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Structural Dynamics (Melville, N.Y.)

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https://read.qxmd.com/read/30931347/svd-aided-non-orthogonal-decomposition-sanod-method-to-exploit-prior-knowledge-of-spectral-components-in-the-analysis-of-time-resolved-data
#1
H Ki, Y Lee, E H Choi, S Lee, H Ihee
Analysis of time-resolved data typically involves discriminating noise against the signal and extracting time-independent components and their time-dependent contributions. Singular value decomposition (SVD) serves this purpose well, but the extracted time-independent components are not necessarily the physically meaningful spectra directly representing the actual dynamic or kinetic processes but rather a mathematically orthogonal set necessary for constituting the physically meaningful spectra. Converting the orthogonal components into physically meaningful spectra requires subsequent posterior analyses such as linear combination fitting (LCF) and global fitting (GF), which takes advantage of prior knowledge about the data but requires that all components are known or satisfactory components are guessed...
March 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30915389/generation-of-a-large-compressive-strain-wave-in-graphite-by-ultrashort-pulse-laser-irradiation
#2
Xiaocui Wang, A Jarnac, J C Ekström, Å U J Bengtsson, F Dorchies, H Enquist, A Jurgilaitis, M N Pedersen, C-M Tu, M Wulff, J Larsson
We have studied strain wave generation in graphite induced by an intense ultrashort laser pulse. The study was performed in the intensity regime above the ablation threshold of graphite. The aim was to maximize the strain and, thus, also the internal pressure (stress). Laser pulses with a 1 ps temporal duration melt the surface of graphite resulting in a molten material which initially exists at the solid density. As the molten material expands, a compressive strain wave starts propagating into the crystal below the molten layer...
March 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30915388/ultrafast-structural-dynamics-of-photo-reactions-observed-by-time-resolved-x-ray-cross-correlation-analysis
#3
Peter Vester, Ivan A Zaluzhnyy, Ruslan P Kurta, Klaus B Møller, Elisa Biasin, Kristoffer Haldrup, Martin Meedom Nielsen, Ivan A Vartanyants
We applied angular X-ray Cross-Correlation analysis (XCCA) to scattering images from a femtosecond resolution X-ray free-electron laser pump-probe experiment with solvated PtPOP {[Pt2 (P2 O5 H2 )4 ]4- } metal complex molecules. The molecules were pumped with linear polarized laser pulses creating an excited state population with a preferred orientational (alignment) direction. Two time scales of 1.9 ± 1.5 ps and 46 ± 10 ps were revealed by angular XCCA associated with structural changes and rotational dephasing of the solvent molecules, respectively...
March 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30915387/time-resolved-x-ray-optical-pump-probe-simulations-on-n-2-molecules
#4
Athiya Mahmud Hanna, Oriol Vendrell, Robin Santra
The dynamics of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msup> <mml:mrow> <mml:msub> <mml:mi>N</mml:mi> <mml:mn>2</mml:mn> </mml:msub> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> <mml:mo>+</mml:mo> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> dications after x-ray-induced Auger decay and their probing with a delayed infrared probe pulse are theoretically investigated based on a quantum-mechanical model including all relevant electronic states for which wave-packet calculations on ab-initio potential energy curves are performed...
March 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868089/time-resolved-x-ray-crystallography-capture-of-a-slow-reaction-tetrahydrofolate-intermediate
#5
Hongnan Cao, Jeffrey Skolnick
Time-resolved crystallography is a powerful technique to elucidate molecular mechanisms at both spatial (angstroms) and temporal (picoseconds to seconds) resolutions. We recently discovered an unusually slow reaction at room temperature that occurs on the order of days: the in crystalline reverse oxidative decay of the chemically labile (6S)-5,6,7,8-tetrahydrofolate in complex with its producing enzyme Escherichia coli dihydrofolate reductase. Here, we report the critical analysis of a representative dataset at an intermediate reaction time point...
