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

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

Nonlinear Kinetic Energy Harvesting

Abstract Harvesting of kinetic energy present in the form of random vibrations is an interesting option due to the almost universal presence of this kind of motion. Traditional generators based on piezoelectric effect are built with linear oscillators made by a piezoelectric beam and a mass used to tune the resonance frequency on the predominant frequency of the vibrations spectrum. However, in most cases the ambient random vibrations have their energy distributed over a wide spectrum of frequencies, being rich especially at low frequency. Furthermore frequency tuning is not always possible due to geometrical/dynamical constraints. In this work we present a different method based on the exploitation of the nonlinear dynamical features of bistable oscillator. The experimental results and the digital simulations show that nonlinear harvester (e.g. bistable oscillators) can overcome some of the most severe limitations of generators based on linear dynamics

Saturable Absorption of Free-Electron Laser Radiation by Graphite near the Carbon K-Edge

The interaction of intense light with matter gives rise to competing nonlinear responses that can dynamically change material properties. Prominent examples are saturable absorption (SA) and two-photon absorption (TPA), which dynamically increase and decrease the transmission of a sample depending on pulse intensity, respectively. The availability of intense soft X-ray pulses from free-electron lasers (FELs) has led to observations of SA and TPA in separate experiments, leaving open questions about the possible interplay between and relative strength of the two phenomena. Here, we systematically study both phenomena in one experiment by exposing graphite films to soft X-ray FEL pulses of varying intensity. By applying real-time electronic structure calculations, we find that for lower intensities the nonlinear contribution to the absorption is dominated by SA attributed to ground-state depletion; our model suggests that TPA becomes more dominant for larger intensities (\u3e1014 W/cm2). Our results demonstrate an approach of general utility for interpreting FEL spectroscopies

{\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

Transient grating spectroscopy on a DyCo5_5 thin film with femtosecond extreme ultraviolet pulses

Surface acoustic waves (SAWs) are excited by femtosecond extreme ultraviolet (EUV) transient gratings (TGs) in a room-temperature ferrimagnetic DyCo$_5$ alloy. TGs are generated by crossing a pair of EUV pulses from a free electron laser (FEL) with the wavelength of 20.8\,nm matching the Co $M$-edge, resulting in a SAW wavelength of $\Lambda=44$\,nm. Using the pump-probe transient grating scheme in a reflection geometry the excited SAWs could be followed in the time range of -10 to 100\,ps in the thin film. Coherent generation of TGs by ultrafast EUV pulses allows to excite SAW in any material and to investigate their couplings to other dynamics such as spin waves and orbital dynamics

Ultrafast dynamics in (TaSe4)2I triggered by valence and core-level excitation

Dimensionality plays a key role in the emergence of ordered phases, such as charge density-waves (CDW), which can couple to, and modulate, the topological properties of matter. In this work, we study the out-of-equilibrium dynamics of the paradigmatic quasi-one-dimensional material (TaSe4)2I, which exhibits a transition into an incommensurate CDW phase when cooled to just below room temperature, namely at TCDW = 263 K. We make use of both optical laser and free-electron laser (FEL) based time-resolved spectroscopies in order to study the effect of a selective excitation on the normal-state and on the CDW phases by probing the near-infrared/visible optical properties both along and perpendicularly to the direction of the CDW, where the system is metallic and insulating, respectively. Excitation of the core-levels by ultrashort X-ray FEL pulses at 47 eV and 119 eV induces reflectivity transients resembling those recorded when only exciting the valence band of the compound - by near-infrared pulses at 1.55 eV - in the case of the insulating sub-system. Conversely, the metallic sub-system displays relaxation dynamics which depend on the energy of photo-excitation. Moreover, excitation of the CDW amplitude mode is recorded only for excitation at a low-photon-energy. This fact suggests that the coupling of light to ordered states of matter can predominantly be achieved when directly injecting delocalized carriers in the valence band, rather than localized excitations in the core levels. Complementing this, table-top experiments allow us to prove the quasi-unidirectional nature of the CDW phase in (TaSe4)2I, whose fingerprints are detected along its c-axis only. Our results provide new insights into the symmetry of the ordered phase of (TaSe4)2I perturbed by a selective excitation, and suggest a novel approach based on complementary table-top and FEL spectroscopies for the study of complex materials

Nanoscale transient polarization gratings

We present the generation of transient polarization gratings at the nanoscale, achieved using a tailored accelerator configuration of the FERMI free electron laser. We demonstrate the capabilities of such a transient polarization grating by comparing its induced dynamics with the ones triggered by a more conventional intensity grating on a thin film ferrimagnetic alloy. While the signal of the intensity grating is dominated by the thermoelastic response of the system, such a contribution is suppressed in the case of the polarization grating. This exposes helicity-dependent magnetization dynamics that have so-far remained hidden under the large thermally driven response. We anticipate nanoscale transient polarization gratings to become useful for the study of any physical, chemical and biological systems possessing chiral symmetry

FEL stochastic spectroscopy revealing silicon bond softening dynamics

Time-resolved X-ray Emission/Absorption Spectroscopy (Tr-XES/XAS) is an informative experimental tool sensitive to electronic dynamics in materials, widely exploited in diverse research fields. Typically, Tr-XES/XAS requires X-ray pulses with both a narrow bandwidth and sub-picosecond pulse duration, a combination that in principle finds its optimum with Fourier transform-limited pulses. In this work, we explore an alternative xperimental approach, capable of simultaneously retrieving information about unoccupied (XAS) and occupied (XES) states from the stochastic fluctuations of broadband extreme ultraviolet pulses of a free-electron laser. We used this method, in combination with singular value decomposition and Tikhonov regularization procedures, to determine the XAS/XES response from a crystalline silicon sample at the L2,3-edge, with an energy resolution of a few tens of meV. Finally, we combined this spectroscopic method with a pump-probe approach to measure structural and electronic dynamics of a silicon membrane. Tr-XAS/XES data obtained after photoexcitation with an optical laser pulse at 390 nm allowed us to observe perturbations of the band structure, which are compatible with the formation of the predicted precursor state of a non-thermal solid-liquid phase transition associated with a bond softening phenomenon