Helmut, Gärtner, Klaus, Richter, Rainer, Foucar, Lutz, Shoeman, Robert L., Schlichting, Ilme, and Ullrich, Joachim

Published
2010
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19. Demonstration of a dual-range photon detector with SDD and La[Br.sup.3]([Ce.sup.3+]) scintillator

Author

Pausch, Guntram, Plettner, Cristina, Herbach, Claus-Michael, Stein, Juergen, Moszynski, Marek, Nassalski, Antoni, Swiderski, Lukasz, Szczesniak, Tomasz, Niculae, Adrian, and Soltau, Heike

Subjects
Silicon diodes -- Research, Photon detectors -- Research, Gamma ray spectrometry -- Methods, Business, Electronics, Electronics and electrical industries
Abstract

A novel concept for improving gamma ray spectroscopy in compact instruments is presented. The dual-range photon detector (DRPD) consists of a silicon drift detector (SDD) which is optically coupled with a La[Br.sup.3]([Ce.sup.3+]) crystal. In contrast to similar configurations investigated so far the SDD points to the radiation source. Pulse shape discrimination allows separating the distinct detection mechanisms which correspond to gamma absorption in the SDD or in the scintillator, respectively. This arrangement combines for the first time the excellent performance of an SDD as X-ray detector on its own with the striking energy resolution of a La[Br.sub.3] ([Ce.sup.3+]) scintillator read out by an SDD. The concept was successfully demonstrated with two experimental SDD-La[Br.sub.3]([Ce.sup.3+]) systems. An energy resolution (FWHM) of 2.7% and 2.9% at 662 keV was measured with the two distinct systems operated in scintillator mode whereas scintillator-photomultiplier combinations with the same crystals yielded only 3.3% and 3.1%, respectively. The SDD mode provided an energy resolution surpassing the scintillator resolution by about one order of magnitude in the limited energy range up to 100 keV. Measurements with various radioactive sources demonstrated that this mode uncovers line structures which could never be resolved with scintillators or CZT detectors. Homeland security programs could profit from the proposed detector concept. Index Terms--Energy resolution, gamma-ray spectroscopy, homeland security, pulse shape discrimination, radioisotope identification, scintillation detectors, silicon detectors.

Published
2009

22. A pulse shape discrimination gamma-ray detector based on a silicon drift chamber coupled to a CsI(Tl) scintillator: prospects for a 1 keV-1 MeV monolithic detector

Author

Marisaldi, Martino, Labanti, Claudio, and Soltau, Heike

Subjects
Silicon diodes -- Analysis, Detectors -- Analysis, Business, Electronics, Electronics and electrical industries
Abstract

In this paper, an X- and gamma-ray detector based on a silicon drift detector (SDD) coupled to a CsI(Tl) scintillating crystal is presented. The SDD is operated both as a direct X-ray detector for photons interacting in silicon and as an indirect detector for photons interacting in the scintillator. As interactions in silicon and in CsI yield different amounts of charge per unit energy deposited, discrimination of the place of interaction is necessary to obtain the correct energy. Discrimination of the interaction type is carried out by means of pulse shape discrimination performed with two parallel processing chains with different shaping times. The performance of the detectors are described and discussed. Pulse shape discrimination is possible throughout the detector energy range. Index Terms--Gamma-ray detectors, pulse shape discrimination, silicon drift detectors, X-ray detectors.

