Above threshold ionization by few-cycle spatially inhomogeneous fields

We present theoretical studies of above threshold ionization (ATI) produced by spatially inhomogeneous fields. This kind of field appears as a result of the illumination of plasmonic nanostructures and metal nanoparticles with a short laser pulse. We use the time-dependent Schr\"odinger equation (TDSE) in reduced dimensions to understand and characterize the ATI features in these fields. It is demonstrated that the inhomogeneity of the laser electric field plays an important role in the ATI process and it produces appreciable modifications to the energy-resolved photoelectron spectra. In fact, our numerical simulations reveal that high energy electrons can be generated. Specifically, using a linear approximation for the spatial dependence of the enhanced plasmonic field and with a near infrared laser with intensities in the mid- 10^{14} W/cm^{2} range, we show it is possible to drive electrons with energies in the near-keV regime. Furthermore, we study how the carrier envelope phase influences the emission of ATI photoelectrons for few-cycle pulses. Our quantum mechanical calculations are supported by their classical counterparts

Enhanced optical conductivity and many-body effects in strongly-driven photo-excited semi-metallic graphite

The excitation of quasi-particles near the extrema of the electronic band structure is a gateway to electronic phase transitions in condensed matter. In a many-body system, quasi-particle dynamics are strongly influenced by the electronic single-particle structure and have been extensively studied in the weak optical excitation regime. Yet, under strong optical excitation, where light fields coherently drive carriers, the dynamics of many-body interactions that can lead to new quantum phases remain largely unresolved. Here, we induce such a highly non-equilibrium many-body state through strong optical excitation of charge carriers near the van Hove singularity in graphite. We investigate the system's evolution into a strongly-driven photo-excited state with attosecond soft X-ray core-level spectroscopy. Surprisingly, we find an enhancement of the optical conductivity of nearly ten times the quantum conductivity and pinpoint it to carrier excitations in flat bands. This interaction regime is robust against carrier-carrier interaction with coherent optical phonons acting as an attractive force reminiscent of superconductivity. The strongly-driven non-equilibrium state is markedly different from the single-particle structure and macroscopic conductivity and is a consequence of the non-adiabatic many-body state

BioRuby: bioinformatics software for the Ruby programming language

Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser

Molecular structure retrieval directly from laboratory-frame photoelectron spectra in laser-induced electron diffraction

Ubiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically exacerbated when imaging larger molecules or for dynamic systems with little a priori knowledge. Here, we employ laser-induced electron diffraction (LIED) which is a powerful means to determine the precise atomic configuration of an isolated gas-phase molecule with picometre spatial and attosecond temporal precision. We introduce a simple molecular retrieval method, which is based only on the identification of critical points in the oscillating molecular interference scattering signal that is extracted directly from the laboratory-frame photoelectron spectrum. The method is compared with a Fourier-based retrieval method, and we show that both methods correctly retrieve the asymmetrically stretched and bent field-dressed configuration of the asymmetric top molecule carbonyl sulfide (OCS), which is confirmed by our quantum-classical calculations

Imaging an isolated water molecule using a single electron wave packet

Observing changes in molecular structure requires atomic-scale Ångstrom and femtosecond spatio-temporal resolution. We use the Fourier transform (FT) variant of laser-induced electron diffraction (LIED), FT-LIED, to directly retrieve the molecular structure of H2O+ with picometer and femtosecond resolution without a priori knowledge of the molecular structure nor the use of retrieval algorithms or ab initio calculations. We identify a symmetrically stretched H2O+ field-dressed structure that is most likely in the ground electronic state. We subsequently study the nuclear response of an isolated water molecule to an external laser field at four different field strengths. We show that upon increasing the laser field strength from 2.5 to 3.8 V/Å, the O–H bond is further stretched and the molecule slightly bends. The observed ultrafast structural changes lead to an increase in the dipole moment of water and, in turn, a stronger dipole interaction between the nuclear framework of the molecule and the intense laser field. Our results provide important insights into the coupling of the nuclear framework to a laser field as the molecular geometry of H2O+ is altered in the presence of an external field

Influence of orbital symmetry on diffraction imaging with rescattering electron wave packets

Citation: Pullen, M. G., Wolter, B., Le, A. T., Baudisch, M., Sclafani, M., Pires, H., . . . Biegert, J. (2016). Influence of orbital symmetry on diffraction imaging with rescattering electron wave packets. Nature Communications, 7, 6. doi:10.1038/ncomms11922The ability to directly follow and time-resolve the rearrangement of the nuclei within molecules is a frontier of science that requires atomic spatial and few-femtosecond temporal resolutions. While laser-induced electron diffraction can meet these requirements, it was recently concluded that molecules with particular orbital symmetries (such as pi(g)) cannot be imaged using purely backscattering electron wave packets without molecular alignment. Here, we demonstrate, in direct contradiction to these findings, that the orientation and shape of molecular orbitals presents no impediment for retrieving molecular structure with adequate sampling of the momentum transfer space. We overcome previous issues by showcasing retrieval of the structure of randomly oriented O-2 and C2H2 molecules, with pi(g) and pi(u) symmetries, respectively, and where their ionization probabilities do not maximize along their molecular axes. While this removes a serious bottleneck for laser-induced diffraction imaging, we find unexpectedly strong backscattering contributions from low-Z atoms

Ultrafast electron diffraction imaging of bond breaking in di-ionized acetylene

Visualizing chemical reactions as they occur requires atomic spatial and femtosecond temporal resolution. Here, we report imaging of the molecular structure of acetylene (C2H2) 9 femtoseconds after ionization. Using mid-infrared laser–induced electron diffraction (LIED), we obtained snapshots as a proton departs the [C2H2]2+ ion. By introducing an additional laser field, we also demonstrate control over the ultrafast dissociation process and resolve different bond dynamics for molecules oriented parallel versus perpendicular to the LIED field. These measurements are in excellent agreement with a quantum chemical description of field-dressed molecular dynamicsPostprint (author's final draft

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

Motivation: Phospholipid scramblases (PLSCRs) constitute a family of cytoplasmic membrane-associated proteins that were identified based upon their capacity to mediate a Ca2+-dependent bidirectional movement of phospholipids across membrane bilayers, thereby collapsing the normally asymmetric distribution of such lipids in cell membranes. The exact function and mechanism(s) of these proteins nevertheless remains obscure: data from several laboratories now suggest that in addition to their putative role in mediating transbilayer flip/flop of membrane lipids, the PLSCRs may also function to regulate diverse processes including signaling, apoptosis, cell proliferation and transcription. A major impediment to deducing the molecular details underlying the seemingly disparate biology of these proteins is the current absence of any representative molecular structures to provide guidance to the experimental investigation of their function