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195 results on '"Boutet, Sebastien"'

1. Attosecond Inner-Shell Lasing at Angstrom Wavelengths

Author

Linker, Thomas M., Halavanau, Aliaksei, Kroll, Thomas, Benediktovitch, Andrei, Zhang, Yu, Michine, Yurina, Chuchurka, Stasis, Abhari, Zain, Ronchetti, Daniele, Fransson, Thomas, Weninger, Clemens, Fuller, Franklin D., Aquila, Andy, Alonso-Mori, Roberto, Boutet, Sebastien, Guetg, Marc W., Marinelli, Agostino, Lutman, Alberto A., Yabashi, Makina, Inoue, Ichiro, Osaka, Taito, Yamada, Jumpei, Inubushi, Yuichi, Yamaguchi, Gota, Hara, Toru, Babu, Ganguli, Salpekar, Devashish, Sayed, Farheen N., Ajayan, Pulickel M., Kern, Jan, Yano, Junko, Yachandra, Vittal K., Kling, Matthias F., Pellegrini, Claudio, Yoneda, Hitoki, Rohringer, Nina, and Bergmann, Uwe

Subjects
Physics - Optics, Physics - Atomic Physics
Abstract

Since the invention of the laser nonlinear effects such as filamentation, Rabi-cycling and collective emission have been explored in the optical regime leading to a wide range of scientific and industrial applications. X-ray free electron lasers (XFELs) have led to the extension of many optical techniques to X-rays for their advantages of angstrom scale spatial resolution and elemental specificity. One such example is XFEL driven population inversion of 1s core hole states resulting in inner-shell K${\alpha}$ (2p to 1s) X-ray lasing in elements ranging from neon to copper, which has been utilized for nonlinear spectroscopy and development of next generation X-ray laser sources. Here we show that strong lasing effects, similar to those observed in the optical regime, can occur at 1.5 to 2.1 angstrom wavelengths during high intensity (> ${10^{19}}$ W/cm${^{2}}$) XFEL driven inner-shell lasing and superfluorescence of copper and manganese. Depending on the temporal substructure of the XFEL pump pulses, the resulting inner-shell X-ray laser pulses can exhibit strong spatial inhomogeneities as well as spectral inhomogeneities and broadening. Through 3D Maxwell Bloch theory we show that the observed spatial inhomogeneities result from X-ray filamentation, and that the spectral broadening is driven by Rabi cycling with sub-femtosecond periods. These findings indicate that we have generated Angstrom-wavelength x-ray pulses (containing ${10^{6}}$ - ${10^{8}}$ photons) in the strong lasing regime, some of them with pulse lengths of less than 100 attoseconds.

Published
2024

2. Distinct transient structural rearrangement of ionized water revealed by XFEL X-ray pump X-ray probe experiment

Author

Stransky, Michal, Lane, Thomas J., Gorel, Alexander, Boutet, Sébastien, Schlichting, Ilme, Mancuso, Adrian P., Jurek, Zoltan, and Ziaja, Beata

Subjects
Physics - Plasma Physics
Abstract

Using X-ray free electron laser (XFEL) radiation to conduct an X-ray pump X-ray probe experiment, we studied strongly ionized water as part of our ongoing work on radiation damage. After irradiance with a pump pulse with a nominal fluence of ~$5 \times 10^5$ J/cm$^2$, we observed for pump-probe delays of 75 fs and longer an unexpected structural rearrangement, exhibiting a characteristic length scale of ~9 \r{A}. Simulations suggest that the experiment probes a superposition of ionized water in two distinct regimes. In the first, fluences expected at the X-ray focus create nearly completely ionized water, which as a result becomes effectively transparent to the probe. In the second regime, out of focus pump radiation produces O$^{1+}$ and O$^{2+}$ ions, which rearrange due to Coulombic repulsion over 10s of fs. Importantly, structural changes in the low fluence regime have implications for the design of two-pulse X-ray experiments that aim to study unperturbed liquid samples. Our simulations account for two key observations in the experimental data: the decrease in ambient water signal and an increase in low-angle X-ray scattering. They cannot, however, account for the experimentally observed 9 \r{A} feature. A satisfactory account of this feature presents a new challenge for theory., Comment: 24 main text pages, 6 supplement pages (30 total), 4 main text figures, 3 supplemental figures, 2 supplemental tables

Published
2024

3. Resolving Length Scale Dependent Transient Disorder Through an Ultrafast Phase Transition

Author

Griffiths, Jack, Suzana, Ana Flávia, Wu, Longlong, Marks, Samuel D., Esposito, Vincent, Boutet, Sébastien, Evans, Paul G., Mitchell, J. F., Dean, Mark P. M., Keen, David A., Robinson, Ian, Billinge, Simon J. L., and Bozin, Emil S.

Subjects
Condensed Matter - Materials Science
Abstract

Material functionality can be strongly determined by structure extending only over nanoscale distances. The pair distribution function presents an opportunity to shift structural studies beyond idealized crystal models and investigate structure over varying length scales. Applying this method with ultrafast time resolution has the potential to similarly disrupt the study of structural dynamics and phase transitions. Here, we demonstrate such a measurement of CuIr$_{2}$S$_{4}$ optically pumped from its low temperature Ir-dimerized phase. Dimers are optically suppressed without spatial correlation, generating a structure whose level of disorder depends strongly on length scale. The re-development of structural ordering over tens of picoseconds is directly tracked over both space and time as a transient state is approached. This measurement demonstrates both the crucial role of local structure and disorder in non-equilibrium processes and the feasibility of accessing this information with state-of-the-art XFEL facilities., Comment: 14 page manuscript with 4 figures. 13 page Supplementary with 17 figures. 27 pages and 21 figures in total

Published
2023
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4. Optical control of ultrafast structural dynamics in a fluorescent protein.

Author

Hutchison, Christopher, Baxter, James, Fitzpatrick, Ann, Dorlhiac, Gabriel, Fadini, Alisia, Perrett, Samuel, Maghlaoui, Karim, Lefèvre, Salomé, Cordon-Preciado, Violeta, Ferreira, Josie, Chukhutsina, Volha, Garratt, Douglas, Barnard, Jonathan, Galinis, Gediminas, Glencross, Flo, Morgan, Rhodri, Stockton, Sian, Taylor, Ben, Yuan, Letong, Romei, Matthew, Lin, Chi-Yun, Marangos, Jon, Schmidt, Marius, Chatrchyan, Viktoria, Buckup, Tiago, Morozov, Dmitry, Park, Jaehyun, Park, Sehan, Eom, Intae, Kim, Minseok, Jang, Dogeun, Choi, Hyeongi, Hyun, HyoJung, Park, Gisu, Nango, Eriko, Tanaka, Rie, Owada, Shigeki, Tono, Kensuke, DePonte, Daniel, Carbajo, Sergio, Seaberg, Matt, Aquila, Andrew, Boutet, Sebastien, Barty, Anton, Iwata, So, Boxer, Steven, Groenhof, Gerrit, and van Thor, Jasper

Subjects
Motion, Vibration, Rhodopsin, Hydrogen Bonding
Abstract

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Published
2023

5. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.

