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

Comparative Structural Analysis of GFRP, Reinforced Concrete, and Steel Frames under Seismic Loads

Fibre-reinforced polymer composites in general, and especially glass fibre-reinforced polymer (GFRP), have increasingly been used in recent decades in construction. The advantages of GFRP as an alternative construction material are its high strength-to-weight ratio, corrosive resistance, high durability, and ease of installation. The main purpose of this study is to evaluate the response of GFRP under dynamic conditions (more specifically, under seismic loads) and to compare the performance of this composite material with that of two traditional building materials: reinforced concrete and structural steel. To this aim, a finite element analysis is carried out on a two-dimensional frame modelled with steel, reinforced concrete (RC), or GFRP pultruded materials and subjected to a seismic input. The dynamic response of the structure is evaluated for the three building materials in terms of displacements, inter-storey drift, base shear, and stress. The results show a good performance of the GFRP frame, with stress distribution and displacements halfway between those of RC and steel. Most importantly, the GFRP frame outperforms the other materials in terms of reduced weight and, thus, base shear (-40% compared to steel and -88.5% compared to RC)

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

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

Short-wavelength four wave mixing experiments using single and two-color schemes at FERMI

The development of ultra-bright extreme ultraviolet (EUV) and X-ray free electron laser (FEL) sources has enabled the extension of wave-mixing approaches into the short wavelength regime. Such a class of experiments relies upon nonlinear interactions among multiple light pulses offering a unique tool for exploring the dynamics of ultrafast processes and correlations between selected excitations at relevant length and time scales adding elemental and site selectivity as well. Besides the availability of a suitable photon source, the implementation of wave mixing methodology requires efforts in developing the instrumental set-up. We have realized at the FERMI FEL two dedicated set-ups to handle multiple FEL beams with preselected parameters in a non-collinear fashion and control their interaction sequence at the target. These unique apparatuses, combined with the exceptional characteristics of the seeded FERMI FEL, have allowed us to make the first steps into this field and further advances are foreseen in the near future