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Structural Dynamics (Melville, N.Y.)

Jérémy R Rouxel, Markus Kowalewski, Shaul Mukamel
Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state...
July 2017: Structural Dynamics (Melville, N.Y.)
Ariel Alcides Petruk, Kostyantyn Pichugin, Germán Sciaini
An electrostatic electron source design capable of producing sub-20 femtoseconds (rms) multi-electron pulses is presented. The photoelectron gun concept builds upon geometrical electric field enhancement at the cathode surface. Particle tracer simulations indicate the generation of extremely short bunches even beyond 40 cm of propagation. Comparisons with compact electron sources commonly used for femtosecond electron diffraction are made.
July 2017: Structural Dynamics (Melville, N.Y.)
Laurent P René de Cotret, Bradley J Siwick
The general problem of background subtraction in ultrafast electron powder diffraction (UEPD) is presented with a focus on the diffraction patterns obtained from materials of moderately complex structure which contain many overlapping peaks and effectively no scattering vector regions that can be considered exclusively background. We compare the performance of background subtraction algorithms based on discrete and dual-tree complex (DTCWT) wavelet transforms when applied to simulated UEPD data on the M1-R phase transition in VO2 with a time-varying background...
July 2017: Structural Dynamics (Melville, N.Y.)
Christopher Kupitz, Jose L Olmos, Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthür, Mark Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Calvey, Andrea Katz, Yujie Chen, Max O Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor Poudyal, Thomas Grant, Mitchell D Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose M Martin-Garcia, James D Zook, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Thomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N Chapman, Nadia Zatsepin, Garrett Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N Phillips, Marius Schmidt
Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated...
July 2017: Structural Dynamics (Melville, N.Y.)
Fabio G Santomauro, Jakob Grilj, Lars Mewes, Georgian Nedelcu, Sergii Yakunin, Thomas Rossi, Gloria Capano, André Al Haddad, James Budarz, Dominik Kinschel, Dario S Ferreira, Giacomo Rossi, Mario Gutierrez Tovar, Daniel Grolimund, Valerie Samson, Maarten Nachtegaal, Grigory Smolentsev, Maksym V Kovalenko, Majed Chergui
We report on an element-selective study of the fate of charge carriers in photoexcited inorganic CsPbBr3 and CsPb(ClBr)3 perovskite nanocrystals in toluene solutions using time-resolved X-ray absorption spectroscopy with 80 ps time resolution. Probing the Br K-edge, the Pb L3-edge, and the Cs L2-edge, we find that holes in the valence band are localized at Br atoms, forming small polarons, while electrons appear as delocalized in the conduction band. No signature of either electronic or structural changes is observed at the Cs L2-edge...
July 2017: Structural Dynamics (Melville, N.Y.)
Monique M Tirion
The α and β subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only β subunits are catalytically active. Why? We re-examine their internal symmetry axes and observe interesting differences. Dividing each chain into an N-terminal head region, a C-terminal foot region, and a central torso, we observe (1) that while the foot and head regions in all chains obtain high and similar mobility, the torsos obtain different mobility profiles, with the β subunits exhibiting a higher motility compared to the α subunits, a trend supported by the crystallographic B-factors...
July 2017: Structural Dynamics (Melville, N.Y.)
Srinivas Niranj Chandrasekaran, Charles W Carter
PATH algorithms for identifying conformational transition states provide computational parameters-time to the transition state, conformational free energy differences, and transition state activation energies-for comparison to experimental data and can be carried out sufficiently rapidly to use in the "high throughput" mode. These advantages are especially useful for interpreting results from combinatorial mutagenesis experiments. This report updates the previously published algorithm with enhancements that improve correlations between PATH convergence parameters derived from virtual variant structures generated by RosettaBackrub and previously published kinetic data for a complete, four-way combinatorial mutagenesis of a conformational switch in Tryptophanyl-tRNA synthetase...
May 2017: Structural Dynamics (Melville, N.Y.)
Marius Schmidt
The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.
May 2017: Structural Dynamics (Melville, N.Y.)
Philip Coppens
A short description of some of the paradigm-changing developments of the study of light-induced structural changes in molecular crystals is presented. The review is by no means comprehensive. The extensive literature on the subject should be consulted for further information.
May 2017: Structural Dynamics (Melville, N.Y.)
Charles W Carter, Srinivas Niranj Chandrasekaran, Violetta Weinreb, Li Li, Tishan Williams
We measured and cross-validated the energetics of networks in Bacillus stearothermophilus Tryptophanyl-tRNA synthetase (TrpRS) using both multi-mutant and modular thermodynamic cycles. Multi-dimensional combinatorial mutagenesis showed that four side chains from this "molecular switch" move coordinately with the active-site Mg(2+) ion as the active site preorganizes to stabilize the transition state for amino acid activation. A modular thermodynamic cycle consisting of full-length TrpRS, its Urzyme, and the Urzyme plus each of the two domains deleted in the Urzyme gives similar energetics...