Author

Jernigan, Rebecca J, Logeswaran, Dhenugen, Doppler, Diandra, Nagaratnam, Nirupa, Sonker, Mukul, Yang, Jay-How, Ketawala, Gihan, Martin-Garcia, Jose M, Shelby, Megan L, Grant, Thomas D, Mariani, Valerio, Tolstikova, Alexandra, Sheikh, Michelle Z, Yung, Mimi Cho, Coleman, Matthew A, Zaare, Sahba, Kaschner, Emily K, Rabbani, Mohammad Towshif, Nazari, Reza, Zacks, Michele A, Hayes, Brandon, Sierra, Raymond G, Hunter, Mark S, Lisova, Stella, Batyuk, Alexander, Kupitz, Christopher, Boutet, Sebastien, Hansen, Debra T, Kirian, Richard A, Schmidt, Marius, Fromme, Raimund, Frank, Matthias, Ros, Alexandra, Chen, Julian J-L, Botha, Sabine, and Fromme, Petra

Subjects
Humans, Crystallography, X-Ray, Lasers, Temperature, Electrons, COVID-19, SARS-CoV-2, NSP15, NendoU, X-ray free-electron laser, serial femtosecond crystallography, Prevention, Infectious Diseases, Emerging Infectious Diseases, Vaccine Related, Biodefense, Infection, Chemical Sciences, Biological Sciences, Information and Computing Sciences, Biophysics
Abstract

NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

Published
2023

6. In-Situ Observation of the Formation of Laser-Induced Periodic Surface Structures with Extreme Spatial and Temporal Resolution

Author

Sokolowski-Tinten, Klaus, Bonse, Jörn, Barty, Anton, Chapman, Henry N., Bajt, Saša, Bogan, Mike J., Boutet, Sebastien, Cavalleri, Andrea, Düsterer, Stefan, Frank, Matthias, Hajdu, Janos, Hau-Riege, Stefan, Marchesini, Stefano, Stojanovic, Nikola, Treusch, Rolf, Lotsch, H.K.V., Founding Editor, Rhodes, William T., Editor-in-Chief, Adibi, Ali, Series Editor, Asakura, Toshimitsu, Series Editor, Hänsch, Theodor W., Series Editor, Krausz, Ferenc, Series Editor, Masters, Barry R., Series Editor, Midorikawa, Katsumi, Series Editor, Venghaus, Herbert, Series Editor, Weber, Horst, Series Editor, Weinfurter, Harald, Series Editor, Kobayashi, Kazuya, Series Editor, Markel, Vadim, Series Editor, Stoian, Razvan, editor, and Bonse, Jörn, editor

Published
2023
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7. X-ray diffractive imaging of controlled gas-phase molecules: Toward imaging of dynamics in the molecular frame

Author

Kierspel, Thomas, Morgan, Andrew, Wiese, Joss, Mullins, Terry, Aquila, Andy, Barty, Anton, Bean, Richard, Boll, Rebecca, Boutet, Sébastien, Bucksbaum, Philip, Chapman, Henry N., Christensen, Lauge, Fry, Alan, Hunter, Mark, Koglin, Jason E., Liang, Mengning, Mariani, Valerio, Natan, Adi, Robinson, Joseph, Rolles, Daniel, Rudenko, Artem, Schnorr, Kirsten, Stapelfeldt, Henrik, Stern, Stephan, Thøgersen, Jan, Yoon, Chun Hong, Wang, Fenglin, and Küpper, Jochen

Subjects
Physics - Atomic and Molecular Clusters, Physics - Chemical Physics
Abstract

We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV ($\lambda\approx130 \text{pm}$) provided by the Linac Coherent Light Source. Diffracted photons were recorded on the CSPAD detector and a two-dimensional diffraction pattern of the equilibrium structure of 2,5-diiodothiophene was recorded. The retrieved distance between the two iodine atoms agrees with the quantum-chemically calculated molecular structure to within 5 %. The experimental approach allows for the imaging of intrinsic molecular dynamics in the molecular frame, albeit this requires more experimental data which should be readily available at upcoming high-repetition-rate facilities.

Published
2019
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8. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Author

Kovacs, Gabriela Nass, Colletier, Jacques-Philippe, Grünbein, Marie, Yang, Yang, Stensitzki, Till, Batyuk, Alexander, Carbajo, Sergio, Doak, R, Ehrenberg, David, Foucar, Lutz, Gasper, Raphael, Gorel, Alexander, Hilpert, Mario, Kloos, Marco, Koglin, Jason, Reinstein, Jochen, Roome, Christopher, Schlesinger, Ramona, Seaberg, Matthew, Shoeman, Robert, Stricker, Miriam, Boutet, Sébastien, Haacke, Stefan, Heberle, Joachim, Heyne, Karsten, Domratcheva, Tatiana, Barends, Thomas, and Schlichting, Ilme

Subjects
Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy allow identifying a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multi-photon effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.

Published
2019
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9. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Author

Wolff, Alexander M, Young, Iris D, Sierra, Raymond G, Brewster, Aaron S, Martynowycz, Michael W, Nango, Eriko, Sugahara, Michihiro, Nakane, Takanori, Ito, Kazutaka, Aquila, Andrew, Bhowmick, Asmit, Biel, Justin T, Carbajo, Sergio, Cohen, Aina E, Cortez, Saul, Gonzalez, Ana, Hino, Tomoya, Im, Dohyun, Koralek, Jake D, Kubo, Minoru, Lazarou, Tomas S, Nomura, Takashi, Owada, Shigeki, Samelson, Avi J, Tanaka, Tomoyuki, Tanaka, Rie, Thompson, Erin M, van den Bedem, Henry, Woldeyes, Rahel A, Yumoto, Fumiaki, Zhao, Wei, Tono, Kensuke, Boutet, Sebastien, Iwata, So, Gonen, Tamir, Sauter, Nicholas K, Fraser, James S, and Thompson, Michael C

Subjects
Inorganic Chemistry, Chemical Sciences, 1.4 Methodologies and measurements, microcrystals, batch crystallization, serial crystallography, MicroED, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

Published
2020

10. Ultrafast X-ray scattering offers a structural view of excited-state charge transfer

Author

Yong, Haiwang, Xu, Xuan, Ruddock, Jennifer M., Stankus, Brian, Carrascosa, Andrés Moreno, Zotev, Nikola, Bellshaw, Darren, Du, Wenpeng, Goff, Nathan, Chang, Yu, Boutet, Sébastien, Carbajo, Sergio, Koglin, Jason E., Liang, Mengning, Robinson, Joseph S., Kirrander, Adam, Minitti, Michael P., and Weber, Peter M.

