Exploring the Fundamental Spatial Limits of Magnetic All-Optical Switching.

All-optical switching (AOS) results in ultrafast and deterministic magnetization reversal upon single laser pulse excitation, potentially supporting faster and more energy-efficient data storage. To explore the fundamental limits of achievable bit densities in AOS, we have used soft X-ray transient grating spectroscopy to study the ultrafast magnetic response of a GdFe alloy after a spatially structured excitation with a periodicity of 17 nm. The ultrafast spatial evolution of the magnetization in combination with atomistic spin dynamics and microscopic temperature model calculations allows us to derive a detailed phase diagram of AOS as a function of both the absorbed energy density and the nanoscale excitation period. Our results suggest that the minimum size for AOS in GdFe alloys, induced by a nanoscale periodic excitation, is around 25 nm and that this limit is governed by ultrafast lateral electron diffusion and by the threshold for optical damage.

A sub-100†nm thickness flat jet for extreme ultraviolet to soft X-ray absorption spectroscopy.

Experimental characterization of the structural, electronic and dynamic properties of dilute systems in aqueous solvents, such as nanoparticles, molecules and proteins, are nowadays an open challenge. X-ray absorption spectroscopy (XAS) is probably one of the most established approaches to this aim as it is element-specific. However, typical dilute systems of interest are often composed of light elements that require extreme-ultraviolet to soft X-ray photons. In this spectral regime, water and other solvents are rather opaque, thus demanding radical reduction of the solvent volume and removal of the liquid to minimize background absorption. Here, we present an experimental endstation designed to operate a liquid flat jet of sub-micrometre thickness in a vacuum environment compatible with extreme ultraviolet/soft XAS measurements in transmission geometry. The apparatus developed can be easily connected to synchrotron and free-electron-laser user-facility beamlines dedicated to XAS experiments. The conditions for stable generation and control of the liquid flat jet are analyzed and discussed. Preliminary soft XAS measurements on some test solutions are shown.

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.

Stimulated Brillouin Scattering in the Time Domain at 1 nm

We used extreme ultraviolet (EUV) pulses to create transient gratings (TGs) with sub-100 nm spatial periodicity in a ß-Ga_{2}O_{3} single crystal. The EUV TG launches acoustic modes parallel to the sample surface, whose dynamics were revealed via backward diffraction of a third, time-delayed, EUV pulse. In addition, the sharp penetration depth of EUV light launches acoustic modes along the surface normal with a broad wave vector spectrum. The dynamics of selected modes at a wave vector tangibly larger (≈1 nm^{-1}) than the TG one is detected in the time domain via the interference between the backward diffracted TG signal and the stimulated Brillouin backscattering of the EUV probe. While stimulated Brillouin backscattering of an optical probe was reported in previous EUV TG experiments, its extension to shorter wavelengths can be used as a contactless experimental tool for filling the gap between the wave vector range accessible by inelastic hard x-ray and thermal neutron scattering techniques, and the one accessible through Brillouin scattering of visible and UV light.

Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents.

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions.

Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding.

G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.

All-Optical Switching on the Nanometer Scale Excited and Probed with Femtosecond Extreme Ultraviolet Pulses.

Ultrafast control of magnetization on the nanometer length scale, in particular all-optical switching, is key to putting ultrafast magnetism on the path toward future technological application in data storage technology. However, magnetization manipulation with light on this length scale is challenging due to the wavelength limitations of optical radiation. Here, we excite transient magnetic gratings in a GdFe alloy with a periodicity of 87 nm by the interference of two coherent femtosecond light pulses in the extreme ultraviolet spectral range. The subsequent ultrafast evolution of the magnetization pattern is probed by diffraction of a third, time-delayed pulse tuned to the Gd N-edge at a wavelength of 8.3 nm. By examining the simultaneously recorded first and second order diffractions and by performing reference real-space measurements with a wide-field magneto-optical microscope with femtosecond time resolution, we can conclusively demonstrate the ultrafast emergence of all-optical switching on the nanometer length scale.

