High throughput interactome determination via sulfur anomalous scattering

We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in protein structures at lower percentages than the other atomic species. Here, we run an extensive preliminary investigation to probe both the feasibility and the range of usage of the proposed protocol. In particular, we (i) analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus the differences in the patterns produced by bound proteins with respect to their non-bonded states can be exploited to rapidly assess protein complex formation. Next, we (ii) carried out analyses on the abundances of sulfurs in the different proteomes and molecular dynamics simulations on a representative set of protein structures to probe the typical motion of sulfur atoms. Finally, we (iii) suggest a possible experimental procedure to detect protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale even between other biological molecules, thus paving the way to the development of a novel field of research based on a synchrotron light source.Comment: 9 pages, 4 figure

BGO relaxation dynamics probed with heterodyne detected optical transient gratings

We used optical laser pulses to create transient gratings (TGs) with sub-10 {\mu}m spatial periodicity in a Bismuth Germanate (310) (Bi4Ge3O12) single crystal at room temperature. The TG launches phonon modes, whose dynamics were revealed via forward diffraction of a third, time-delayed, heterodyne-detected optical pulse. Acoustic oscillations have been clearly identified in a time-frequency window not covered by previous spectroscopic studies and their characteristic dynamic parameters have been measured as a function of transferred momenta magnitude and direction.Comment: 6 pages, 4 figure

High-throughput interactome determination via sulfur anomalous scattering

We propose a novel approach for detecting the binding between proteins making use of the anomalous diffraction of natively present heavy elements, e.g., sulfurs, inside molecular three-dimensional structures. In particular, we analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus, the differences in the patterns produced by bound proteins with respect to their nonbonded states can be exploited to rapidly assess protein complex formation. On the basis of our results, we suggest a possible experimental procedure for detecting protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale, thus paving the way for the development of a novel field of research based on a synchrotron light source

Roadmap of ultrafast x-ray atomic and molecular physics

X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (1020 W cm−2) of x-rays at wavelengths down to ~1 Ångstrom, and HHG provides unprecedented time resolution (~50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ~280 eV (44 Ångstroms) and the bond length in methane of ~1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since its discovery roughly 30 years ago, showcasing experiments in AMO physics and other applications. Here we capture the perspectives of 17 leading groups and organize the contributions into four categories: ultrafast molecular dynamics, multidimensional x-ray spectroscopies; high-intensity x-ray phenomena; attosecond x-ray science

Stimulated Brillouin scattering at 1 nm-1 wavevector by extreme ultraviolet transient gratings

We crossed two femtosecond extreme ultraviolet (EUV) pulses in a beta - Ga2O3 (001) single crystal to create transient gratings (TG) of light intensity with sub-100 nm spatial periodicity. The EUV TG excitation launches phonon modes, whose dynamics were revealed via the backward diffraction of a third, time-delayed, EUV probe pulse. In addition to the modes typically observed in this kind of experiment, the phase-matching condition imposed by the TG, combined with the sharp penetration depth of the EUV excitation pulses, permitted to generate and detect phonons with a wavevector tangibly larger (approximately 1 nm-1) than the EUV TG one, via stimulated Brillouin back-scattering (SBBS) of the EUV probe. While SBBS of an optical probe was reported in previous EUV TG experiments, the extension of SBBS to short wavelength radiation can be used as a contact-less experimental tool for filling the gap between the wavevector range accessible through inelastic hard X-ray and thermal neutron scattering techniques, and the one accessible through Brillouin scattering of visible and UV light.Comment: 7 pages, 3 figure

Long-lived nonthermal electron distribution in aluminum excited by femtosecond extreme ultraviolet radiation

We report a time-resolved study of the relaxation dynamics of Al films excited by ultrashort intense free-electron laser (FEL) extreme ultraviolet pulses. The system response was measured through a pump-probe detection scheme, in which an intense FEL pulse tuned around the Al L2,3 edge (72.5 eV) acted as the pump, while a time-delayed ultrafast pulse probed the near-infrared (NIR) reflectivity of the Al film. Remarkably, following the intense FEL excitation, the reflectivity of the film exhibited no detectable variation for hundreds of femtoseconds. Following this latency time, sizable reflectivity changes were observed. Exploiting recent theoretical calculations of the EUV-excited electron dynamics [N. Medvedev et al., Phys. Rev. Lett. 107, 165003 (2011)], the delayed NIR-reflectivity evolution is interpreted invoking the formation of very-long-living nonthermal hot electron distributions in Al after exposure to EUV pulses. Our data represent the first evidence in the time domain of such an intriguing behavior

Optical constants modelling in silicon nitride membrane transiently excited by EUV radiation.

We hereby report on a set of transient optical reflectivity and transmissivity measurements performed on silicon nitride thin membranes excited by extreme ultraviolet (EUV) radiation from a free electron laser (FEL). Experimental data were acquired as a function of the membrane thickness, FEL fluence and probe polarization. The time dependence of the refractive index, retrieved using Jones matrix formalism, encodes the dynamics of electron and lattice excitation following the FEL interaction. The observed dynamics are interpreted in the framework of a two temperature model, which permits to extract the relevant time scales and magnitudes of the processes. We also found that in order to explain the experimental data thermo-optical effects and inter-band filling must be phenomenologically added to the model

{\AA}ngstr\"om-resolved Interfacial Structure in Organic-Inorganic Junctions

Charge transport processes at interfaces which are governed by complex interfacial electronic structure play a crucial role in catalytic reactions, energy storage, photovoltaics, and many biological processes. Here, the first soft X-ray second harmonic generation (SXR-SHG) interfacial spectrum of a buried interface (boron/Parylene-N) is reported. SXR-SHG shows distinct spectral features that are not observed in X-ray absorption spectra, demonstrating its extraordinary interfacial sensitivity. Comparison to electronic structure calculations indicates a boron-organic separation distance of 1.9 {\AA}, wherein changes as small as 0.1 {\AA} result in easily detectable SXR-SHG spectral shifts (ca. 100s of meV). As SXR-SHG is inherently ultrafast and sensitive to individual atomic layers, it creates the possibility to study a variety of interfacial processes, e.g. catalysis, with ultrafast time resolution and bond specificity.Comment: 19 page

Towards jitter-free pump-probe measurements at seeded free electron laser facilities

X-ray free electron lasers (FEL) coupled with optical lasers have opened unprecedented opportunities for studying ultrafast dynamics in matter. The major challenge in pump-probe experiments using FEL and optical lasers is synchronizing the arrival time of the two pulses. Here we report a technique that benefits from the seeded-FEL scheme and uses the optical seed laser for nearly jitter-free pump-probe experiments. Timing jitter as small as 6 fs has been achieved and confirmed by measurements of FEL-induced transient reflectivity changes of Si3N4 using both collinear and non-collinear geometries. Planned improvements of the experimental set-up are expected to further reduce the timing jitter between the two pulses down to fs level