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We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.

We experimentally study the interaction between intense infrared few-cycle laser pulses and an ultrathin (∼2 µm) flat liquid sheet of isopropanol running in vacuum. We observe a rapid decline in transmission above a critical peak intensity of 50 TW/cm2 of the initially transparent liquid sheet, and the emission of a plume of material. We find both events are due to the creation of a surface plasma and are similar to processes observed in dielectric solids. After calculating the electron density for different laser peak intensities, we find an electron scattering rate of 0.3 fs-1 in liquid isopropanol to be consistent with our data. We study the dynamics of the plasma plume to find the expansion velocity of the plume front.

An atomic-level picture of molecular and bulk processes, such as chemical bonding and charge transfer, necessitates an understanding of the dynamical evolution of these systems. On the ultrafast timescales associated with nuclear and electronic motion, the temporal behaviour of a system is often interrogated in a 'pump-probe' scheme. Here, an initial 'pump' pulse triggers dynamics through photoexcitation, and after a carefully controlled delay a 'probe' pulse initiates projection of the instantaneous state of the evolving system onto an informative measurable quantity, such as electron binding energy. In this paper, we apply spectral ghost imaging to a pump-probe time-resolved experiment at an X-ray free-electron laser (XFEL) facility, where the observable is spectral absorption in the X-ray regime. By exploiting the correlation present in the shot-to-shot fluctuations in the incoming X-ray pulses and measured electron kinetic energies, we show that spectral ghost imaging can be applied to time-resolved pump-probe measurements. In the experiment presented, interpretation of the measurement is simplified because spectral ghost imaging separates the overlapping contributions to the photoelectron spectrum from the pump and probe pulse.

The photoelectron spectra of both liquid and gas phase aromatic molecules are reported. The spectra were obtained using a 34.1 eV source produced by high harmonic generation and analysed with the help of high-level ab initio simulations using the reflection principle combined with path integral molecular dynamics simulations accounting for nuclear quantum effects for the gas phase. We demonstrate the suitability of three trimethylbenzenes (1,3,5-trimethylbenzene, 1,2,3-trimethylbenzene and 1,2,4-trimethylbenzene) as a solvent for liquid photoelectron spectroscopy of solute species. We also discuss the electrokinetic charging of a non-polar liquid jet.

Even within the sudden approximation, the removal of one neutral Hartree-Fock orbital does not leave the molecule in a pure one-hole state of the cation; coupling to virtual orbitals leads to a breakdown in the molecular orbital picture. This can be understood as interaction with two-hole one-particle states (singly excited cations) and becomes significant when those states are energetically similar to the one-hole states. This splitting of states is most relevant for inner valence holes which lie above the double ionisation potential. As such, impulsive creation of an inner valence hole (IVH) wavepacket results in a time dependent charge density which is purely electronic in nature (charge migration) [1] , [2] , though it depends on the nuclear geometry at the time of excitation, and subsequent nuclear motion will result in decoherence [3] .

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

We have generated isolated attosecond pulses and performed attosecond streaking measurements using a two-colour synthesized laser field consisting of a strong near-infrared few-cycle pulse and a weaker multi-cycle pulse centred at 400 nm. An actively stabilized interferometer was used to coherently combine the two pulses. Using attosecond streaking we characterised the electric fields of the two pulses and accurately retrieved the spectrum of the multi-cycle pulse. We demonstrated a two-fold increase in the flux of isolated attosecond pulses produced and show that their duration was minimally affected by the presence of the weaker field due to spectral filtering by a multilayer mirror.

International audience

The development of attosecond pulses across different photon energies is an essential precursor to performing pump–probe attosecond experiments in complex systems, where the potential of attosecond science1 can be further developed2,3. We report the generation and characterization of synchronized extreme ultraviolet (90 eV) and vacuum ultraviolet (20 eV) pulses, generated simultaneously via high-harmonic generation. The vacuum ultraviolet pulses are well suited for pump–probe experiments that exploit the high photo-ionization cross-sections of many molecules in this spectral region4 as well as the higher photon flux due to the higher conversion efficiency of the high harmonic generation process at these energies5. We temporally characterized all pulses using the attosecond streaking technique6 and the FROG-CRAB retrieval method7. We report 576 ± 16 as pulses at 20 eV and 257 ± 21 as pulses at 90 eV. Our demonstration of synchronized attosecond pulses at different photon energies, which are inherently jitter-free due to the common-path geometry implemented, offers unprecedented possibilities for pump–probe studies.

We demonstrate angle-resolved coherent (ARC) wave mixing using 4 fs light pulses derived from a laser source that spans 550-1000 nm. We believe this to be the shortest pulse duration used to date in coherent multi-dimensional spectroscopy. The marriage of this ultra-broad band, few-cycle coherent source with the ARC technique will permit new investigations of the interplay between energy transfers and quantum superposition states spanning 8200 cmsup-1/sup. We applied this configuration to measurements on the photosynthetic low light (LL) complex from Rhodopseudomonas palustris in solution at ambient temperature. We observe bi-exponential population dynamics for energy transfer across 5500 cmsup-1/sup(0.65 eV), which we attribute to energy transfer from the Qsubx/subtransition of bacteriochlorophylls to the B850 pigment of the complex. We believe for the first time, to the best of our knowledge, we demonstrate that ARC maps can be recorded using a single laser pulse.

