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  • Direct imaging of plasma waves using ultrafast electron microscopy
    Struct. Dyn. (IF 3.216) Pub Date : 2020-12-28
    Shuaishuai Sun; Xiaoyi Sun; Daniel Bartles; Elliot Wozniak; Joseph Williams; Peng Zhang; Chong-Yu Ruan

    A femtosecond plasma imaging modality based on a new development of ultrafast electron microscope is introduced. We investigated the laser-induced formation of high-temperature electron microplasmas and their subsequent non-equilibrium evolution. Based on a straightforward field imaging principle, we directly retrieve detailed information about the plasma dynamics, including plasma wave structures

  • Photodissociation of aqueousI3−observed with liquid-phase ultrafast mega-electron-volt electron diffraction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-12-28
    K. Ledbetter; E. Biasin; J. P. F. Nunes; M. Centurion; K. J. Gaffney; M. Kozina; M.-F. Lin; X. Shen; J. Yang; X. J. Wang; T. J. A. Wolf; A. A. Cordones

    Developing femtosecond resolution methods for directly observing structural dynamics is critical to understanding complex photochemical reaction mechanisms in solution. We have used two recent developments, ultrafast mega-electron-volt electron sources and vacuum compatible sub-micron thick liquid sheet jets, to enable liquid-phase ultrafast electron diffraction (LUED). We have demonstrated the viability

  • Detection of femtosecond spin voltage pulses in a thin iron film
    Struct. Dyn. (IF 3.216) Pub Date : 2020-11-05
    K. Bühlmann; G. Saerens; A. Vaterlaus; Y. Acremann

    We present experimental evidence of a spin voltage—a difference between the chemical potentials of the two spin directions—in a thin iron film based on spin- and time-resolved photoemission spectroscopy. This voltage is the driving force for a spin current during the ultrafast demagnetization of the sample. The observed magnitude is on the order of 50 mV, a value that is quite consistent with predictions

  • Effect of gold nanoparticle incorporation into oil-swollen surfactant lamellar membranes
    Struct. Dyn. (IF 3.216) Pub Date : 2020-12-15
    Michihiro Nagao; Robert Bradbury; Siyam M. Ansar; Christopher L. Kitchens

    An oil-swollen surfactant membrane is employed to measure the effects of incorporated hydrophobically functionalized gold nanoparticles (AuNPs) on the structure and dynamics of the membranes. While maintaining an average AuNP diameter of approximately 5 nm, the membrane thickness was varied from 5 nm to 7.5 nm by changing the amount of oil in the membrane. The membranes become softer as the proportion

  • Dioctadecyldimethylammonium bromide, a surfactant model for the cell membrane: Importance of microscopic dynamics
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-22
    V. K. Sharma; H. Srinivasan; V. García Sakai; S. Mitra

    Cationic lipid membranes have recently attracted huge attention both from a fundamental point of view and due to their practical applications in drug delivery and gene therapy. The dynamical behavior of the lipids in the membrane is a key parameter controlling various physiological processes and drug release kinetics. Here, we review the dynamical and thermotropic phase behavior of an archetypal cationic

  • The TRIXS end-station for femtosecond time-resolved resonant inelastic x-ray scattering experiments at the soft x-ray free-electron laser FLASH
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-16
    S. Dziarzhytski; M. Biednov; B. Dicke; A. Wang; P. S. Miedema; R. Y. Engel; J. O. Schunck; H. Redlin; H. Weigelt; F. Siewert; C. Behrens; M. Sinha; A. Schulte; B. Grimm-Lebsanft; S. G. Chiuzbăian; W. Wurth; M. Beye; M. Rübhausen; G. Brenner

    We present the experimental end-station TRIXS dedicated to time-resolved soft x-ray resonant inelastic x-ray scattering (RIXS) experiments on solid samples at the free-electron laser FLASH. Using monochromatized ultrashort femtosecond XUV/soft x-ray photon pulses in combination with a synchronized optical laser in a pump-probe scheme, the TRIXS setup allows measuring sub-picosecond time-resolved high-resolution