Published
2021

11. Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

Author

Yun, Ji-Hye, Li, Xuanxuan, Yue, Jianing, Park, Jae-Hyun, Jin, Zeyu, Li, Chufeng, Hu, Hao, Shi, Yingchen, Pandey, Suraj, Carbajo, Sergio, Boutet, Sébastien, Hunter, Mark S., Liang, Mengning, Sierra, Raymond G., Lane, Thomas J., Zhou, Liang, Weierstall, Uwe, Zatsepin, Nadia A., Ohki, Mio, Tame, Jeremy R. H., Park, Sam-Yong, Spence, John C. H., Zhang, Wenkai, Schmidt, Marius, Lee, Weontae, and Liu, Haiguang

Published
2021

12. Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Author

Dasgupta, Medhanjali, Budday, Dominik, de Oliveira, Saulo H. P., Madzelan, Peter, Marchany-Rivera, Darya, Seravalli, Javier, Hayes, Brandon, Sierra, Raymond G., Boutet, Sébastien, Hunter, Mark S., Alonso-Mori, Roberto, Batyuk, Alexander, Wierman, Jennifer, Lyubimov, Artem, Brewster, Aaron S., Sauter, Nicholas K., Applegate, Gregory A., Tiwari, Virendra K., Berkowitz, David B., Thompson, Michael C., Cohen, Aina E., Fraser, James S., Wall, Michael E., van den Bedem, Henry, and Wilson, Mark A.

Published
2019

13. Analysis of XFEL serial diffraction data from individual crystalline fibrils

Author

Wojtas, David H, Ayyer, Kartik, Liang, Mengning, Mossou, Estelle, Romoli, Filippo, Seuring, Carolin, Beyerlein, Kenneth R, Bean, Richard J, Morgan, Andrew J, Oberthuer, Dominik, Fleckenstein, Holger, Heymann, Michael, Gati, Cornelius, Yefanov, Oleksandr, Barthelmess, Miriam, Ornithopoulou, Eirini, Galli, Lorenzo, Xavier, P Lourdu, Ling, Wai Li, Frank, Matthias, Yoon, Chun Hong, White, Thomas A, Bajt, Saša, Mitraki, Anna, Boutet, Sebastien, Aquila, Andrew, Barty, Anton, Forsyth, V Trevor, Chapman, Henry N, and Millane, Rick P

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Brain Disorders, Neurodegenerative, serial crystallography, coherent X-ray diffractive imaging, single particles, molecular orientation determination, crystalline fibrils, amyloid, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

Published
2017

14. Strongly aligned gas-phase molecules at Free-Electron Lasers

Author

Kierspel, Thomas, Wiese, Joss, Mullins, Terry, Robinson, Joseph, Aquila, Andy, Barty, Anton, Bean, Richard, Boll, Rebecca, Boutet, Sébastien, Bucksbaum, Philip, Chapman, Henry N., Christensen, Lauge, Fry, Alan, Hunter, Mark, Koglin, Jason E., Liang, Mengning, Mariani, Valerio, Morgan, Andrew, Natan, Adi, Petrovic, Vladimir, Rolles, Daniel, Rudenko, Artem, Schnorr, Kirsten, Stapelfeldt, Henrik, Stern, Stephan, Thøgersen, Jan, Yoon, Chun Hong, Wang, Fenglin, Trippel, Sebastian, and Küpper, Jochen

Subjects
Physics - Atomic and Molecular Clusters
Abstract

We demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the Linac Coherent Light Source. Chirped laser pulses, i. e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2,5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment of $\left<\cos^2\!\theta_{2D}\right>$ = 0.85 was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses., Comment: 10 pages, 5 figures

Published
2015
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15. Nonlinear X-ray Compton Scattering

Author

Fuchs, Matthias, Trigo, Mariano, Chen, Jian, Ghimire, Shambhu, Shwartz, Sharon, Kozina, Michael, Jiang, Mason, Henighan, Thomas, Bray, Crystal, Ndabashimiye, Georges, Bucksbaum, P. H., Feng, Yiping, Herrmann, Sven, Carini, Gabriella, Pines, Jack, Hart, Philip, Kenney, Christopher, Guillet, Serge, Boutet, Sebastien, Williams, Garth, Messerschmidt, Marc, Seibert, Marvin, Moeller, Stefan, Hastings, Jerome B., and Reis, David A.

Subjects
Physics - Optics, Physics - Atomic Physics, Physics - Instrumentation and Detectors
Abstract

X-ray scattering is a weak linear probe of matter. It is primarily sensitive to the position of electrons and their momentum distribution. Elastic X-ray scattering forms the basis of atomic structural determination while inelastic Compton scattering is often used as a spectroscopic probe of both single-particle excitations and collective modes. X-ray free-electron lasers (XFELs) are unique tools for studying matter on its natural time and length scales due to their bright and coherent ultrashort pulses. However, in the focus of an XFEL the assumption of a weak linear probe breaks down, and nonlinear light-matter interactions can become ubiquitous. The field can be sufficiently high that even non-resonant multiphoton interactions at hard X-rays wavelengths become relevant. Here we report the observation of one of the most fundamental nonlinear X-ray-matter interactions, the simultaneous Compton scattering of two identical photons producing a single photon at nearly twice the photon energy. We measure scattered photons with an energy near 18 keV generated from solid beryllium irradiated by 8.8-9.75 keV XFEL pulses. The intensity in the X-ray focus reaches up to 4x20 W/cm2, which corresponds to a peak electric field two orders of magnitude higher than the atomic unit of field-strength and within four orders of magnitude of the quantum electrodynamic critical field. The observed signal scales quadratically in intensity and is emitted into a non-dipolar pattern, consistent with the simultaneous two-photon scattering from free electrons. However, the energy of the generated photons shows an anomalously large redshift only present at high intensities. This indicates that the instantaneous high-intensity scattering effectively interacts with a different electron momentum distribution than linear Compton scattering, with implications for the study of atomic-scale structure and dynamics of matter

Published
2015

17. X-ray diffraction of metastable structures from supercooled liquid hydrogen.

Author

Fletcher, Luke B., Levitan, Abraham L., McBride, Emma E., Kim, Jongjin B., Alves, Eduardo P., Aquila, Andrew, Frost, Mungo, Goede, Sebastian, King, Grace, Lane, Thomas J., Liang, Mengning, MacDonald, Michael J., Ofori-Okai, Benjamin K., Schönwälder, Christopher, Sun, Peihao, Hastings, Jerome B., Boutet, Sebastien, and Glenzer, Siegfried H.

Subjects
LIQUID hydrogen, X-ray diffraction, SUPERCOOLED liquids, LIQUID density, SUPERCOOLING, COHERENCE (Optics)
Abstract

We report time resolved observations of the crystallization from liquid hydrogen, supercooled to temperatures below the melting point, using 11.2 keV X-ray diffraction from the Linac Coherent Light Source (LCLS). Changes to the metastable solid and liquid structure factors have been dynamically measured. This allows for a direct determination of the lowest energy crystal polymorphs, the stacking probabilities, as well as the liquid and solid densities and temperatures. Such measurements provide experimental evidence of an Arrhenius-like growth kinetics along the stacking direction during supercooling. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase

Author

Ishigami, Izumi, Lewis-Ballester, Ariel, Echelmeier, Austin, Brehm, Gerrit, Zatsepin, Nadia A., Grant, Thomas D., Coe, Jesse D., Lisova, Stella, Nelson, Garrett, Zhang, Shangji, Dobson, Zachary F., Boutet, Sébastien, Sierra, Raymond G., Batyuk, Alexander, Fromme, Petra, Fromme, Raimund, Spence, John C. H., Ros, Alexandra, Yeh, Syun-Ru, and Rousseau, Denis L.