Angstrom-Resolved Interfacial Structure in Buried Organic-Inorganic Junctions.

Charge transport processes at interfaces play a crucial role in many 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 Å, with changes of less than 1 Å resulting in easily detectable SXR SHG spectral shifts (ca. hundreds of milli-electron volts).

UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction.

Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the ß-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.

Hydrogen Bonding and Solvation of a Proline-Based Peptide Model in Salt Solutions.

The hydrogen bonding of water and water/salt mixtures around the proline-based tripeptide model glycyl-l-prolyl-glycinamide·HCl (GPG-NH2) is investigated here by multi-wavelength UV resonance Raman spectroscopy (UVRR) to clarify the role of ion-peptide interactions in affecting the conformational stability of this peptide. The unique sensitivity and selectivity of the UVRR technique allow us to efficiently probe the hydrogen bond interaction between water molecules and proline residues in different solvation conditions, along with its influence on trans to cis isomerism in the hydrated tripeptide. The spectroscopic data suggest a relevant role played by the cations in altering the solvation shell at the carbonyl site of proline., while the fluoride and chloride anions were found to promote the establishment of the strongest interactions on the C=O site of proline. This latter effect is reflected in the greater stabilization of the trans conformers of the tripeptide in the presence of these specific ions. The molecular view provided by UVRR experiments was complemented by the results of circular dichroism (CD) measurements that show a strong structural stabilizing effect on the ß-turn motif of GPG-NH2 observed in the presence of KF as a co-solute.

Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments.

The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.

Non-linear self-driven spectral tuning of Extreme Ultraviolet Femtosecond Pulses in monoatomic materials.

Self-action nonlinearity is a key aspect - either as a foundational element or a detrimental factor - of several optical spectroscopies and photonic devices. Supercontinuum generation, wavelength converters, and chirped pulse amplification are just a few examples. The recent advent of Free Electron Lasers (FEL) fostered building on nonlinearity to propose new concepts and extend optical wavelengths paradigms for extreme ultraviolet (EUV) and X-ray regimes. No evidence for intrapulse dynamics, however, has been reported at such short wavelengths, where the light-matter interactions are ruled by the sharp absorption edges of core electrons. Here, we provide experimental evidence for self-phase modulation of femtosecond FEL pulses, which we exploit for fine self-driven spectral tunability by interaction with sub-micrometric foils of selected monoatomic materials. Moving the pulse wavelength across the absorption edge, the spectral profile changes from a non-linear spectral blue-shift to a red-shifted broadening. These findings are rationalized accounting for ultrafast ionization and delayed thermal response of highly excited electrons above and below threshold, respectively.

Nanoscale Transient Magnetization Gratings Created and Probed by Femtosecond Extreme Ultraviolet Pulses.

We utilize coherent femtosecond extreme ultraviolet (EUV) pulses from a free electron laser (FEL) to generate transient periodic magnetization patterns with periods as short as 44 nm. Combining spatially periodic excitation with resonant probing at the M-edge of cobalt allows us to create and probe transient gratings of electronic and magnetic excitations in a CoGd alloy. In a demagnetized sample, we observe an electronic excitation with a rise time close to the FEL pulse duration and ∼0.5 ps decay time indicative of electron-phonon relaxation. When the sample is magnetized to saturation in an external field, we observe a magnetization grating, which appears on a subpicosecond time scale as the sample is demagnetized at the maxima of the EUV intensity and then decays on the time scale of tens of picoseconds via thermal diffusion. The described approach opens multiple avenues for studying dynamics of ultrafast magnetic phenomena on nanometer length scales.

Ultrafast Dynamics of Plasmon-Mediated Charge Transfer in Ag@CeO2 Studied by Free Electron Laser Time-Resolved X-ray Absorption Spectroscopy.

