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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.)
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.)
Daniel Schick, Sebastian Eckert, Niko Pontius, Rolf Mitzner, Alexander Föhlisch, Karsten Holldack, Florian Sorgenfrei
We present an X-ray-optical cross-correlator for the soft ([Formula: see text]) up to the hard X-ray regime based on a molybdenum-silicon superlattice. The cross-correlation is done by probing intensity and position changes of superlattice Bragg peaks caused by photoexcitation of coherent phonons. This approach is applicable for a wide range of X-ray photon energies as well as for a broad range of excitation wavelengths and requires no external fields or changes of temperature. Moreover, the cross-correlator can be employed on a 10 ps or 100 fs time scale featuring up to 50% total X-ray reflectivity and transient signal changes of more than 20%...
September 2016: Structural Dynamics (Melville, N.Y.)
W Verhoeven, J F M van Rens, M A W van Ninhuijs, W F Toonen, E R Kieft, P H A Mutsaers, O J Luiten
We demonstrate the use of two TM110 resonant cavities to generate ultrashort electron pulses and subsequently measure electron energy losses in a time-of-flight type of setup. The method utilizes two synchronized microwave cavities separated by a drift space of 1.45 m. The setup has an energy resolution of 12 ± 2 eV FWHM at 30 keV, with an upper limit for the temporal resolution of 2.7 ± 0.4 ps. Both the time and energy resolution are currently limited by the brightness of the tungsten filament electron gun used...
September 2016: Structural Dynamics (Melville, N.Y.)
S Höfer, T Kämpfer, E Förster, T Stöhlker, I Uschmann
We explore the InSb-semiconductor lattice dynamics after excitation of high density electron-hole plasma with an ultrashort and intense laser pulse. By using time resolved x-ray diffraction, a sub-mÅ and sub-ps resolution was achieved. Thus, a strain of 4% was measured in a 3 nm thin surface layer 2 ps after excitation. The lattice strain was observed for the first 5 ps as exponentially decaying, changing rapidly by time and by depth. The observed phenomena can only be understood assuming nonlinear time dependent laser absorption where the absorption depth decreases by a factor of twenty compared to linear absorption...
September 2016: Structural Dynamics (Melville, N.Y.)
Heikki Takala, Stephan Niebling, Oskar Berntsson, Alexander Björling, Heli Lehtivuori, Heikki Häkkänen, Matthijs Panman, Emil Gustavsson, Maria Hoernke, Gemma Newby, Federico Zontone, Michael Wulff, Andreas Menzel, Janne A Ihalainen, Sebastian Westenhoff
Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains...
September 2016: Structural Dynamics (Melville, N.Y.)
A von Reppert, J Pudell, A Koc, M Reinhardt, W Leitenberger, K Dumesnil, F Zamponi, M Bargheer
We present a temperature and fluence dependent Ultrafast X-Ray Diffraction study of a laser-heated antiferromagnetic dysprosium thin film. The loss of antiferromagnetic order is evidenced by a pronounced lattice contraction. We devise a method to determine the energy flow between the phonon and spin system from calibrated Bragg peak positions in thermal equilibrium. Reestablishing the magnetic order is much slower than the cooling of the lattice, especially around the Néel temperature. Despite the pronounced magnetostriction, the transfer of energy from the spin system to the phonons in Dy is slow after the spin-order is lost...
September 2016: Structural Dynamics (Melville, N.Y.)
George D Calvey, Andrea M Katz, Chris B Schaffer, Lois Pollack
Knowledge of protein structure provides essential insight into function, enhancing our understanding of diseases and enabling new treatment development. X-ray crystallography has been used to solve the structures of more than 100 000 proteins; however, the vast majority represent long-lived states that do not capture the functional motions of these molecular machines. Reactions triggered by the addition of a ligand can be the most challenging to detect with crystallography because of the difficulty of synchronizing reactions to create detectable quantities of transient states...
September 2016: Structural Dynamics (Melville, N.Y.)