  • Simultaneous two-color snapshot view on ultrafast charge and spin dynamics in a Fe-Cu-Ni tri-layer
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-22
    Benedikt Rösner; Boris Vodungbo; Valentin Chardonnet; Florian Döring; Vitaliy A. Guzenko; Marcel Hennes; Armin Kleibert; Maxime Lebugle; Jan Lüning; Nicola Mahne; Aladine Merhe; Denys Naumenko; Ivaylo P. Nikolov; Ignacio Lopez-Quintas; Emanuele Pedersoli; Primož R. Ribič; Tatiana Savchenko; Benjamin Watts; Marco Zangrando; Flavio Capotondi; Christian David; Emmanuelle Jal

    Ultrafast phenomena on a femtosecond timescale are commonly examined by pump-probe experiments. This implies multiple measurements, where the sample under investigation is pumped with a short light pulse and then probed with a second pulse at various time delays to follow its dynamics. Recently, the principle of streaking extreme ultraviolet (XUV) pulses in the temporal domain has enabled recording

  • Repetitive non-thermal melting as a timing monitor for femtosecond pump/probe X-ray experiments
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-22
    Å. U. J. Bengtsson; J. C. Ekström; Xiaocui Wang; A. Jurgilaitis; Van-Thai Pham; D. Kroon; J. Larsson

    Time-resolved optical pump/X-ray probe experiments are often used to study structural dynamics. To ensure high temporal resolution, it is necessary to monitor the timing between the X-ray pulses and the laser pulses. The transition from a crystalline solid material to a disordered state in a non-thermal melting process can be used as a reliable timing monitor. We have performed a study of the non-thermal

  • Characterization of a time-resolved electron microscope with a Schottky field emission gun
    Struct. Dyn. (IF 3.216) Pub Date : 2020-10-01
    Pavel K. Olshin; Marcel Drabbels; Ulrich J. Lorenz

    The rapid growth of the field of time-resolved and ultrafast electron microscopy has been accompanied by the active development of new instrumentation. Recently, time-resolved microscopes equipped with a field emission gun have been introduced, demonstrating great potential for experiments that benefit from the high brightness and coherence of the electron source. Here, we describe a straightforward

  • Transient magnetic gratings on the nanometer scale
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-08
    D. Weder; C. von Korff Schmising; C. M. Günther; M. Schneider; D. Engel; P. Hessing; C. Strüber; M. Weigand; B. Vodungbo; E. Jal; X. Liu; A. Merhe; E. Pedersoli; F. Capotondi; J. Lüning; B. Pfau; S. Eisebitt

    Laser-driven non-local electron dynamics in ultrathin magnetic samples on a sub-10 nm length scale is a key process in ultrafast magnetism. However, the experimental access has been challenging due to the nanoscopic and femtosecond nature of such transport processes. Here, we present a scattering-based experiment relying on a laser-induced electro- and magneto-optical grating in a Co/Pd ferromagnetic

  • Role of intracellular water in the normal-to-cancer transition in human cells—insights from quasi-elastic neutron scattering
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-08
    M. P. M. Marques; A. L. M. Batista de Carvalho; A. P. Mamede; A. Dopplapudi; V. García Sakai; L. A. E. Batista de Carvalho

    The transition from normal to malignant state in human cells is still a poorly understood process. Changes in the dynamical activity of intracellular water between healthy and cancerous human cells were probed as an innovative approach for unveiling particular features of malignancy and identifying specific reporters of cancer. Androgen-unresponsive prostate and triple-negative breast carcinomas were

  • Real-time tracking of protein unfolding with time-resolved x-ray solution scattering
    Struct. Dyn. (IF 3.216) Pub Date : 2020-09-22
    L. Henry; M. R. Panman; L. Isaksson; E. Claesson; I. Kosheleva; R. Henning; S. Westenhoff; O. Berntsson