Expanding the activity of wide bandgap semiconductors from the UV into the visible range has become a central goal for their application in green solar photocatalysis. The hybrid plasmonic/semiconductor system, based on silver nanoparticles (Ag NPs) embedded in a film of CeO2, is an example of a functional material developed with this aim. In this work, we take advantage of the chemical sensitivity of free electron laser (FEL) time-resolved soft X-ray absorption spectroscopy (TRXAS) to investigate the electron transfer process from the Ag NPs to the CeO2 film generated by the NPs plasmonic resonance photoexcitation. Ultrafast changes (<200 fs) of the Ce N4,5 absorption edge allowed us to conclude that the excited Ag NPs transfer electrons to the Ce atoms of the CeO2 film through a highly efficient electron-based mechanism. These results demonstrate the potential of FEL-based TRXAS measurements for the characterization of energy transfer in novel hybrid plasmonic/semiconductor materials.

Impact of lockdown on Covid-19 case fatality rate and viral mutations spread in 7 countries in Europe and North America.

BACKGROUND: Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11th, 2020 and the same month several Countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus. METHODS: The calculation of the Case Fatality Rate of SARS-CoV-2 in the Countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data . Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the Country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between Countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p value was adjusted using Holm method. We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the Countries selected. RESULTS: In this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each Country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy. CONCLUSIONS: Strict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different Countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.

Investigation of genomic DNA methylation by ultraviolet resonant Raman spectroscopy.

Cytosine plays a preeminent role in DNA methylation, an epigenetic mechanism that regulates gene expression, the misregulation of which can lead to severe diseases. Several methods are nowadays employed for assessing the global DNA methylation levels, but none of them combines simplicity, high sensitivity, and low operating costs to be translated into clinical applications. Ultraviolet (UV) resonant Raman measurements at excitation wavelengths of 272 nm, 260 nm, 250 nm, and 228 nm have been carried out on isolated deoxynucleoside triphosphates (dNTPs), on a dNTP mixture as well as on genomic DNA (gDNA) samples, commercial from salmon sperm and non-commercial from B16 murine melanoma cell line. The 228 nm excitation wavelength was identified as the most suitable energy for enhancing cytosine signals over the other DNA bases. The UV Raman measurements performed at this excitation wavelength on hyper-methylated and hypo-methylated DNA from Jurkat leukemic T-cell line have revealed significant spectral differences with respect to gDNA isolated from salmon sperm and mouse melanoma B16 cells. This demonstrates how the proper choice of the excitation wavelength, combined with optimized extraction protocols, makes UV Raman spectroscopy a suitable technique for highlighting the chemical modifications undergone by cytosine nucleotides in gDNA upon hyper- and hypo-methylation events.

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant.

BACKGROUND: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS: We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann-Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS: We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). CONCLUSIONS: These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates.

Laser-slicing at a low-emittance storage ring.

Laser-slicing at a diffraction-limited storage ring light source in the soft X-ray region is investigated with theoretical and numerical modelling. It turns out that the slicing efficiency is favoured by the ultra-low beam emittance, and that slicing can be implemented without interference to the standard multi-bunch operation. Spatial and spectral separation of the sub-picosecond radiation pulse from a hundreds of picosecond-long background is achieved by virtue of 1:1 imaging of the radiation source. The spectral separation is enhanced when the radiator is a transverse gradient undulator. The proposed configuration applied to the Elettra 2.0 six-bend achromatic lattice envisages total slicing efficiency as high as 10-7, one order of magnitude larger than the demonstrated state-of-the-art, at the expense of pulse durations as long as 0.4 ps FWHM and average laser power as high as ∼40 W.

Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway.

A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.

Impulsive UV-pump/X-ray probe study of vibrational dynamics in glycine.

We report an ab-initio study of a pump-probe experiment on the amino-acid glycine. We consider an UV pump followed by an X-ray probe tuned to carbon K-edge and study the vibronic structure of the core transition. The simulated experiment is feasible using existing free electron laser or high harmonic generation sources and thanks to the localization of the core orbitals posseses chemical selectivity. The present theory applies to other experimental schemes, including the use of a THz probe, available with present soft X-ray free electron lasers and/or high harmonic generation sources.