May 2017: Structural Dynamics (Melville, N.Y.)
Felix Willems, Clemens von Korff Schmising, David Weder, Christian M Günther, Michael Schneider, Bastian Pfau, Sven Meise, Erik Guehrs, Jan Geilhufe, Alaa El Din Merhe, Emmanuelle Jal, Boris Vodungbo, Jan Lüning, Benoit Mahieu, Flavio Capotondi, Emanuele Pedersoli, David Gauthier, Michele Manfredda, Stefan Eisebitt
We present an element specific and spatially resolved view of magnetic domains in Co/Pt heterostructures in the extreme ultraviolet spectral range. Resonant small-angle scattering and coherent imaging with Fourier-transform holography reveal nanoscale magnetic domain networks via magnetic dichroism of Co at the M2,3 edges as well as via strong dichroic signals at the O2,3 and N6,7 edges of Pt. We demonstrate for the first time simultaneous, two-color coherent imaging at a free-electron laser facility paving the way for a direct real space access to ultrafast magnetization dynamics in complex multicomponent material systems...
January 2017: Structural Dynamics (Melville, N.Y.)
A Schuler, M Greif, A P Seitsonen, G Mette, L Castiglioni, J Osterwalder, M Hengsberger
Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate...
January 2017: Structural Dynamics (Melville, N.Y.)
G Salvatella, R Gort, K Bühlmann, S Däster, A Vaterlaus, Y Acremann
[This corrects the article DOI: 10.1063/1.4964892.].
January 2017: Structural Dynamics (Melville, N.Y.)
A Nakamura, T Shimojima, M Nakano, Y Iwasa, K Ishizaka
We report the ultrafast dynamics of electrons and lattice in transition metal thin films (Au, Cu, and Mo) investigated by a combination of ultrafast electron diffraction (UED) and pump-probe optical methods. For a single-crystalline Au thin film, we observe the suppression of the diffraction intensity occuring in 10 ps, which direcly reflects the lattice thermalization via the electron-phonon interaction. By using the two-temperature model, the electron-phonon coupling constant (g) and the electron and lattice temperatures (Te, Tl) are evaluated from UED, with which we simulate the transient optical transmittance...
November 2016: Structural Dynamics (Melville, N.Y.)
Edoardo Baldini, Andreas Mann, Simone Borroni, Christopher Arrell, Frank van Mourik, Fabrizio Carbone
A femtosecond pump-probe setup is described that is optimised for broadband transient reflectivity experiments on solid samples over a wide temperature range. By combining high temporal resolution and a broad detection window, this apparatus can investigate the interplay between coherent collective modes and high-energy electronic excitations, which is a distinctive characteristic of correlated electron systems. Using a single-shot readout array detector at frame rates of 10 kHz allows resolving coherent oscillations with amplitudes <10(-4)...
November 2016: Structural Dynamics (Melville, N.Y.)
A S Johnson, L Miseikis, D A Wood, D R Austin, C Brahms, S Jarosch, C S Strüber, P Ye, J P Marangos
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...
November 2016: Structural Dynamics (Melville, N.Y.)
Mizuho Fushitani, Akiyoshi Hishikawa
We present applications of extreme ultraviolet (XUV) single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules...
November 2016: Structural Dynamics (Melville, N.Y.)
Marie Preuße, Sergey I Bokarev, Saadullah G Aziz, Oliver Kühn
The Frenkel exciton model was adapted to describe X-ray absorption and resonant inelastic scattering spectra of polynuclear transition metal complexes by means of the restricted active space self-consistent field method. The proposed approach allows to substantially decrease the requirements on computational resources if compared to a full supermolecular quantum chemical treatment. This holds true, in particular, in cases where the dipole approximation to the electronic transition charge density can be applied...
November 2016: Structural Dynamics (Melville, N.Y.)
Isabella Gierz, Andrea Cavalleri
We review our recent time- and angle-resolved photoemission spectroscopy experiments, which measure the transient electronic structure of optically driven graphene. For pump photon energies in the near infrared ([Formula: see text]), we have discovered the formation of a population-inverted state near the Dirac point, which may be of interest for the design of THz lasing devices and optical amplifiers. At lower pump photon energies ([Formula: see text]), for which interband absorption is not possible in doped samples, we find evidence for free carrier absorption...
September 2016: Structural Dynamics (Melville, N.Y.)
G Salvatella, R Gort, K Bühlmann, S Däster, A Vaterlaus, Y Acremann
Ultrafast demagnetization of ferromagnetic metals can be achieved by a heat pulse propagating in the electron gas of a non-magnetic metal layer, which absorbs a pump laser pulse. Demagnetization by electronic heating is investigated on samples with different thicknesses of the absorber layer on nickel. This allows us to separate the contribution of thermalized hot electrons compared to non-thermal electrons. An analytical model describes the demagnetization amplitude as a function of the absorber thickness...
September 2016: Structural Dynamics (Melville, N.Y.)
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