Published
2019

19. Toxicity of Eosinophil MBP Is Repressed by Intracellular Crystallization and Promoted by Extracellular Aggregation

Author

Soragni, Alice, Yousefi, Shida, Stoeckle, Christina, Soriaga, Angela B, Sawaya, Michael R, Kozlowski, Evelyne, Schmid, Inès, Radonjic-Hoesli, Susanne, Boutet, Sebastien, Williams, Garth J, Messerschmidt, Marc, Seibert, M Marvin, Cascio, Duilio, Zatsepin, Nadia A, Burghammer, Manfred, Riekel, Christian, Colletier, Jacques-Philippe, Riek, Roland, Eisenberg, David S, and Simon, Hans-Uwe

Subjects
Biochemistry and Cell Biology, Biological Sciences, Neurodegenerative, Brain Disorders, Neurosciences, Inflammatory and immune system, Animals, Cell Death, Cell Line, Cell Membrane, Cellulitis, DNA-Binding Proteins, Dermatitis, Atopic, Eosinophilia, Eosinophils, Epithelial Cells, Escherichia coli, Host-Pathogen Interactions, Humans, Immunity, Innate, Mice, Inbred C57BL, Nanoparticles, Secretory Vesicles, Skin, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Eosinophils are white blood cells that function in innate immunity and participate in the pathogenesis of various inflammatory and neoplastic disorders. Their secretory granules contain four cytotoxic proteins, including the eosinophil major basic protein (MBP-1). How MBP-1 toxicity is controlled within the eosinophil itself and activated upon extracellular release is unknown. Here we show how intragranular MBP-1 nanocrystals restrain toxicity, enabling its safe storage, and characterize them with an X-ray-free electron laser. Following eosinophil activation, MBP-1 toxicity is triggered by granule acidification, followed by extracellular aggregation, which mediates the damage to pathogens and host cells. Larger non-toxic amyloid plaques are also present in tissues of eosinophilic patients in a feedback mechanism that likely limits tissue damage under pathological conditions of MBP-1 oversecretion. Our results suggest that MBP-1 aggregation is important for innate immunity and immunopathology mediated by eosinophils and clarify how its polymorphic self-association pathways regulate toxicity intra- and extracellularly.

Published
2015

20. Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser

Author

Beyerlein, Kenneth R., Jönsson, H. Olof, Alonso-Mori, Roberto, Aquila, Andrew, Bajt, Saša, Barty, Anton, Bean, Richard, Koglin, Jason E., Messerschmidt, Marc, Ragazzon, Davide, Sokaras, Dimosthenis, Williams, Garth J., Hau-Riege, Stefan, Boutet, Sébastien, Chapman, Henry N., Tîmneanu, Nicuşor, and Caleman, Carl

Published
2018

21. Femtosecond Diffractive Imaging with a Soft-X-ray Free-Electron Laser

Author

Chapman, Henry N., Barty, Anton, Bogan, Michael J., Boutet, Sebastien, Frank, Matthias, Hau-Riege, Stefan P., Marchesini, Stefano, Woods, Bruce W., Bajt, Sasa, Benner, W. Henry, London, Richard A., Plonjes, Elke, Kuhlmann, Marion, Treusch, Rolf, Dusterer, Stefan, Tschentscher, Thomas, Schneider, Jochen R., Spiller, Eberhard, Moller, Thomas, Bostedt, Christoph, Hoener, Matthias, Shapiro, David A., Hodgson, Keith O., van der Spoel, David, Burmeister, Florian, Bergh, Magnus, Caleman, Carl, Huldt, Gosta, Seibert, M. Marvin, Maia, Filipe R. N. C., Lee, Richard W., Szoke, Abraham, Timneanu, Nicusor, and Hajdu, Janos

Subjects
Physics - Optics
Abstract

Theory predicts that with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus, or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft X-ray free-electron laser. An intense 25 fs, 4 10^13 W/cm^2 pulse, containing 10^12 photons at 32 nm wavelength, produced a coherent diffraction pattern from a nano-structured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling, shows no measurable damage, and extends to diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one., Comment: revtex, 6 pages, 4 figures

Published
2006
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22. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

Author

Gati, Cornelius, Oberthuer, Dominik, Yefanov, Oleksandr, Bunker, Richard D., Stellato, Francesco, Chiu, Elaine, Yeh, Shin-Mei, Aquila, Andrew, Basu, Shibom, Bean, Richard, Beyerlein, Kenneth R., Botha, Sabine, Boutet, Sébastien, DePonte, Daniel P., Doak, R. Bruce, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, James, Daniel R., Kupitz, Christopher, Lomb, Lukas, Messerschmidt, Marc, Nass, Karol, Rendek, Kimberly, Shoeman, Robert L., Wang, Dingjie, Weierstall, Uwe, White, Thomas A., Williams, Garth J., Zatsepin, Nadia A., Fromme, Petra, Spence, John C. H., Goldie, Kenneth N., Jehle, Johannes A., Metcalf, Peter, Barty, Anton, and Chapman, Henry N.

Published
2017

23. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher D. M., Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S., Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P., Liang, Mengning, White, Thomas A., Zatsepin, Nadia A., Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D., Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D., Koglin, Jason E., Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John C. H., Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N., Moffat, Keith, van Thor, Jasper J., and Schmidt, Marius

Published
2016

24. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

Author

Sonker, Mukul, primary, Doppler, Diandra, additional, Egatz-Gomez, Ana, additional, Zaare, Sahba, additional, Rabbani, Mohammad T., additional, Manna, Abhik, additional, Cruz Villarreal, Jorvani, additional, Nelson, Garrett, additional, Ketawala, Gihan K., additional, Karpos, Konstantinos, additional, Alvarez, Roberto C., additional, Nazari, Reza, additional, Thifault, Darren, additional, Jernigan, Rebecca, additional, Oberthür, Dominik, additional, Han, Huijong, additional, Sierra, Raymond, additional, Hunter, Mark S., additional, Batyuk, Alexander, additional, Kupitz, Christopher J., additional, Sublett, Robert E., additional, Poitevin, Frederic, additional, Lisova, Stella, additional, Mariani, Valerio, additional, Tolstikova, Alexandra, additional, Boutet, Sebastien, additional, Messerschmidt, Marc, additional, Meza-Aguilar, J. Domingo, additional, Fromme, Raimund, additional, Martin-Garcia, Jose M., additional, Botha, Sabine, additional, Fromme, Petra, additional, Grant, Thomas D., additional, Kirian, Richard A., additional, and Ros, Alexandra, additional

Published
2022
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25. Speckle contrast of interfering fluorescence X-rays

Author

Trost, Fabian, Ayyer, Kartik, Oberthür, Dominik, Yefanov, Oleksandr, Bajt, Sasa, Caleman, Carl, Weimer, Agnes, Feld, Artur, Weller, Horst, Boutet, Sebastien, Koglin, Jason, Timneanu, Nicusor, Von Zanthier, Joachim, Roehlsberger, Ralf, and Chapman, Henry N.

