Search

Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and dosed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; 1001 Scientific and Technological Research Projects Funding Program; U.S. Department of Energy; Office of Science; Office of Basic Energy Sciences; European Union (EU); Horizon 2020 ; European Research Council (ERC); SYBORG; U.S. Department of Energy Joint Genome Institute; DOE Office of Science User Facility; Max Planck Society; a Max-Planck-Partner Group; CONICYT; CONICYT Doctorado Nacional Grant; Fondo Nacional de Desarrollo Científico y Tecnológico (Fondecyt) Postdoctoral Fellowship; DOE Office of Science, Biological Environmental Research; National Institutes of Health; National Science Foundation Major Research Instrument Grant; NIGMS; Stanford PRECOURT Institute

Using electron and ion spectroscopy, we studied the electron and nuclear dynamics in ~50 000-atom large krypton clusters, following excitation with an intense hard x-ray pulse. Beyond the single pulse experiment, we also present the results of a time-resolved, x-ray pump–near-infrared probe measurement that allows one to learn about the time evolution of the system. After core ionization of the atoms by x-ray photons, trapped Auger and secondary electrons form a nanoplasma in which the krypton ions are embedded, according to the already published scenario. While the ion data show expected features, the electron emission spectra miss the expected pump–probe delay-dependent enhancement except for a slight enhancement in the energy range below 2 eV. Theoretical simulations help to reveal that, due to the deep trapping potential of the ions during the long time expansion accompanied by electron–ion recombination, thermal emission from the transient nanoplasma becomes quenched.

We present results from the SPring-8 Angstrom Compact free electron LAser facility, where we used a high intensity (∼10^20 W/cm2) x-ray pump x-ray probe scheme to observe changes in the ionic structure of silicon induced by x-ray heating of the electrons. By avoiding Laue spots in the scattering signal from a single crystalline sample, we observe a rapid rise in diffuse scattering and a transition to a disordered, liquidlike state with a structure significantly different from liquid silicon. The disordering occurs within 100 fs of irradiation, a timescale that agrees well with first principles simulations, and is faster than that predicted by purely inertial behavior, suggesting that both the phase change and disordered state reached are dominated by Coulomb forces. This method is capable of observing liquid scattering without masking signal from the ambient solid, allowing the liquid structure to be measured throughout and beyond the phase change.

High intensity X-ray Free Electron Lasers (XFEL) are an ideal tool to heat materials directly and isochorically, which can cause them to be modified and damaged irreversibly. During XFEL-matter interactions, the energy of an XFEL beam will be mainly absorbed by photoionization, creating numerous high-energy photo- and Auger electrons. Modelling this process is quite complex since both atomic physics and plasma physics are involved. Atomic collisional-radiative (CR) codes such as FLYCHK are widely used to simulate such processes. However, the CR codes typically assume local thermodynamic equilibrium (LTE) and are limited to zero dimension. In order to understand the sample damaging mechanisms, we performed two-dimensional kinetic particle-in-cell simulations with radiation transport (PIC-RT) to retrieve the temporal processes of XFEL-matter interactions. The dynamics of XFEL-Matter interactions can roughly divide into three different time scales: 1) electron heating and photoionization by XFEL in ~ 10 fs ; 2) collisional heating and ionization by high-energy photo- and Auger electrons with several keV energy in tens of fs to sub-ps; and 3) collective hydrodynamic explosion driven by ~ TPa thermal pressure from ~100 fs to nanoseconds. The simulation results are compared to our recent experiment that a variety of samples were irradiated by Japanese XFEL SACLA with intensities on the order of 10^20 W/cm^2. The post-analysis of the irradiated samples showed that large holes with radius sizes more than one order of magnitude higher than the XFEL spot were created for metallic samples. The hole size is also much larger than the stopping range of high energy electrons. According to our PIC-RT simulations, we attribute the generation of such large holes to the micro-explosion process. Kinect simulation of the hole generation with multiple time scales is also useful and complementary to understand the change of X-Ray diffraction pattern in the experiment that infers significa

We present results from the SPring-8 Angstrom Compact free electron LAser (SACLA) X-ray free electron laser (XFEL) facility, using an X-ray pump, X-ray probe scheme to observe ultrafast changes in the structure of heated graphite. The 9.8 keV XFEL beam was focused to give an intensity on the order of 10^19 W/cm2, and the evolution of the diffraction pattern observed up to delays of 300 fs. The interplanar diffraction peaks weaken significantly within 10s of femtoseconds, but in-plane diffraction orders i.e. those with Miller Index (hk0), persist up to 300 fs, with the observed signal increasing. We interpret this as nonthermal damage through the breaking of interplanar bonds, which at longer timescales leads to ablation by removal of intact graphite sheets. Post-experiment examination of the graphite samples shows damage which is comparable in size to the range of the excited photoelectrons. These results highlight the challenges of accurately modelling X-ray driven heating, as it becomes a routine approach to generating high energy density states.