    The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly

  • Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells
    Struct. Dyn. (IF 3.216) Pub Date : 2020-10-12
    Rui Li; Zhuo Liu; Like Li; Juan Huang; Takeshi Yamada; Victoria García Sakai; Pan Tan; Liang Hong

    Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated

  • Enhanced dynamics in the anomalous melting regime of DMPG lipid membranes
    Struct. Dyn. (IF 3.216) Pub Date : 2020-10-16
    Elizabeth G. Kelley; Michihiro Nagao; Paul D. Butler; Lionel Porcar; Bela Farago

    Like many soft materials, lipids undergo a melting transition associated with a significant increase in their dynamics. At temperatures below the main melting transition (Tm), all molecular and collective dynamics are suppressed, while above Tm the alkyl tail motions, lipid diffusivity, and collective membrane undulations are at least an order of magnitude faster. Here we study the collective dynamics

  • Shear-induced ordering in liquid microjets seen by x-ray cross correlation analysis
    Struct. Dyn. (IF 3.216) Pub Date : 2020-10-16
    V. Markmann; M. Dartsch; J. Valerio; L. Frenzel; I. Lokteva; M. Walther; F. Westermeier; G. Grübel; F. Lehmkühler

    We applied shear to a silica nanoparticle dispersion in a microfluidic jet device and observed direction-dependent structure along and across the flow direction. The asymmetries of the diffraction patterns were evaluated by x-ray cross correlation analysis. For different Rayleigh nozzle sizes and shapes, we measured the decay of the shear-induced ordering after the cessation of the shear. At large

  • Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-08-06
    Johan Bielecki,Filipe R N C Maia,Adrian P Mancuso

    X-ray free electron lasers (XFELs) now routinely produce millijoule level pulses of x-ray photons with tens of femtoseconds duration. Such x-ray intensities gave rise to the idea that weakly scattering particles—perhaps single biomolecules or viruses—could be investigated free of radiation damage. Here, we examine elements from the past decade of so-called single particle imaging with hard XFELs. We

  • Simulation of time-resolved x-ray absorption spectroscopy of ultrafast dynamics in particle-hole-excited 4‐(2-thienyl)-2,1,3-benzothiadiazole
    Struct. Dyn. (IF 3.216) Pub Date : 2020-07-06
    Khadijeh Khalili; Ludger Inhester; Caroline Arnold; Anders S. Gertsen; Jens Wenzel Andreasen; Robin Santra

    To date, alternating co-polymers based on electron-rich and electron-poor units are the most attractive materials to control functionality of organic semiconductor layers in which ultrafast excited-state processes play a key role. We present a computational study of the photoinduced excited-state dynamics of the 4-(2-thienyl)-2,1,3-benzothiadiazole (BT-1T) molecule, which is a common building block

  • Origin of core-to-core x-ray emission spectroscopy sensitivity to structural dynamics
    Struct. Dyn. (IF 3.216) Pub Date : 2020-07-06
    Morgane Vacher; Kristjan Kunnus; Mickaël G. Delcey; Kelly J. Gaffney; Marcus Lundberg

    Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of Kα x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for

  • Water structure near the surface of Weyl semimetals as catalysts in photocatalytic proton reduction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-05-12
    Jure Gujt; Peter Zimmer; Frederik Zysk; Vicky Süß; Claudia Felser; Matthias Bauer; Thomas D. Kühne

    In this work, second-generation Car–Parrinello-based mixed quantum-classical mechanics molecular dynamics simulations of small nanoparticles of NbP, NbAs, TaAs, and 1T-TaS2 in water are presented. The first three materials are topological Weyl semimetals, which were recently discovered to be active catalysts in photocatalytic water splitting. The aim of this research was to correlate potential differences

  • Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-23
    Lingyu Ma,Haiwang Yong,Joseph D Geiser,Andrés Moreno Carrascosa,Nathan Goff,Peter M Weber

    Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions

  • Method for developing a sub-10 fs ultrafast electron diffraction technology
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-09
    Hyun Woo Kim; In Hyung Baek; Junho Shin; Sunjeong Park; Hyeon Sang Bark; Key Young Oang; Kyu-Ha Jang; Kitae Lee; Nikolay Vinokurov; Young Uk Jeong

    The experimental observation of femtosecond dynamics in atoms and molecules by stroboscopic technologies utilizing x ray or electron flashes has attracted much attention and has rapidly developed. We propose a feasible ultrafast electron diffraction (UED) technology with high brightness and a sub-10 fs temporal resolution. We previously demonstrated a UED system with an overall temporal resolution

  • Fluctuation suppression in microgels by polymer electrolytes
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-15
    S. Pasini; S. Maccarrone; N. K. Székely; L. R. Stingaciu; A. P. H. Gelissen; W. Richtering; M. Monkenbusch; O. Holderer

    Structural details of thermoresponsive, cationically poly(N-iso-propylacrylamide-co-methacrylamido propyl trimethyl ammonium chloride) microgels and the influence of the anionic electrolyte polystyrene sulfonate (PSS) on the internal structure and dynamics of the cationic microgels have been studied with a combination of small angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy

  • Imaging plasma formation in isolated nanoparticles with ultrafast resonant scattering.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-18
    Daniela Rupp,Leonie Flückiger,Marcus Adolph,Alessandro Colombo,Tais Gorkhover,Marion Harmand,Maria Krikunova,Jan Philippe Müller,Tim Oelze,Yevheniy Ovcharenko,Maria Richter,Mario Sauppe,Sebastian Schorb,Rolf Treusch,David Wolter,Christoph Bostedt,Thomas Möller

    We have recorded the diffraction patterns from individual xenon clusters irradiated with intense extreme ultraviolet pulses to investigate the influence of light-induced electronic changes on the scattering response. The clusters were irradiated with short wavelength pulses in the wavelength regime of different 4d inner-shell resonances of neutral and ionic xenon, resulting in distinctly different

  • Structural dynamics of incommensurate charge-density waves tracked by ultrafast low-energy electron diffraction.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-22
    G Storeck,J G Horstmann,T Diekmann,S Vogelgesang,G von Witte,S V Yalunin,K Rossnagel,C Ropers

    We study the non-equilibrium structural dynamics of the incommensurate and nearly commensurate charge-density wave (CDW) phases in 1T- TaS 2. Employing ultrafast low-energy electron diffraction with 1 ps temporal resolution, we investigate the ultrafast quench and recovery of the CDW-coupled periodic lattice distortion (PLD). Sequential structural relaxation processes are observed by tracking the intensities

  • Determination of the dehydration pathway in a flexible metal-organic framework by dynamic in situ x-ray diffraction.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-06-23
    Ian M Walton,Jordan M Cox,Shea D Myers,Cassidy A Benson,Travis B Mitchell,Gage S Bateman,Eric D Sylvester,Yu-Sheng Chen,Jason B Benedict

    Understanding guest exchange processes in metal–organic frameworks is an important step toward the rational design of functional materials with tailor-made properties. The dehydration of the flexible metal-organic framework [Co(AIP)(bpy)0.5(H2O)]•2H2O was studied by novel in situ dynamic x-ray diffraction techniques. The complex mechanism of dehydration, along with the as-yet unreported metastable

  • Imaging phonon dynamics with ultrafast electron microscopy: Kinematical and dynamical simulations.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-17
    Daniel X Du,David J Flannigan

    Ultrafast x-ray and electron scattering techniques have proven to be useful for probing the transient elastic lattice deformations associated with photoexcited coherent acoustic phonons. Indeed, femtosecond electron imaging using an ultrafast electron microscope (UEM) has been used to directly image the influence of nanoscale structural and morphological discontinuities on the emergence, propagation

  • Controlled beams of shock-frozen, isolated, biological and artificial nanoparticles.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-17
    Amit K Samanta,Muhamed Amin,Armando D Estillore,Nils Roth,Lena Worbs,Daniel A Horke,Jochen Küpper