Subjects
Atom and Molecular Physics and Optics, ddc:550, X-ray fluorescence, incoherent diffraction imaging, Atom- och molekylfysik och optik, XPCS, speckle contrast estimation
Abstract

Journal of synchrotron radiation 30(1), 11 - 23 (2023). doi:10.1107/S1600577522009997, With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity–intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-ray beam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration., Published by Wiley-Blackwell, [S.l.]

Published
2023

26. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

Author

Barends, Thomas R. M., Foucar, Lutz, Ardevol, Albert, Nass, Karol, Aquila, Andrew, Botha, Sabine, Doak, R. Bruce, Falahati, Konstantin, Hartmann, Elisabeth, Hilpert, Mario, Heinz, Marcel, Hoffmann, Matthias C., Köfinger, Jürgen, Koglin, Jason E., Kovacsova, Gabriela, Liang, Mengning, Milathianaki, Despina, Lemke, Henrik T., Reinstein, Jochen, Roome, Christopher M., Shoeman, Robert L., Williams, Garth J., Burghardt, Irene, Hummer, Gerhard, Boutet, Sébastien, and Schlichting, Ilme

Published
2015

27. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Author

Tenboer, Jason, Basu, Shibom, Zatsepin, Nadia, Pande, Kanupriya, Milathianaki, Despina, Frank, Matthias, Hunter, Mark, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Oberthuer, Dominik, Heymann, Michael, Kupitz, Christopher, Conrad, Chelsie, Coe, Jesse, Roy-Chowdhury, Shatabdi, Weierstall, Uwe, James, Daniel, Wang, Dingjie, Grant, Thomas, Barty, Anton, Yefanov, Oleksandr, Scales, Jennifer, Gati, Cornelius, Seuring, Carolin, Srajer, Vukica, Henning, Robert, Schwander, Peter, Fromme, Raimund, Ourmazd, Abbas, Moffat, Keith, Van Thor, Jasper J., Spence, John C. H., Fromme, Petra, Chapman, Henry N., and Schmidt, Marius

Published
2014

28. Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

Author

Sawaya, Michael R., Cascio, Duilio, Gingery, Mari, Rodriguez, Jose, Goldschmidt, Lukasz, Colletier, Jacques-Philippe, Messerschmidt, Marc M., Boutet, Sébastien, Koglin, Jason E., Williams, Garth J., Brewster, Aaron S., Nass, Karol, Hattne, Johan, Botha, Sabine, Doak, R. Bruce, Shoeman, Robert L., DePonte, Daniel P., Park, Hyun-Woo, Federici, Brian A., Sauter, Nicholas K., Schlichting, Ilme, and Eisenberg, David S.

Published
2014

29. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

Author

Pedrini, Bill, Tsai, Ching-Ju, Capitani, Guido, Padeste, Celestino, Hunter, Mark S., Zatsepin, Nadia A., Barty, Anton, Benner, W. Henry, Boutet, Sébastien, Feld, Geoffrey K., Hau-Riege, Stefan P., Kirian, Richard A., Kupitz, Christopher, Messerschmitt, Marc, Ogren, John I., Pardini, Tommaso, Segelke, Brent, Williams, Garth J., Spence, John C. H., Abela, Rafael, Coleman, Matthew, Evans, James E., Schertler, Gebhard F. X., Frank, Matthias, and Li, Xiao-Dan

Published
2014

30. Serial Femtosecond Crystallography of G Protein-Coupled Receptors

Author

Liu, Wei, Wacker, Daniel, Gati, Cornelius, Han, Gye Won, James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Katritch, Vsevolod, Barty, Anton, Zatsepin, Nadia A., Li, Dianfan, Messerschmidt, Marc, Boutet, Sébastien, Williams, Garth J., Koglin, Jason E., Seibert, M. Marvin, Wang, Chong, Shah, Syed T. A., Basu, Shibom, Fromme, Raimund, Kupitz, Christopher, Rendek, Kimberley N., Grotjohann, Ingo, Fromme, Petra, Kirian, Richard A., Beyerlein, Kenneth R., White, Thomas A., Chapman, Henry N., Caffrey, Martin, Spence, John C. H., Stevens, Raymond C., and Cherezov, Vadim

Published
2013
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31. Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature

Author

Kern, Jan, Alonso-Mori, Roberto, Tran, Rosalie, Hattne, Johan, Gildea, Richard J., Echols, Nathaniel, Glöckner, Carina, Hellmich, Julia, Laksmono, Hartawan, Sierra, Raymond G., Lassalle-Kaiser, Benedikt, Koroidov, Sergey, Lampe, Alyssa, Han, Guangye, Gul, Sheraz, DiFiore, Dörte, Milathianaki, Despina, Fry, Alan R., Miahnahri, Alan, Schafer, Donald W., Messerschmidt, Marc, Seibert, M. Marvin, Koglin, Jason E., Sokaras, Dimosthenis, Weng, Tsu-Chien, Sellberg, Jonas, Latimer, Matthew J., Grosse-Kunstleve, Ralf W., Zwart, Petrus H., White, William E., Glatzel, Pieter, Adams, Paul D., Bogan, Michael J., Williams, Garth J., Boutet, Sébastien, Messinger, Johannes, Zouni, Athina, Sauter, Nicholas K., Yachandra, Vittal K., Bergmann, Uwe, and Yano, Junko

Published
2013
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32. Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser

Author

Redecke, Lars, Nass, Karol, Deponte, Daniel P., White, Thomas A., Rehders, Dirk, Barty, Anton, Stellato, Francesco, Liang, Mengning, Barends, Thomas R.M., Boutet, Sébastien, Williams, Garth J., Messerschmidt, Marc, Seibert, M. Marvin, Aquila, Andrew, Arnlund, David, Bajt, Sasa, Barth, Torsten, Bogan, Michael J., Caleman, Carl, Chao, Tzu-Chiao, Doak, R. Bruce, Fleckenstein, Holger, Frank, Matthias, Fromme, Raimund, Galli, Lorenzo, Grotjohann, Ingo, Hunter, Mark S., Johansson, Linda C., Kassemeyer, Stephan, Katona, Gergely, Kirian, Richard A., Koopmann, Rudolf, Kupitz, Chris, Lomb, Lukas, Martin, Andrew V., Mogk, Stefan, Neutze, Richard, Shoeman, Robert L., Steinbrener, Jan, Timneanu, Nicusor, Wang, Dingjie, Weierstall, Uwe, Zatsepin, Nadia A., Spence, John C. H., Fromme, Petra, Schlichting, Ilme, Duszenko, Michael, Betzel, Christian, and Chapman, Henry N.