International audience

International audience; We theoretically study high-harmonic generation in toluene, ortho-xylene and fluorobenzene driven by a 1.8 μm ultrashort pulse. We find that the chemical substitutions have a strong influence on the amplitude and phase of the emission from the highest occupied molecular orbital, despite having a small influence on the orbital itself. We show that this influence is due to the tunnel ionization step, which depends critically on the sign and amplitude of the asymptotic part of the wave function. We discuss how these effects would manifest in phase-sensitive high-harmonic generation spectroscopy experiments.

The interaction of intense laser pulses with nanoscale particles leads to the production of high-energy electrons, ions, neutral atoms, neutrons and photons. Up to now, investigations have focused on near-infrared to X-ray laser pulses consisting of many optical cycles. Here we study strong-field ionization of rare-gas clusters (103 to 105 atoms) using two-cycle 1.8 μm laser pulses to access a new interaction regime in the limit where the electron dynamics are dominated by the laser field and the cluster atoms do not have time to move significantly. The emission of fast electrons with kinetic energies exceeding 3 keV is observed using laser pulses with a wavelength of 1.8 μm and an intensity of 1 × 1015 W/cm2, whereas only electrons below 500 eV are observed at 800 nm using a similar intensity and pulse duration. Fast electrons are preferentially emitted along the laser polarization direction, showing that they are driven out from the cluster by the laser field. In addition to direct electron emission, an electron rescattering plateau is observed. Scaling to even longer wavelengths is expected to result in a highly directional current of energetic electrons on a few-femtosecond timescale.

We report, to the best of our knowledge, the first application of time-domain ptychography for the characterization of few-cycle laser pulses. Our method enables zero-additional phase measurements of over-octave-spanning laser pulses in the single cycle regime. The spectral phase is recovered using a robust ptychography algorithm that requires no input apart from the measured data trace. In addition to numerical tests, we validate our new device experimentally by reconstructing the complex electric field of a 1.5 cycle laser pulse with a bandwidth spanning 490 to 1060 nm. We further check the accuracy of our device by comparing the measured phases of octave-spanning chirped pulses to the known dispersion of fused silica glass.

Wepresent the first measurement of the vectorial response of strongly dressed helium atoms probed by an attosecond pulse train (APT) polarised either parallel or perpendicular to the dressing field polarisation. The transient absorption is probed as a function of delay between the APT and the Linearly polarised 800 nmfield of peak intensity 1.3∗1014 W cm-2. The APT spans the photon energy range 1642 eV, covering the first ionisation energy of helium (24.59 eV). With parallel polarised dressing and probing fields, we observe modulations with periods of one half and one quarter of the dressing field period. When the polarisation of the dressing field is altered from parallel to perpendicular with respect to the APT polarisation we observe a large suppression in the Modulation depth of the above ionisation threshold absorption. In addition to this we present the intensity dependence of the harmonic modulation depth as a function of delay between the dressing and probe fields, with dressing field peak intensities ranging from 2∗1012 to 2∗1014 W cm-2.We compare our experimental results with a full-dimensional solution of the single-atom time-dependent (TD) Schrdinger equation obtained using the recently developed abinitio TDB-spline ADCmethod and find good qualitative agreement for the above threshold harmonics.

The challenge of measuring ultrafast electron dynamics will be explained. Recent progress on soft X-ray sources based upon XFELs and HHG and their appication to time resolved absorption spectroscopy and related techniques will be described.

We report on the characterization of space-time couplings in high energy sub-2-cycle 770nm laser pulses using a self-referencing single-shot method. Using spatially-encoded arrangement filter-based spectral phase interferometry for direct electric field reconstruction (SEA-F-SPIDER) we characterize few-cycle pulses with a wave-front rotation of 2.8x?10^11 rev/sec (1.38 mrad per half-cycle) and pulses with pulse front tilts ranging from to -0.33 fs/um to -3.03 fs/um., Comment: 6 pages, 6 figures

A surprisingly dominant contribution of slow electrons is observed following NIR strong-field ionization of clusters. This is consistent with highly efficient intra-Rydberg correlated electronic decay processes, from which the emission of low-energy electrons is expected.