    X-ray free-electron lasers promise diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred

  • A tool for visualizing protein motions in time-resolved crystallography
    Struct. Dyn. (IF 3.216) Pub Date : 2020-04-01
    Cecilia Wickstrand, Gergely Katona, Takanori Nakane, Przemyslaw Nogly, Joerg Standfuss, Eriko Nango, Richard Neutze

    Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature

  • Ultrafast electron imaging of surface charge carrier dynamics at low voltage
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-30
    Jianfeng Zhao, Osman M. Bakr, Omar F. Mohammed

    The performance of optoelectronic devices strongly depends on charge carrier dynamics on top of surfaces of the absorber layers. Unfortunately, this information cannot be selectively probed using conventional ultrafast laser spectroscopic methods, due to the large penetration depth (tens of nm to μm) of the photon pulses in the pump-probe configurations. Therefore, ultrafast time-resolved approaches

  • Unconventional picosecond strain pulses resulting from the saturation of magnetic stress within a photoexcited rare earth layer
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-27
    A. von Reppert, M. Mattern, J.-E. Pudell, S. P. Zeuschner, K. Dumesnil, M. Bargheer

    Optical excitation of spin-ordered rare earth metals triggers a complex response of the crystal lattice since expansive stresses from electron and phonon excitations compete with a contractive stress induced by spin disorder. Using ultrafast x-ray diffraction experiments, we study the layer specific strain response of a dysprosium film within a metallic heterostructure upon femtosecond laser-excitation

  • Single-particle imaging by x-ray free-electron lasers—How many snapshots are needed?
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-20
    I. Poudyal, M. Schmidt, P. Schwander

    X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense x-ray pulses that are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns, the three-dimensional electron density

  • Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    Jesper Norell, Michael Odelius, Morgane Vacher

    Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n ,   π *) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both

  • Secondary structure effects on internal proton transfer in poly-peptides
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    M. Bouakil, F. Chirot, M. Girod, P. Dugourd, L. MacAleese

    A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always

  • Nanoscale thermal transport across an GaAs/AlGaAs heterostructure interface
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-17
    Matthew Gorfien, Hailong Wang, Long Chen, Hamidreza Rahmani, Junxiao Yu, Pengfei Zhu, Jie Chen, Xuan Wang, Jianhua Zhao, Jianming Cao

    We studied the thermal transport across a GaAs/AlGaAs interface using time-resolved Reflection High Energy Electron Diffraction. The lattice temperature change of the GaAs nanofilm was directly monitored and numerically simulated using diffusive heat equations based on Fourier's Law. The extracted thermal boundary resistances (TBRs) were found to decrease with increasing lattice temperature imbalance

  • Liquid-phase mega-electron-volt ultrafast electron diffraction
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-09
    J. P. F. Nunes, K. Ledbetter, M. Lin, M. Kozina, D. P. DePonte, E. Biasin, M. Centurion, C. J. Crissman, M. Dunning, S. Guillet, K. Jobe, Y. Liu, M. Mo, X. Shen, R. Sublett, S. Weathersby, C. Yoneda, T. J. A. Wolf, J. Yang, A. A. Cordones, X. J. Wang

    The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure–function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast

  • Discovering a rotational barrier within a charge-transfer state of a photoexcited chromophore in solution
    Struct. Dyn. (IF 3.216) Pub Date : 2020-03-04
    Taylor D. Krueger, Sean A. Boulanger, Liangdong Zhu, Longteng Tang, Chong Fang

    Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS)

  • JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-26
    Filip Leonarski,Aldo Mozzanica,Martin Brückner,Carlos Lopez-Cuenca,Sophie Redford,Leonardo Sala,Andrej Babic,Heinrich Billich,Oliver Bunk,Bernd Schmitt,Meitian Wang