Published
2013
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33. Observations of phase changes in monoolein during high viscous injection

Author

Wells, Daniel J., Berntsen, Peter, Balaur, Eugeniu, Kewish, Cameron M., Adams, Patrick, Aquila, Andrew, Binns, Jack, Boutet, Sebastien, Broomhall, Hayden, Caleman, Carl, Christofferson, Andrew, Conn, Charlotte E., Dahlqvist, Caroline, Flueckiger, Leonie, Roque, Francisco Gian, Greaves, Tamar L., Hejazian, Majid, Hunter, Mark, Jazi, Marjan Hadian, Jönsson, H. Olof, Pathirannahalage, Sachini Kadaoluwa, Kirian, Richard A., Kozlov, Alex, Kurta, Ruslan P., Marman, Hugh, Mendez, Derek, Morgan, Andrew, Nugent, Keith, Oberthuer, Dominik, Quiney, Harry, Reinhardt, Juliane, Saha, Saumitra, Sellberg, Jonas A., Sierra, Raymond, Wiedorn, Max, Abbey, Brian, Martin, Andrew, V, Darmanin, Connie, Wells, Daniel J., Berntsen, Peter, Balaur, Eugeniu, Kewish, Cameron M., Adams, Patrick, Aquila, Andrew, Binns, Jack, Boutet, Sebastien, Broomhall, Hayden, Caleman, Carl, Christofferson, Andrew, Conn, Charlotte E., Dahlqvist, Caroline, Flueckiger, Leonie, Roque, Francisco Gian, Greaves, Tamar L., Hejazian, Majid, Hunter, Mark, Jazi, Marjan Hadian, Jönsson, H. Olof, Pathirannahalage, Sachini Kadaoluwa, Kirian, Richard A., Kozlov, Alex, Kurta, Ruslan P., Marman, Hugh, Mendez, Derek, Morgan, Andrew, Nugent, Keith, Oberthuer, Dominik, Quiney, Harry, Reinhardt, Juliane, Saha, Saumitra, Sellberg, Jonas A., Sierra, Raymond, Wiedorn, Max, Abbey, Brian, Martin, Andrew, V, and Darmanin, Connie

Abstract

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Published
2022
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34. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

Author

National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Sonker, Mukul, Doppler, Diandra, Egatz-Gomez, Ana, Zaare, Sahba, Rabbani, Mohammad T., Manna, Abhik, Cruz Villarreal, Jorvani, Nelson, Garrett, Ketawala, Gihan K., Karpos, Konstantinos, Alvarez, Roberto C., Nazari, Reza, Thifault, Darren, Jernigan, Rebecca, Oberthür, Dominik, Han, Huijong, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Poitevin, Frederic, Lisova, Stella, Mariani, Valerio, Tolstikova, Alexandra, Boutet, Sebastien, Messerschmidt, Marc, Meza-Aguilar, J Domingo, Fromme, Raimund, Martín-García, Jose Manuel, Botha, Sabine, Fromme, Petra, Grant, Thomas D., Kirian, Richard A., Ros, Alexandra, National Science Foundation (US), National Institutes of Health (US), Department of Energy (US), Max Planck Institute for Medical Research, Sonker, Mukul, Doppler, Diandra, Egatz-Gomez, Ana, Zaare, Sahba, Rabbani, Mohammad T., Manna, Abhik, Cruz Villarreal, Jorvani, Nelson, Garrett, Ketawala, Gihan K., Karpos, Konstantinos, Alvarez, Roberto C., Nazari, Reza, Thifault, Darren, Jernigan, Rebecca, Oberthür, Dominik, Han, Huijong, Sierra, Raymond, Hunter, Mark S., Batyuk, Alexander, Kupitz, Christopher J., Sublett, Robert E., Poitevin, Frederic, Lisova, Stella, Mariani, Valerio, Tolstikova, Alexandra, Boutet, Sebastien, Messerschmidt, Marc, Meza-Aguilar, J Domingo, Fromme, Raimund, Martín-García, Jose Manuel, Botha, Sabine, Fromme, Petra, Grant, Thomas D., Kirian, Richard A., and Ros, Alexandra

Abstract

With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.

Published
2022

35. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

Author

Alonso-Mori, Roberto, Kern, Jan, Gildea, Richard J., Sokaras, Dimosthenis, Weng, Tsu-Chien, Lassalle-Kaiser, Benedikt, Tran, Rosalie, Hattne, Johan, Laksmono, Hartawan, Hellmich, Julia, Glöckner, Carina, Echols, Nathaniel, Sierra, Raymond G., Schafer, Donald W., Sellberg, Jonas, Kenney, Christopher, Herbst, Ryan, Pines, Jack, Hart, Philip, Herrmann, Sven, Grosse-Kunstleve, Ralf W., Latimer, Matthew J., Fry, Alan R., Messerschmidt, Marc M., Miahnahri, Alan, Seibert, M. Marvin, Zwart, Petrus H., White, William E., Adams, Paul D., Bogan, Michael J., Boutet, Sébastien, Williams, Garth J., Zouni, Athina, Messinger, Johannes, Glatzel, Pieter, Sauter, Nicholas K., Yachandra, Vittal K., Yano, Junko, and Bergmann, Uwe

Published
2012

36. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Author

Boutet, Sébastien, Lomb, Lukas, Williams, Garth J., Barends, Thomas R. M., Aquila, Andrew, Doak, R. Bruce, Weierstall, Uwe, DePonte, Daniel P., Steinbrener, Jan, Shoeman, Robert L., Messerschmidt, Marc, Barty, Anton, White, Thomas A., Kassemeyer, Stephan, Kirian, Richard A., Seibert, M. Marvin, Montanez, Paul A., Kenney, Chris, Herbst, Ryan, Hart, Philip, Pines, Jack, Haller, Gunther, Gruner, Sol M., Philipp, Hugh T., Tate, Mark W., Hromalik, Marianne, Koerner, Lucas J., van Bakel, Niels, Morse, John, Ghonsalves, Wilfred, Arnlund, David, Bogan, Michael J., Caleman, Carl, Fromme, Raimund, Hampton, Christina Y., Hunter, Mark S., Johansson, Linda C., Katona, Gergely, Kupitz, Christopher, Liang, Mengning, Martin, Andrew V., Nass, Karol, Redecke, Lars, Stellato, Francesco, Timneanu, Nicusor, Wang, Dingjie, Zatsepin, Nadia A., Schafer, Donald, Defever, James, Neutze, Richard, Fromme, Petra, Spence, John C. H., Chapman, Henry N., and Schlichting, Ilme

Published
2012
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37. Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

Author

Kern, Jan, Alonso-Mori, Roberto, Hellmich, Julia, Tran, Rosalie, Hattne, Johan, Laksmono, Hartawan, Glöckner, Carina, Echols, Nathaniel, Sierra, Raymond G., Sellberg, Jonas, Lassalle-Kaiser, Benedikt, Gildea, Richard J., Glatzel, Pieter, Grosse-Kunstleve, Ralf W., Latimer, Matthew J., McQueen, Trevor A., DiFiore, Dörte, Fry, Alan R., Messerschmidt, Marc, Miahnahri, Alan, Schafer, Donald W., Seibert, M. Marvin, Sokaras, Dimosthenis, Weng, Tsu-Chien, Zwart, Petrus H., White, William E., Adams, Paul D., Bogan, Michael J., Boutet, Sébastien, Williams, Garth J., Messinger, Johannes, Sauter, Nicholas K., Zouni, Athina, Bergmann, Uwe, Yano, Junko, and Yachandra, Vittal K.