March 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868088/phonon-driven-charge-dynamics-in-polycrystalline-acetylsalicylic-acid-mapped-by-ultrafast-x-ray-diffraction
#6
Christoph Hauf, Antonio-Andres Hernandez Salvador, Marcel Holtz, Michael Woerner, Thomas Elsaesser
The coupled lattice and charge dynamics induced by phonon excitation in polycrystalline acetylsalicylic acid (aspirin) are mapped by femtosecond x-ray powder diffraction. The hybrid-mode character of the 0.9 ± 0.1 THz methyl rotation in the aspirin molecules is evident from collective charge relocations over distances of some 100 pm, much larger than the sub-picometer nuclear displacements. Oscillatory charge relocations around the methyl group generate a torque on the latter, thus coupling electronic and nuclear motions...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868087/structural-dynamics-of-lavo-3-on-the-nanosecond-time-scale
#7
Matthew Brahlek, Vladimir A Stoica, Jason Lapano, Lei Zhang, Hirofumi Akamatsu, I-Cheng Tung, Venkatraman Gopalan, Donald A Walko, Haidan Wen, John W Freeland, Roman Engel-Herbert
Due to the strong dependence of electronic properties on the local bonding environment, a full characterization of the structural dynamics in ultrafast experiments is critical. Here, we report the dynamics and structural refinement at nanosecond time scales of a perovskite thin film by combining optical excitation with time-resolved X-ray diffraction. This is achieved by monitoring the temporal response of both integer and half-integer diffraction peaks of LaVO3 in response to an above-band-gap 800 nm pump pulse...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868086/intermittent-plasticity-in-individual-grains-a-study-using-high-energy-x-ray-diffraction
#8
K Chatterjee, A J Beaudoin, D C Pagan, P A Shade, H T Philipp, M W Tate, S M Gruner, P Kenesei, J-S Park
Long-standing evidence suggests that plasticity in metals may proceed in an intermittent fashion. While the documentation of intermittency in plastically deforming materials has been achieved in several experimental settings, efforts to draw connections from dislocation motion and structure development to stress relaxation have been limited, especially in the bulk of deforming polycrystals. This work uses high energy x-ray diffraction measurements to build these links by characterizing plastic deformation events inside individual deforming grains in both the titanium alloy, Ti-7Al, and the magnesium alloy, AZ31...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868085/coulomb-interactions-in-high-coherence-femtosecond-electron-pulses-from-tip-emitters
#9
Nora Bach, Till Domröse, Armin Feist, Thomas Rittmann, Stefanie Strauch, Claus Ropers, Sascha Schäfer
Tip-based photoemission electron sources offer unique properties for ultrafast imaging, diffraction, and spectroscopy experiments with highly coherent few-electron pulses. Extending this approach to increased bunch-charges requires a comprehensive experimental study on Coulomb interactions in nanoscale electron pulses and their impact on beam quality. For a laser-driven Schottky field emitter, we assess the transverse and longitudinal electron pulse properties in an ultrafast transmission electron microscope at a high photoemission current density...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868084/-ab-initio-investigation-of-br-3-d-core-excited-states-in-hbr-and-hbr-toward-xuv-probing-of-photochemical-dynamics
#10
Yuki Kobayashi, Tao Zeng, Daniel M Neumark, Stephen R Leone
Ultrafast X-ray/XUV transient absorption spectroscopy is a powerful tool for real-time probing of chemical dynamics. Interpretation of the transient absorption spectra requires knowledge of core-excited potentials, which necessitates assistance from high-level electronic-structure computations. In this study, we investigate Br-3 d core-excited electronic structures of hydrogen bromide (HBr) using spin-orbit general multiconfigurational quasidegenerate perturbation theory (SO-GMC-QDPT). Potential energy curves and transition dipole moments are calculated from the Franck-Condon region to the asymptotic limit and used to construct core-to-valence absorption strengths for five electronic states of HBr ( <mml:math xmlns:mml="http://www...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868083/perspective-towards-single-shot-time-resolved-microscopy-using-short-wavelength-table-top-light-sources
#11
T Helk, M Zürch, C Spielmann
Time-resolved imaging allows revealing the interaction mechanisms in the microcosm of both inorganic and biological objects. While X-ray microscopy has proven its advantages for resolving objects beyond what can be achieved using optical microscopes, dynamic studies using full-field imaging at the nanometer scale are still in their infancy. In this perspective, we present the current state of the art techniques for full-field imaging in the extreme-ultraviolet- and soft X-ray-regime which are suitable for single exposure applications as they are paramount for studying dynamics in nanoscale systems...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868082/perspective-how-can-ultrafast-laser-spectroscopy-inform-the-design-of-new-organic-photoredox-catalysts-for-chemical-and-materials-synthesis
#12
Andrew J Orr-Ewing
Photoredox catalysis of chemical reactions, using light-activated molecules which serve as electron donors or acceptors to initiate chemical transformations under mild conditions, is finding widespread use in the synthesis of organic compounds and materials. The transition-metal-centred complexes first developed for these photoredox-catalysed applications are steadily being superseded by more sustainable and lower toxicity organic photocatalysts. While the diversity of possible structures for photoredox-active organic molecules brings benefits of design flexibility, it also presents considerable challenges for optimization of the photocatalyst molecular architecture...
January 2019: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868081/dynamics-of-the-photoinduced-insulator-to-metal-transition-in-a-nickelate-film
#13
Vincent Esposito, Laurenz Rettig, Elisabeth M Bothschafter, Yunpei Deng, Christian Dornes, Lucas Huber, Tim Huber, Gerhard Ingold, Yuichi Inubushi, Tetsuo Katayama, Tomoya Kawaguchi, Henrik Lemke, Kanade Ogawa, Shigeki Owada, Milan Radovic, Mahesh Ramakrishnan, Zoran Ristic, Valerio Scagnoli, Yoshikazu Tanaka, Tadashi Togashi, Kensuke Tono, Ivan Usov, Yoav W Windsor, Makina Yabashi, Steven L Johnson, Paul Beaud, Urs Staub
Material properties can be controlled via strain, pressure, chemical composition, or dimensionality. Nickelates are particularly susceptible due to their strong variations of the electronic and magnetic properties on such external stimuli. Here, we analyze the photoinduced dynamics in a single crystalline NdNiO3 film upon excitation across the electronic gap. Using time-resolved reflectivity and resonant x-ray diffraction, we show that the pump pulse induces an insulator-to-metal transition, accompanied by the melting of the charge order...