1 pags. -- Correction to: Scientific Reports https://doi.org/10.1038/s41598-018-22055-9, published online 28 February 2018, A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a ‘molecular movie’ of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy., United States. Dept. of Energy. Office of Basic Energy Sciences

We present a technical review of a beamline built to perform pump-probe experiments with a temporal resolution of < 200 attosecond. This is designed specifically to use the technique of attosecond transient absorption spectroscopy (ATAS) to resolve ultra-fast electron dynamics in atoms and molecules. A non-collinear, interferometrically stable geometry is adopted to allow us to individually control the characteristics of each of the pump and probe arms independent from each other. With the use of an auxiliary interferometer to correct for long-term drifts between the pump and probe arms we measure better than 150as resolution for our time-corrected delay despite having separated beam paths of over 4m in length. In our first experiment we have focused on the time dependence of the electronic states of an atom in a strong laser field. An extreme ultra-violet (XUV) attosecond pulse train (APT) and a precisely synchronized 30fs IR pulse are used in this work. Delay-dependent absorption modulations are observed at even multiples (2 and 4) of the IR dressing field frequency as the pump-probe delay is scanned. We investigate the dependence of the 2ω order absorption modulation amplitude from the transient absorption of laser-dressed helium as the IR dressing field ellipticity is varied, and we discuss the issues in obtaining such results. We present qualitative data indicating a clear anisotropy in the response of the atom to an IR dressing field, and discuss how we will improve this measurement in future experiments.

Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~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., 超強力X線による極微小プラズマ生成を発見 -X線自由電子レーザーを利用したイメージングに重要なメッセージ-. 京都大学プレスリリース. 2015-07-07.

The response of solids to electromagnetic fields is of crucial importance in many areas of science and technology. Many fundamental questions remain to be answered about the dynamics of the photoexcited electrons that underpin this response, which can evolve on timescales of tens to hundreds of attoseconds. How, for example, is the photoexcited electron affected by the periodic potential as it travels in the solid, and how do the other electrons respond in these strongly correlated systems? Furthermore, control of electronic motion in solids with attosecond precision would pave the way for the development of ultrafast optoelectronics. Attosecond electron dynamics can be traced using streaking, a technique in which a strong near-infrared laser field accelerates an attosecond electron wavepacket photoemitted by an extreme ultraviolet light pulse, imprinting timing information onto it. We present attosecond streaking measurements on the wide-bandgap semiconductor tungsten trioxide, and on gold, a metal used in many nanoplasmonic devices. Information about electronic motion in the solid is encoded on the temporal properties of the photoemitted electron wavepackets, which are consistent with a spread of electron transport times to the surface following photoexcitation. (C) 2015 Optical Society of America

We investigate high-order harmonic spectra from aligned diatomic molecules in intense driving fields whose components have orthogonal polarizations. We focus on how the driving-field ellipticity influences structural interference patterns in a macroscopic medium. In a previous publication [Phys. Rev. A 88, 023404 (2013)] we have shown that the non-vanishing ellipticity introduces an effective dynamic shift in the angle for which the two-center interference maxima and minima occur, with regard to the existing condition for linearly polarized fields. In this work we show through simulation that it is still possible to observe this shift in harmonic spectra that have undergone macroscopic propagation, and discuss the parameter range for doing so. These features are investigated for $H_2$ in a bichromatic field composed of two orthogonally polarized waves. The shift is visible both in the near- and in the far-field regime, so that, in principle, it can be observed in experiments., Comment: 9 pages, 6 figures

Peptides are irradiated by femtosecond near-infrared pulses, initiating tunnel ionisation and non-ergodic molecular dissociation. Mass spectrometric analysis of the fragments gives unique structural and dynamical information for femtosecond molecular dynamics research and bioanalytical applications.

The International Year of Light (IYL) in 2015 is a unique opportunity to celebrate and broadcast the enormous contribution of optics to science, technology and culture. The Journal of Modern Optics...

We use a high harmonic generated supercontinuum in the soft X-ray region to measure X-ray absorption near edge structure (XANES) spectra in polythiophene (poly(3-hexylthiophene)) films at multiple absorption edges. A few-cycle carrier-envelope phase-stable laser pulse centered at 1800 nm was used to generate a stable soft X-ray supercontinuum, with amplitude gating limiting the generated pulse duration to a single optical half-cycle. We report a quantitative transmission measurement of the sulfur L2,3 edge over the range 160-200 eV and the carbon K edge from 280 to 330 eV. These spectra show all the features previously reported in the XANES spectra of polythiophene, but for the first time they are measured with a source that has an approximately 1 fs pulse duration. This study opens the door to measurements that can fully time-resolve the photoexcited electronic dynamics in these systems.

We present a variant of spatially encoded spectral shearing interferometry for measuring two-dimensional spatio-temporal slices of few-cycle pulses centered around 2 μm. We demonstrate experimentally that the device accurately retrieves the pulse-front tilt caused by angular dispersion of two-cycle pulses. We then use the technique to characterize 500-650 μJ pulses from a hollow fiber pulse compressor, with durations as short as 7.1 fs (1.3 optical cycles).

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.

International audience; We report the first measurement of the near oxygen K-edge auger spectrum of the glycine molecule. Our work employed an x-ray free electron laser as the photon source operated with input photon energies tunable between 527 and 547 eV. Complete electron spectra were recorded at each photon energy in the tuning range, revealing resonant and non-resonant auger structures. Finally ab initio theoretical predictions are compared with the measured above the edge auger spectrum and an assignment of auger decay channels is performed.