Published
2012

38. Observations of phase changes in monoolein during high viscous injection

Author

Wells, Daniel, Berntsen, Peter, Balaur, Eugeniu, Kewish, Cameron, Adams, Patrick, Boutet, Sebastien, Broomhall, Hayden, Caleman, Carl, Christofferson, Andrew, Conn, Charlotte E, Dahlqvist, Caroline, Flueckiger, Leonie, Roque, Francisco Gian, Greaves, Tamar, Hejazian, Majid, Hunter, Mark, Hadian Jazi, Marjan, Jonsson, H Olof, Pathirannahalage, Sachini Kadaoluwa, Kirian, Richard, Kozlov, Alex, Kurta, Ruslan, Marman, Hugh, Mendez, Derek, Morgan, Andrew, Nugent, Keith, Oberthuer, Dominik, Quinney, Harry, Reinhardt, Juliane, Saha, Sumitra, Selberg, Jonas, Sierra, Raymond, Wiedorn, Max, Abbey, Brian, Andrew, Martin, and Darmanin, Connie

Subjects
29999 Physical Sciences not elsewhere classified, FOS: Physical sciences
Abstract

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Published
2022
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39. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Author

Edlund, Petra, Takala, Heikki, Claesson, Elin, Henry, Léocadie, Dods, Robert, Lehtivuori, Heli, Panman, Matthijs, Pande, Kanupriya, White, Thomas, Nakane, Takanori, Berntsson, Oskar, Gustavsson, Emil, Båth, Petra, Modi, Vaibhav, Roy-Chowdhury, Shatabdi, Zook, James, Berntsen, Peter, Pandey, Suraj, Poudyal, Ishwor, Tenboer, Jason, Kupitz, Christopher, Barty, Anton, Fromme, Petra, Koralek, Jake D., Tanaka, Tomoyuki, Spence, John, Liang, Mengning, Hunter, Mark S., Boutet, Sebastien, Nango, Eriko, Moffat, Keith, Groenhof, Gerrit, Ihalainen, Janne, Stojković, Emina A., Schmidt, Marius, and Westenhoff, Sebastian

Published
2016
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40. De novo protein crystal structure determination from X-ray free-electron laser data

Author

Barends, Thomas R.M., Foucar, Lutz, Botha, Sabine, Doak, R. Bruce, Shoeman, Robert L., Nass, Karol, Koglin, Jason E., Williams, Garth J., Boutet, Sebastien, Messerschmidt, Marc, and Schlichting, Ilme

Subjects
Proteins -- Structure, X-rays -- Diffraction, Crystals -- Structure, X-ray crystallography -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The determination of protein crystal structures is hampered by the need for macroscopic crystals. X-ray free-electron lasers (FELs) provide extremely intense pulses of femtosecond duration, which allow data collection from [...]

Published
2014
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41. Ultrafast structural changes within a photosynthetic reaction centre

Author

Dods, Robert, Bath, Petra, Morozov, Dmitry, Gagner, Viktor Ahlberg, Arnlund, David, Luk, Hoi Ling, Kubel, Joachim, Maj, Michal, Vallejos, Adams, Wickstrand, Cecilia, Bosman, Robert, Beyerlein, Kenneth R., Nelson, Garrett, Liang, Mengning, Milathianaki, Despina, Robinson, Joseph, Harimoorthy, Rajiv, Berntsen, Peter, Malmerberg, Erik, Johansson, Linda, Andersson, Rebecka, Carbajo, Sergio, Claesson, Elin, Conrad, Chelsie E., Dahl, Peter, Hammarin, Greger, Hunter, Mark S., Li, Chufeng, Lisova, Stella, Royant, Antoine, Safari, Cecilia, Sharma, Amit, Williams, Garth J., Yefanov, Oleksandr, Westenhoff, Sebastian, Davidsson, Jan, DePonte, Daniel P., Boutet, Sebastien, Barty, Anton, Katona, Gergely, Groenhof, Gerrit, Branden, Gisela, Neutze, Richard, Dods, Robert, Bath, Petra, Morozov, Dmitry, Gagner, Viktor Ahlberg, Arnlund, David, Luk, Hoi Ling, Kubel, Joachim, Maj, Michal, Vallejos, Adams, Wickstrand, Cecilia, Bosman, Robert, Beyerlein, Kenneth R., Nelson, Garrett, Liang, Mengning, Milathianaki, Despina, Robinson, Joseph, Harimoorthy, Rajiv, Berntsen, Peter, Malmerberg, Erik, Johansson, Linda, Andersson, Rebecka, Carbajo, Sergio, Claesson, Elin, Conrad, Chelsie E., Dahl, Peter, Hammarin, Greger, Hunter, Mark S., Li, Chufeng, Lisova, Stella, Royant, Antoine, Safari, Cecilia, Sharma, Amit, Williams, Garth J., Yefanov, Oleksandr, Westenhoff, Sebastian, Davidsson, Jan, DePonte, Daniel P., Boutet, Sebastien, Barty, Anton, Katona, Gergely, Groenhof, Gerrit, Branden, Gisela, and Neutze, Richard

Abstract

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography(1) using an X-ray free-electron laser(2) to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions. Time-resolved serial femtosecond crystallography is used to reveal the structural changes that stabilize the charge-separation steps of electron-transfer reactions in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds.