Nonlinear optical frequency conversion has been challenged to move down to the extreme ultraviolet and x-ray region. However, the extremely low signals have allowed researchers to only perform transmission experiments of the gas phase or ultrathin films. Here, we report second harmonic generation (SHG) of the reflected beam of a soft x-ray free-electron laser from a solid, which is enhanced by the resonant effect. The observation revealed that the double resonance condition can be met by absorption edges for transition metal oxides in the soft x-ray range, and this suggests that the resonant SHG technique can be applicable to a wide range of materials.We discuss the possibility of element-selective SHG spectroscopy measurements in the soft x-ray range.

Time-resolved magneto-optical Kerr effect (MOKE) measurement was demonstrated on a sample of the Au/Fe/Au heterostructure with the Fe layer of 0.35nm thickness under Fe M-edge resonance condition. An ultrabrilliant free electron laser (FEL) in the soft X-ray range was facilitated for the detection of transient signals of resonant MOKE from the ultrathin Fe film. A variation in the Kerr rotation angle was successfully observed on the femtosecond timescale. This technique enables us to reveal the transient magnetization dynamics of such a-few-monolayer magnetic films, which promote the development of spintronic devices.

We have measured electron energy spectra and asymmetry parameters of Ar clusters and Xe clusters illuminated by intense x-rays at 5 and 5.5 keV. A velocity map imaging spectrometer was developed for this purpose and employed at an x-ray free-electron laser facility, SACLA in Japan. The cluster size dependence and the peak fluence dependence of the electron spectra and asymmetry parameters are discussed.

Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at similar to 5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo-and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays.

We have investigated multiphoton multiple ionization of argon and xenon atoms at 5 keV using a new x-ray free electron laser (XFEL) facility, the SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan. The experimental results are compared with the new theoretical results presented here. The absolute fluence of the XFEL pulse has been determined with the help of the calculations utilizing two-photon processes in the argon atom. The high charge states up to +22 observed for Xe in comparison with the calculations point to the occurrence of sequential L-shell multiphoton absorption and of resonance-enabled x-ray multiple ionization.

We have investigated multiphoton multiple ionization dynamics of xenon atoms using a new x-ray free-electron laser facility, SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan, and identified that Xen+ with n up to 26 is produced at a photon energy of 5.5 keV. The observed high charge states (n >= 24) are produced via five-photon absorption, evidencing the occurrence of multiphoton absorption involving deep inner shells. A newly developed theoretical model, which shows good agreement with the experiment, elucidates the complex pathways of sequential electronic decay cascades accessible in heavy atoms. The present study of heavy-atom ionization dynamics in high-intensity hard-x-ray pulses makes a step forward towards molecular structure determination with x-ray free-electron lasers.

T. Koyama, H. Yumoto, K. Tono, T. Sato, T. Togashi, Y. Inubushi, T. Katayama, J. Kim, S. Matsuyama, H. Mimura, M. Yabashi, K. Yamauchi, and H. Ohashi "Damage threshold investigation using grazing incidence irradiation by hard x-ray free electron laser", Proc. SPIE 8848, Advances in X-Ray/EUV Optics and Components VIII, 88480T (27 September 2013); https://doi.org/10.1117/12.2025377.

Multiple photoionization processes of giant rare-gas clusters are investigated in the wavelength region of 51 to 61nm at Spring8. We report here some latest results of our investigation; the frustration of photoionization for giant xenon clusters and the charge transfer in Ar-core Ne-shell clusters.

A mechanism for three-photon double ionization of atoms by extreme-ultraviolet free-electron laser pulses is revealed, where in a sequential process the second ionization step, proceeding via resonant two-photon ionization of ions, is strongly enhanced by the excitation of ionic autoionizing states. In contrast to the conventional model, the mechanism explains the observed relative intensities of photoelectron peaks and their angular dependence in three-photon double ionization of argon.

T. Koyama, H. Yumoto, K. Tono, T. Sato, T. Togashi, Y. Inubushi, T. Katayama, J. Kim, S. Matsuyama, H. Mimura, M. Yabashi, K. Yamauchi, and H. Ohashi "Damage threshold investigation using grazing incidence irradiation by hard x-ray free electron laser", Proc. SPIE 8848, Advances in X-Ray/EUV Optics and Components VIII, 88480T (27 September 2013); https://doi.org/10.1117/12.2025377.

T. Koyama, H. Yumoto, K. Tono, T. Sato, T. Togashi, Y. Inubushi, T. Katayama, J. Kim, S. Matsuyama, H. Mimura, M. Yabashi, K. Yamauchi, and H. Ohashi "Damage threshold investigation using grazing incidence irradiation by hard x-ray free electron laser", Proc. SPIE 8848, Advances in X-Ray/EUV Optics and Components VIII, 88480T (27 September 2013); https://doi.org/10.1117/12.2025377.