Michael Greif, Tibor Nagy, Maksym Soloviov, Luca Castiglioni, Matthias Hengsberger, Markus Meuwly, Jürg Osterwalder
[This corrects the article DOI: 10.1063/1.4922611.].
September 2016: Structural Dynamics (Melville, N.Y.)
Malik Muhammad Abdullah, Zoltan Jurek, Sang-Kil Son, Robin Santra
We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation...
September 2016: Structural Dynamics (Melville, N.Y.)
Terry Mullins, Jochen Küpper
No abstract text is available yet for this article.
July 2016: Structural Dynamics (Melville, N.Y.)
Dimitri Imanbaew, Maxim F Gelin, Christoph Riehn
Excited state dynamics of deprotonated and protonated fluorescein were investigated by polarization dependent femtosecond time-resolved pump-probe photofragmentation in a 3D ion trap. Transients of deprotonated fluorescein exhibit vibrational wavepacket dynamics with weak polarization dependence. Transients of protonated fluorescein show only effects of molecular alignment and rotational dephasing. The time resolved rotational anisotropy of protonated fluorescein is simulated by the calculated orientational correlation function...
July 2016: Structural Dynamics (Melville, N.Y.)
T Stensitzki, Y Yang, A Berg, A Mahammed, Z Gross, K Heyne
We combined femtosecond (fs) VIS pump-IR probe spectroscopy with fs VIS pump-supercontinuum probe spectroscopy to characterize the photoreaction of the hexacoordinated Al(tpfc-Br8)(py)2 in a comprehensive way. Upon fs excitation at ∼400 nm in the Soret band, the excitation energy relaxes with a time constant of (250 ± 80) fs to the S2 and S1 electronic excited states. This is evident from the rise time of the stimulated emission signal in the visible spectral range. On the same time scale, narrowing of broad infrared signals in the C=C stretching region around 1500 cm(-1) is observed...
July 2016: Structural Dynamics (Melville, N.Y.)
Kyung Hwan Kim, Jong Goo Kim, Key Young Oang, Tae Wu Kim, Hosung Ki, Junbeom Jo, Jeongho Kim, Tokushi Sato, Shunsuke Nozawa, Shin-Ichi Adachi, Hyotcherl Ihee
The [Au(CN)2 (-)]3 trimer in water experiences a strong van der Waals interaction between the d(10) gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms...
July 2016: Structural Dynamics (Melville, N.Y.)
T Stensitzki, Y Yang, V Muders, R Schlesinger, J Heberle, K Heyne
Vibrational dynamics of the retinal all-trans to 13-cis photoisomerization in channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by femtosecond visible pump mid-IR probe spectroscopy. After photoexcitation, the transient infrared absorption of C-C stretching modes was detected. The formation of the 13-cis photoproduct marker band at 1193 cm(-1) was observed within the time resolution of 0.3 ps. We estimated the photoisomerization yield to (60 ± 6) %. We found additional time constants of (0...
July 2016: Structural Dynamics (Melville, N.Y.)
Rebecca Boll, Benjamin Erk, Ryan Coffee, Sebastian Trippel, Thomas Kierspel, Cédric Bomme, John D Bozek, Mitchell Burkett, Sebastian Carron, Ken R Ferguson, Lutz Foucar, Jochen Küpper, Tatiana Marchenko, Catalin Miron, Minna Patanen, Timur Osipov, Sebastian Schorb, Marc Simon, Michelle Swiggers, Simone Techert, Kiyoshi Ueda, Christoph Bostedt, Daniel Rolles, Artem Rudenko
Ultrafast electron transfer in dissociating iodomethane and fluoromethane molecules was studied at the Linac Coherent Light Source free-electron laser using an ultraviolet-pump, X-ray-probe scheme. The results for both molecules are discussed with respect to the nature of their UV excitation and different chemical properties. Signatures of long-distance intramolecular charge transfer are observed for both species, and a quantitative analysis of its distance dependence in iodomethane is carried out for charge states up to I(21+)...
July 2016: Structural Dynamics (Melville, N.Y.)
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