Published
2021
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44. Camera for coherent diffractive imaging and holography with a soft-x-ray free-electron laser

Author

Bajt, Sasa, Chapman, Henry N., Spiller, Eberhard A., Alameda, Jennifer B., Woods, Bruce W., Frank, Matthias, Bogan, Michael J., Barty, Anton, Boutet, Sebastien, Marchesini, Stefano, Hau-Riege, Stefan P., Hajdu, Janos, and Shapiro, David

Subjects
Cameras -- Innovations, Diffraction patterns -- Research, Holography -- Research, Imaging systems -- Methods, Free electron lasers -- Usage, X-ray lasers -- Usage, Astronomy, Physics
Abstract

We describe a camera to record coherent scattering patterns with a soft-x-ray free-electron laser (FEL). The camera consists of a laterally graded multilayer mirror, which reflects the diffraction pattern onto a CCD detector. The mirror acts as a bandpass filter for both the wavelength and the angle, which isolates the desired scattering pattern from nonsample scattering or incoherent emission from the sample. The mirror also solves the particular problem of the extreme intensity of the FEL pulses, which are focused to greater than [10.sup.14] W/[cm.sup.2]. The strong undiffracted pulse passes through a hole in the mirror and propagates onto a beam dump at a distance behind the instrument rather than interacting with a beam stop placed near the CCD. The camera concept is extendable for the full range of the ftmdamental wavelength of the free electron laser in Hamburg (FLASH) FEL (i.e., between 6 and 60rim) and into the water window. We have fabricated and tested various multilayer mirrors for wavelengths of 32, 16, 13.5, and 4.5 nm. At the shorter wavelengths mirror roughness must be minimized to reduce scattering from the mirror. We have recorded over 30,000 diffraction patterns at the FLASH FEL with no observable mirror damage or degradation of performance. OCIS codes: 040.1490, 030.1670, 050.1940, 140.2600, 340.7470, 310.1210.

Published
2008

46. Femtosecond time-delay X-ray holography

Author

Chapman, Henry N., Hau-Riege, Stefan P., Bogan, Michael J., Bajt, Saša, Barty, Anton, Boutet, Sebastien, Marchesini, Stefano, Frank, Matthias, Woods, Bruce W., Benner, W. Henry, London, Richard A., Rohner, Urs, Szoke, Abraham, Spiller, Eberhard, Moller, Thomas, Bostedt, Christoph, Shapiro, David A., Kuhlmann, Marion, Treusch, Rolf, Plonjes, Elke, Burmeister, Florian, Bergh, Magnus, Caleman, Carl, Huldt, Gosta, Seibert, M. Marvin, and Hajdu, Janos

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Henry N. Chapman (corresponding author) [1, 2]; Stefan P. Hau-Riege [1]; Michael J. Bogan [1]; Saša Bajt [1]; Anton Barty [1]; Sébastien Boutet [1, 3, 4]; Stefano Marchesini [1, [...]

Published
2007
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47. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.

Author

Wolff, Alexander, Wolff, Alexander, Young, Iris, Sierra, Raymond, Brewster, Aaron, Martynowycz, Michael, Nango, Eriko, Sugahara, Michihiro, Nakane, Takanori, Ito, Kazutaka, Aquila, Andrew, Bhowmick, Asmit, Biel, Justin, Carbajo, Sergio, Cohen, Aina, Cortez, Saul, Gonzalez, Ana, Hino, Tomoya, Im, Dohyun, Koralek, Jake, Kubo, Minoru, Lazarou, Tomas, Nomura, Takashi, Owada, Shigeki, Samelson, Avi, Tanaka, Tomoyuki, Tanaka, Rie, Thompson, Erin, Van Den Bedem, Henry, Woldeyes, Rahel, Yumoto, Fumiaki, Zhao, Wei, Tono, Kensuke, Boutet, Sebastien, Iwata, So, Gonen, Tamir, Sauter, Nicholas, Fraser, James, Thompson, Michael, Wolff, Alexander, Wolff, Alexander, Young, Iris, Sierra, Raymond, Brewster, Aaron, Martynowycz, Michael, Nango, Eriko, Sugahara, Michihiro, Nakane, Takanori, Ito, Kazutaka, Aquila, Andrew, Bhowmick, Asmit, Biel, Justin, Carbajo, Sergio, Cohen, Aina, Cortez, Saul, Gonzalez, Ana, Hino, Tomoya, Im, Dohyun, Koralek, Jake, Kubo, Minoru, Lazarou, Tomas, Nomura, Takashi, Owada, Shigeki, Samelson, Avi, Tanaka, Tomoyuki, Tanaka, Rie, Thompson, Erin, Van Den Bedem, Henry, Woldeyes, Rahel, Yumoto, Fumiaki, Zhao, Wei, Tono, Kensuke, Boutet, Sebastien, Iwata, So, Gonen, Tamir, Sauter, Nicholas, Fraser, James, and Thompson, Michael

Abstract

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

Published
2020

48. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Author

Wolff, Alexander M., primary, Young, Iris D., additional, Sierra, Raymond G., additional, Brewster, Aaron S., additional, Martynowycz, Michael W., additional, Nango, Eriko, additional, Sugahara, Michihiro, additional, Nakane, Takanori, additional, Ito, Kazutaka, additional, Aquila, Andrew, additional, Bhowmick, Asmit, additional, Biel, Justin T., additional, Carbajo, Sergio, additional, Cohen, Aina E., additional, Cortez, Saul, additional, Gonzalez, Ana, additional, Hino, Tomoya, additional, Im, Dohyun, additional, Koralek, Jake D., additional, Kubo, Minoru, additional, Lazarou, Tomas S., additional, Nomura, Takashi, additional, Owada, Shigeki, additional, Samelson, Avi J., additional, Tanaka, Tomoyuki, additional, Tanaka, Rie, additional, Thompson, Erin M., additional, van den Bedem, Henry, additional, Woldeyes, Rahel A., additional, Yumoto, Fumiaki, additional, Zhao, Wei, additional, Tono, Kensuke, additional, Boutet, Sebastien, additional, Iwata, So, additional, Gonen, Tamir, additional, Sauter, Nicholas K., additional, Fraser, James S., additional, and Thompson, Michael C., additional

Published
2020
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49. Science Driven Instrumentation for LCLS-II

Author

Arthur, John, primary, Bergmann, Uwe, additional, Brunger, Axel, additional, Bostedt, Christoph, additional, Boutet, Sebastien, additional, Bozek, John, additional, Cocco, Daniele, additional, Devereaux, Tom, additional, Ding, Yuantao, additional, Durr, Hermann, additional, Fritz, David, additional, Gaffney, Kelly, additional, Galayda, John, additional, Goldstein, Julia, additional, Guhr, Markus, additional, Hastings, Jerome, additional, Heimann, Philip, additional, Hodgson, Keith, additional, Huang, Zirong, additional, Kelez, Nicholas, additional, and Montanez, Paul, additional

Published
2014
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50. Short-pulse laser induced transient structure formation and ablation studied with time-resolved coherent XUV-scattering

Author

Sokolowski-Tinten, Klaus, Barty, Anton, Boutet, Sebastien, Shymanovich, Uladzimir, Chapman, Henry, Bogan, Mike, Marchesini, Stefano, Hau-Riege, Stefan, Stojanovic, Nikola, Bonse, Jörn, Rosandi, Yudi, Urbassek, Herbert M., Tobey, Ra’anan, Ehrke, Henri, Cavalleri, Andrea, Düsterer, Stefan, Redlin, Harald, Frank, Matthias, Bajt, Sasa, Schulz, Joachim, Seibert, Marvin, Hajdu, Janos, Treusch, Rolf, Bostedt, Christoph, Hoener, M., and Möeller, T.

Published
2009
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