    In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU

  • Conformational sampling and kinetics changes across a non-Arrhenius break point in the enzyme thermolysin.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-14
    Ming Dong,Mackenzie L Lauro,Timothy J Koblish,Brian J Bahnson

    Numerous studies have suggested a significant role that protein dynamics play in optimizing enzyme catalysis, and changes in conformational sampling offer a window to explore this role. Thermolysin from Bacillus thermoproteolyticus rokko, which is a heat-stable zinc metalloproteinase, serves here as a model system to study changes of protein function and conformational sampling across a temperature

  • MicroED methodology and development.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-02-13
    Brent L Nannenga

    Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described

  • Coherent narrowband light source for ultrafast photoelectron spectroscopy in the 17-31 eV photon energy range.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-31
    Riccardo Cucini,Tommaso Pincelli,Giancarlo Panaccione,Damir Kopic,Fabio Frassetto,Paolo Miotti,Gian Marco Pierantozzi,Simone Peli,Andrea Fondacaro,Aleksander De Luisa,Alessandro De Vita,Pietro Carrara,Damjan Krizmancic,Daniel T Payne,Federico Salvador,Andrea Sterzi,Luca Poletto,Fulvio Parmigiani,Giorgio Rossi,Federico Cilento

    Here, we report on a novel narrowband High Harmonic Generation (HHG) light source designed for ultrafast photoelectron spectroscopy (PES) on solids. Notably, at 16.9 eV photon energy, the harmonics bandwidth equals 19 meV. This result has been obtained by seeding the HHG process with 230 fs pulses at 515 nm. The ultimate energy resolution achieved on a polycrystalline Au sample at 40 K is ∼22 meV at

  • Evolving data standards for cryo-EM structures.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-24
    Catherine L Lawson,Helen M Berman,Wah Chiu

    Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration

  • Real-time observation of jumping and spinning nanodroplets.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-14
    Pavel K Olshin,Jonathan M Voss,Marcel Drabbels,Ulrich J Lorenz

    The manipulation of liquids at nanoscale dimensions is a central goal of the emergent nanofluidics field. Such endeavors extend to nanodroplets, which are ubiquitous objects involved in many technological applications. Here, we employ time-resolved electron microscopy to elucidate the formation of so-called jumping nanodroplets on a graphene surface. We flash-melt a thin gold nanostructure with a laser

  • Best practices for high data-rate macromolecular crystallography (HDRMX).
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-09
    Herbert J Bernstein,Lawrence C Andrews,Jorge A Diaz,Jean Jakoncic,Thu Nguyen,Nicholas K Sauter,Alexei S Soares,Justin Y Wei,Maciej R Wlodek,Mario A Xerri

    In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations

  • Time-resolved diffraction with an optimized short pulse laser plasma X-ray source.
    Struct. Dyn. (IF 3.216) Pub Date : 2020-01-02
    M Afshari,P Krumey,D Menn,M Nicoul,F Brinks,A Tarasevitch,K Sokolowski-Tinten

    We present a setup for time-resolved X-ray diffraction based on a short pulse, laser-driven plasma X-ray source. The employed modular design provides high flexibility to adapt the setup to the specific requirements (e.g., X-ray optics and sample environment) of particular applications. The configuration discussed here has been optimized toward high angular/momentum resolution and uses K α -radiation

  • Toward time-resolved laser T-jump/X-ray probe spectroscopy in aqueous solutions.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-11
    O Cannelli,C Bacellar,R A Ingle,R Bohinc,D Kinschel,B Bauer,D S Ferreira,D Grolimund,G F Mancini,M Chergui

    Most chemical and biochemical reactions in nature and in industrial processes are driven by thermal effects that bring the reactants above the energy barrier for reaction. In aqueous solutions, this process can also be triggered by the laser driven temperature jump (T-jump) method, in which the water vibrational (stretch, bend, or combination) modes are excited by a short laser pulse, leading to a