November 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868080/the-impact-of-interior-dielectric-constant-and-entropic-change-on-hiv-1-complex-binding-free-energy-prediction
#14
Yuchen Li, Yalong Cong, Guoqiang Feng, Susu Zhong, John Z H Zhang, Huiyong Sun, Lili Duan
At present, the calculated binding free energy obtained using the molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area (MM/PB(GB)SA) method is overestimated due to the lack of knowledge of suitable interior dielectric constants in the simulation on the interaction of Human Immunodeficiency Virus (HIV-1) protease systems with inhibitors. Therefore, the impact of different values of the interior dielectric constant and the entropic contribution when using the MM/PB(GB)SA method to calculate the binding free energy was systemically evaluated...
November 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30868079/perspective-preservation-of-coherence-in-photophysical-processes
#15
Theis I Sølling, Klaus B Møller
Coherence is one of the most important phenomena in ultrafast sciences. We give our perspective on the terminology, observation, and preservation of coherence in photophysical processes with some glimpses to the past and some looking-head to what may pave the way for scaling one of the last bastions in ultrafast science, namely, that of mode specific chemistry where it will be possible to break any specific bond by tailoring the pulse, an accomplishment that obviously would be the dream of any chemist.
November 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30474048/conformation-specific-detection-of-calmodulin-binding-using-the-unnatural-amino-acid-p-azido-phenylalanine-azf-as-an-ir-sensor
#16
Anne Creon, Inokentijs Josts, Stephan Niebling, Nils Huse, Henning Tidow
Calmodulin (CaM) is a very conserved, ubiquitous, eukaryotic protein that binds four Ca2+ ions with high affinity. It acts as a calcium sensor by translating Ca2+ signals into cellular processes such as metabolism, inflammation, immune response, memory, and muscle contraction. Calcium binding to CaM leads to conformational changes that enable Ca2+ /CaM to recognize and bind various target proteins with high affinity. The binding mode and binding partners of CaM are very diverse, and a consensus binding sequence is lacking...
November 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30417027/ultrafast-time-resolved-extreme-ultraviolet-xuv-photoelectron-spectroscopy-of-hole-transfer-in-a-zn-n-gap-schottky-junction
#17
Brett M Marsh, Bethany R Lamoureux, Stephen R Leone
The addition of a metal overlayer to a semiconductor photocatalyst is a frequently used synthetic route to passivate the surface and, via the formation of a Schottky barrier, to enhance catalytic activity of the photocatalyst material. While it is known that Schottky junctions decrease recombination by charge separation, measurements of the depletion region dynamics have remained elusive. Here, we use ultrafast pump-probe transient photoelectron spectroscopy to measure material-specific dynamics of the Zn/n-GaP(100) system...
September 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30364211/demonstration-of-femtosecond-x-ray-pump-x-ray-probe-diffraction-on-protein-crystals
#18
Nadia L Opara, Istvan Mohacsi, Mikako Makita, Daniel Castano-Diez, Ana Diaz, Pavle Juranić, May Marsh, Alke Meents, Christopher J Milne, Aldo Mozzanica, Celestino Padeste, Valérie Panneels, Marcin Sikorski, Sanghoon Song, Henning Stahlberg, Ismo Vartiainen, Laura Vera, Meitian Wang, Philip R Willmott, Christian David
The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals...
September 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30363957/time-of-flight-electron-energy-loss-spectroscopy-by-longitudinal-phase-space-manipulation-with-microwave-cavities
#19
W Verhoeven, J F M van Rens, W F Toonen, E R Kieft, P H A Mutsaers, O J Luiten
The possibility to perform high-resolution time-resolved electron energy loss spectroscopy has the potential to impact a broad range of research fields. Resolving small energy losses with ultrashort electron pulses, however, is an enormous challenge due to the low average brightness of a pulsed beam. In this paper, we propose to use time-of-flight measurements combined with longitudinal phase space manipulation using resonant microwave cavities. This allows for both an accurate detection of energy losses with a high current throughput and efficient monochromation...
September 2018: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/30310825/probing-the-non-equilibrium-transient-state-in-magnetite-by-a-jitter-free-two-color-x-ray-pump-and-x-ray-probe-experiment
#20
N Pontius, M Beye, C Trabant, R Mitzner, F Sorgenfrei, T Kachel, M Wöstmann, S Roling, H Zacharias, R Ivanov, R Treusch, M Buchholz, P Metcalf, C Schüßler-Langeheine, A Föhlisch
We present a general experimental concept for jitter-free pump and probe experiments at free electron lasers. By generating pump and probe pulse from one and the same X-ray pulse using an optical split-and-delay unit, we obtain a temporal resolution that is limited only by the X-ray pulse lengths. In a two-color X-ray pump and X-ray probe experiment with sub 70 fs temporal resolution, we selectively probe the response of orbital and charge degree of freedom in the prototypical functional oxide magnetite after photoexcitation...
September 2018: Structural Dynamics (Melville, N.Y.)
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