Published
2004

24. Femtosecond X-ray protein nanocrystallography

Author

Chapman, Henry N., Fromme, Petra, Barty, Anton, White, Thomas A., Kirian, Richard A., Aquila, Andrew, Hunter, Mark S., Schulz, Joachim, DePonte, Daniel P., Weierstall, Uwe, Doak, Bruce R., Maia, Filipe R. N. C., Martin, Andrew V., Schlichting, Ilme, Lomb, Lukas, Coppola, Nicola, Shoeman, Robert L., Epp, Sascha W., Hartmann, Robert, Rolles, Daniel, Rudenko, Artem, Foucar, Lutz, Kimmel, Nils, Weidenspointner, Georg, Holl, Peter, Liang, Mengning, Barthelmess, Miriam, Caleman, Carl, Boutet, Sébastien, Bogan, Michael J., Krzywinski, Jacek, Bostedt, Christoph, Bajt, Saša, Gumprecht, Lars, Rudek, Benedikt, Erk, Benjamin, Schmidt, Carlo, Hömke, André, Reich, Christian, Pietschner, Daniel, Strüder, Lothar, Hauser, Günter, Gorke, Hubert, Ullrich, Joachim, Herrmann, Sven, Schaller, Gerhard, Schopper, Florian, Soltau, Heike, Kühnel, Kai-Uwe, Messerschmidt, Marc, Bozek, John D., Hau-Riege, Stefan P., Frank, Matthias, Hampton, Christina Y., Sierra, Raymond G., Starodub, Dmitri, Williams, Garth J., Hajdu, Janos, Timneanu, Nicusor, Seibert, Marvin M., Andreasson, Jakob, Rocker, Andrea, Jönsson, Olof, Svenda, Martin, Stern, Stephan, Nass, Karol, Andritschke, Robert, Schröter, Claus-Dieter, Krasniqi, Faton, Bott, Mario, Schmidt, Kevin E., Wang, Xiaoyu, Grotjohann, Ingo, Holton, James M., Barends, Thomas R. M., Neutze, Richard, Marchesini, Stefano, Fromme, Raimund, Schorb, Sebastian, Rupp, Daniela, Adolph, Marcus, Gorkhover, Tais, Andersson, Inger, Hirsemann, Helmut, Potdevin, Guillaume, Graafsma, Heinz, Nilsson, Björn, and Spence, John C. H.

Published
2011
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25. Single mimivirus particles intercepted and imaged with an X-ray laser

Author

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

Published
2011
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28. pnCCDs on XMM-Newton—42 months in orbit

Author

Strüder, Lothar, Englhauser, Jakob, Hartmann, Robert, Holl, Peter, Meidinger, Norbert, Soltau, Heike, Briel, Ulrich, Dennerl, Konrad, Freyberg, Michael, Haberl, Frank, Hartner, Gisela, Pfeffermann, Elmar, Stadlbauer, Thomas, and Kendziorra, Eckehard

Published
2003
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32. Measuring Single Electrons – What Does it Mean?

Author

Ryll, Henning, primary, Huth, Martin, additional, Ritz, Robert, additional, O'Leary, Colum M., additional, Griffiths, Ian, additional, Nellist, Peter, additional, Sagawa, Ryusuke, additional, Kondo, Yukihito, additional, Soltau, Heike, additional, and Strüder, Lothar, additional

Published
2019
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40. Atomic-scale quantification of charge densities in two-dimensional materials

Author

Müller-Caspary, Knut, primary, Duchamp, Martial, additional, Rösner, Malte, additional, Migunov, Vadim, additional, Winkler, Florian, additional, Yang, Hao, additional, Huth, Martin, additional, Ritz, Robert, additional, Simson, Martin, additional, Ihle, Sebastian, additional, Soltau, Heike, additional, Wehling, Tim, additional, Dunin-Borkowski, Rafal E., additional, Van Aert, Sandra, additional, and Rosenauer, Andreas, additional

Published
2018
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43. X-ray Detectors - in Heaven and on Earth

Author

Struder, Lothar, primary, Soltau, Heike, additional, Holl, Peter, additional, Hartmann, Robert, additional, Schlosser, Dieter, additional, Niculae, Adrian, additional, Huth, Martin, additional, and Davis, Jeff, additional

Published
2018
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49. Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution

Author

Yang, Hao, primary, MacLaren, Ian, additional, Jones, Lewys, additional, Martinez, Gerardo T., additional, Simson, Martin, additional, Huth, Martin, additional, Ryll, Henning, additional, Soltau, Heike, additional, Sagawa, Ryusuke, additional, Kondo, Yukihito, additional, Ophus, Colin, additional, Ercius, Peter, additional, Jin, Lei, additional, Kovács, András, additional, and Nellist, Peter D., additional

Published
2017
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