  • Evaluation of serial crystallographic structure determination within megahertz pulse trains.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-04
    Oleksandr Yefanov,Dominik Oberthür,Richard Bean,Max O Wiedorn,Juraj Knoska,Gisel Pena,Salah Awel,Lars Gumprecht,Martin Domaracky,Iosifina Sarrou,P Lourdu Xavier,Markus Metz,Saša Bajt,Valerio Mariani,Yaroslav Gevorkov,Thomas A White,Aleksandra Tolstikova,Pablo Villanueva-Perez,Carolin Seuring,Steve Aplin,Armando D Estillore,Jochen Küpper,Alexander Klyuev,Manuela Kuhn,Torsten Laurus,Heinz Graafsma,Diana

    The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible

  • A shared vision for macromolecular crystallography over the next five years.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-12-04
    Andreas Förster,Clemens Schulze-Briese

    Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron

  • The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-27
    Marek Grabowski,Marcin Cymborowski,Przemyslaw J Porebski,Tomasz Osinski,Ivan G Shabalin,David R Cooper,Wladek Minor

    It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the

  • Fragment screening for a protein-protein interaction inhibitor to WDR5.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-27
    Matthew L Dennis,Benjamin J Morrow,Olan Dolezal,Anthony N Cuzzupe,Alexandra E Stupple,Janet Newman,John Bentley,Meghan Hattarki,Stewart D Nuttall,Richard C Foitzik,Ian P Street,Paul A Stupple,Brendon J Monahan,Thomas S Peat

    The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of

  • Decelerated lattice excitation and absence of bulk phonon modes at surfaces: Ultra-fast electron diffraction from Bi(111) surface upon fs-laser excitation.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-09
    V Tinnemann,C Streubühr,B Hafke,T Witte,A Kalus,A Hanisch-Blicharski,M Ligges,P Zhou,D von der Linde,U Bovensiepen,M Horn-von Hoegen

    Ultrafast reflection high-energy electron diffraction is employed to follow the lattice excitation of a Bi(111) surface upon irradiation with a femtosecond laser pulse. The thermal motion of the atoms is analyzed through the Debye-Waller effect. While the Bi bulk is heated on time scales of 2 to 4 ps, we observe that the excitation of vibrational motion of the surface atoms occurs much slower with

  • Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-09
    François Auvray,David Dennetiere,Alexandre Giuliani,Frédéric Jamme,Frank Wien,Bastien Nay,Séverine Zirah,François Polack,Claude Menneglier,Bruno Lagarde,Jonathan D Hirst,Matthieu Réfrégiers

    Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term time-resolved SRCD (tr-SRCD), which overcomes the limitations of current broadband UV SRCD setups. This technique allows accessing ultrafast time scales

  • FACT and FAIR with Big Data allows objectivity in science: The view of crystallography.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-02
    John R Helliwell

    A publication is an important narrative of the work done and interpretations made by researchers securing a scientific discovery. As The Royal Society neatly states though, "Nullius in verba" ("Take nobody's word for it"), whereby the role of the underpinning data is paramount. Therefore, the objectivity that preserving that data within the article provides is due to readers being able to check the

  • Effect of a bound anion on the structure and dynamics of halorhodopsin from Natronomonas pharaonis.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-11-02
    Misao Mizuno,Yumi Shimoo,Hideki Kandori,Yasuhisa Mizutani

    Active ion transport across membranes is vital to maintaining the electrochemical gradients of ions in cells and is mediated by transmembrane proteins. Halorhodopsin (HR) functions as a light-driven inward pump for chloride ions. The protein contains all-trans-retinal bound to a specific lysine residue through a protonated Schiff base. Interaction between the bound chloride ion and the protonated Schiff

  • Femtosecond gas-phase mega-electron-volt ultrafast electron diffraction.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    X Shen,J P F Nunes,J Yang,R K Jobe,R K Li,Ming-Fu Lin,B Moore,M Niebuhr,S P Weathersby,T J A Wolf,C Yoneda,Markus Guehr,Martin Centurion,X J Wang

    The development of ultrafast gas electron diffraction with nonrelativistic electrons has enabled the determination of molecular structures with atomic spatial resolution. It has, however, been challenging to break the picosecond temporal resolution barrier and achieve the goal that has long been envisioned-making space- and-time resolved molecular movies of chemical reaction in the gas-phase. Recently

  • Make the right measurement: Discovery of an allosteric inhibition site for p300-HAT.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Anna S Gardberg,Annissa J Huhn,Richard Cummings,Archana Bommi-Reddy,Florence Poy,Jeremy Setser,Valerie Vivat,Francois Brucelle,Jonathan Wilson

    Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the dynamic and reversible acetylation of proteins, an epigenetic regulatory mechanism associated with multiple cancers. Indeed, HDAC inhibitors are already approved in the clinic. The HAT paralogs p300 and CREB-binding protein (CBP) have been implicated in human pathological conditions including several hematological malignancies

  • Probing ultrafast C-Br bond fission in the UV photochemistry of bromoform with core-to-valence transient absorption spectroscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Benjamin W Toulson,Mario Borgwardt,Han Wang,Florian Lackner,Adam S Chatterley,C D Pemmaraju,Daniel M Neumark,Stephen R Leone,David Prendergast,Oliver Gessner

    UV pump-extreme UV (XUV) probe femtosecond transient absorption spectroscopy is used to study the 268 nm induced photodissociation dynamics of bromoform (CHBr3). Core-to-valence transitions at the Br(3d) absorption edge (∼70 eV) provide an atomic scale perspective of the reaction, sensitive to changes in the local valence electronic structure, with ultrafast time resolution. The XUV spectra track how

  • The role of transition dipole phase in atomic attosecond transient absorption from the multi-level model.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-28
    Guanglu Yuan,Shicheng Jiang,Ziwen Wang,Weijie Hua,Chao Yu,Cheng Jin,Ruifeng Lu

    Based on a multilevel model considering enough bound electronic states of atoms, we theoretically study the role of the transition dipole phase (TDP) in the attosecond transient absorption (ATA) spectrum of helium in intense laser fields. By solving the stationary Schrödinger equation with B-spline basis sets, we first calculate the transition dipole moments with well-defined phases between the bound

  • Photoemission sources and beam blankers for ultrafast electron microscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-10-09
    Lixin Zhang,Jacob P Hoogenboom,Ben Cook,Pieter Kruit

    Observing atomic motions as they occur is the dream goal of ultrafast electron microscopy (UEM). Great progress has been made so far thanks to the efforts of many scientists in developing the photoemission sources and beam blankers needed to create short pulses of electrons for the UEM experiments. While details on these setups have typically been reported, a systematic overview of methods used to

  • High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-29
    Juan C Sanchez,Melissa Carrillo,Suraj Pandey,Moraima Noda,Luis Aldama,Denisse Feliz,Elin Claesson,Weixiao Yuan Wahlgren,Gregory Tracy,Phu Duong,Angela C Nugent,Andrew Field,Vukica Šrajer,Christopher Kupitz,So Iwata,Eriko Nango,Rie Tanaka,Tomoyuki Tanaka,Luo Fangjia,Kensuke Tono,Shigeki Owada,Sebastian Westenhoff,Marius Schmidt,Emina A Stojković

    Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the

  • Electrostatic subframing and compressive-sensing video in transmission electron microscopy.
    Struct. Dyn. (IF 3.216) Pub Date : 2019-09-29
    B W Reed,A A Moghadam,R S Bloom,S T Park,A M Monterrosa,P M Price,C M Barr,S A Briggs,K Hattar,J T McKeown,D J Masiel

    We present kilohertz-scale video capture rates in a transmission electron microscope, using a camera normally limited to hertz-scale acquisition. An electrostatic deflector rasters a discrete array of images over a large camera, decoupling the acquisition time per subframe from the camera readout time. Total-variation regularization allows features in overlapping subframes to be correctly placed in

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