The analysis of ultrafast electron diffraction (UED) data from low-symmetry single crystals of small molecules is often challenged by the difficulty of assigning unique Laue indices to the observed Bragg reflections. For a variety of technical and physical reasons, UED diffraction images are typically of lower quality when viewed from the perspective of structure determination by single-crystal x-ray or electron diffraction. Nevertheless, time series of UED images can provide valuable insight into structural dynamics, providing that an adequate interpretation of the diffraction patterns can be achieved. Garfield is a collection of tools with a graphical user interface designed to facilitate the interpretation of diffraction patterns and to index Bragg reflections in challenging cases where other indexing tools are ineffective. To this end, Garfield enables the user to interactively create, explore, and optimize sets of parameters that define the diffraction geometry and characteristic properties of the sample.
The energy needed to deform an elastic solid may be recovered, while in Newtonian fluids, like water and glycerol, deformation energy dissipates on timescales of the inter-molecular relaxation time TM . For times considerably longer than zM the existence of shear elasticity requires long -range correlations, which challenge our understanding of the liquid state. We investigated laser-driven free surface bubbles in liquid glycerol by analyzing their expansion and bursting dynamics, in which we found a flow-dominating, rubber -like elasticity unrelated to surface tension forces. In extension to findings of a measurable liquid elasticity at even very low deformation frequencies [L. Noirez, P. Baroni, J. Mol. Struct. 972, 16-21 (2010), A. Zaccone, K. Trachenko, Proc. Natl. Acad. Sci. U.S.A. 117, 19653-19655 (2020)], that is difficult to access under increased strain, we find a robust, strain rate driven elasticity. The recovery of deformation energy allows the bursting bubble to reach Taylor-Culick velocities 20 -fold higher than expected. The elasticity is persistent for microseconds, hence four orders of magnitude longer than 'rM. The dynamic shows that this persistence cannot originate from the far tail of a distribution of relaxation times around zM but must appear by frustrating the short molecular dissipation. The longer time should be interpreted as a relaxation of collective modes of metastable groups of molecules. With strain rates of 106 s-1, we observe a metastable glycerol shell exhibiting a rubber -like solid behavior with similar elasticity values and characteristic tolerance toward large strains, although the molecular inter-action is fundamentally different.
Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. This imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 μm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 109-1011 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.
We present a cryogenic mass spectrometry protocol with the capability to detect peptides in the attomole dilution range from ice films. Our approach employs femtosecond laser pulses and implements neither substrate modification nor proton donor agents in the aqueous solution, known to facilitate analyte detection in mass spectrometry. In a systematic study, we investigated the impact of temperature, substrate composition, and irradiation wavelength (513 and 1026 nm) on the bradykinin signal onset. Our findings show that substrate choice and irradiation wavelength have a minor impact on signal intensity once the preparation protocol is optimized. However, if the temperature is increased from -140 to 0 °C, which is accompanied by ice film thinning, a somehow complex picture of analyte desorption and ionization is recognizable, which has not been described in the literature yet. Under cryogenic conditions (-140 °C), obtaining a signal is only possible from isolated sweet spots across the film. If the thin ice film is between -100 and -70 °C of temperature, these sweet spots appear more frequently. Ice sublimation triggered by temperatures above -70 °C leads to an intense and robust signal onset that could be maintained for several hours. In addition to the above findings, we notice that a vibrant fragmentation pattern produced is strikingly similar with both wavelengths. Our findings suggest that while following an optimized protocol, femtosecond mass spectrometry has excellent potential to analyze small organic molecules and peptides with a mass range of up to 2.5 kDa in aqueous solution without any matrix, as employed in matrix-assisted laser desorption/ionization (MALDI) or any substrate surface modification, found in surface-assisted laser desorption/ionization (SALDI).
Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the 'hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.
Time-resolved X-ray diffraction from Ga091Mn0 09As was recorded with a hard X-ray free-electron-laser. The influence of spin-orders on phonons was investigated; our result suggests a new method for mapping the spin-correlations in low doped magnetic systems, especially the short-range spin-correlation.
Long wavelength vibrational modes in the ferromagnetic semiconductor Ga_{0.91}Mn_{0.09}As are investigated using time resolved x-ray diffraction. At room temperature, we measure oscillations in the x-ray diffraction intensity corresponding to coherent vibrational modes with well-defined wavelengths. When the correlation of magnetic impurities sets in, we observe the transition of the lattice into a disordered state that does not support coherent modes at large wavelengths. Our measurements point toward a magnetically induced broadening of long wavelength vibrational modes in momentum space and their quasilocalization in the real space. More specifically, long wavelength vibrational modes cannot be assigned to a single wavelength but rather should be represented as a superposition of plane waves with different wavelengths. Our findings have strong implications for the phonon-related processes, especially carrier-phonon and phonon-phonon scattering, which govern the electrical conductivity and thermal management of semiconductor-based devices.
Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution scattering data are collected using X-ray exposures below rotational diffusion times, resulting in angularly anisotropic X-ray snapshots that provide several orders of magnitude more information than traditional solution scattering data. Such experiments can be performed using the ultrashort X-ray pulses provided by a free-electron laser source, allowing one to collect a large number of diffraction patterns in a relatively short time. Here, we describe a test data set for FXS, obtained at the Linac Coherent Light Source, consisting of close to 100 000 multi-particle diffraction patterns originating from approximately 50 to 200 Paramecium Bursaria Chlorella virus particles per snapshot. In addition to the raw data, a selection of high-quality pre-processed diffraction patterns and a reference SAXS profile are provided.
* Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität, 07743 Jena, Germany † Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany ‡ TRIUMF, Vancouver, BC V6T 2A3, Canada § QUEST Institute, Physikalisch-Technische Bundesanstalt, 38116 Braunschweig, Germany ¶ Institut für Atomund Molekülphysik, Justus-Liebig-Universität, 35392 Giessen, Germany ◊ Max-Planck-Institut für Struktur und Dynamik der Materie, 22761 Hamburg, Germany
ZusammenfassungBewegungen auf atomarer Ebene und molekulare Strukturveränderungen sind Grundphänomene in Chemie und Physik. Schon lange träumt die Wissenschaft davon, diese Prozesse auf den fundamentalen Längen‐ und Zeitskalen direkt zu beobachten. Solche „Molekülfilme“ werden durch Methoden möglich, bei denen ein kurzer Laser‐Pumppuls eine Reaktion startet und nach einer gewissen Verzögerung ein zweiter kurzer Probepuls ihren momentanen Zustand festhält. Für atomare Auflösung benötigt der Probepuls sehr kurze Wellenlängen, etwa Röntgenstrahlung oder Elektronen. Unsere Methode nutzt ultraschnelle Elektronenbeugung mit dem Vorteil relativ kompakter Experimente im Vergleich zu Freie‐Elektronen‐Lasern für Röntgenstrahlung. Damit gelingen uns erste Molekülfilme, die den Ablauf von Reaktionen im atomaren Detail zeigen. Sie geben Einblick in die Auswahlmechanismen, nach denen chemische Reaktionen einen bestimmten Reaktionspfad unter vielen Pfaden wählen.
A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T0)—the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T0 might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T0. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T0 with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV–IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.
Direct electron detectors are increasingly used to explore the dynamics of macromolecules in real space and real time using transmission electron microscopy. The purpose of this work is to optimize the most suitable detector configuration of a thin silicon detector by Monte Carlo Simulations. Several simulations were performed to achieve an advanced detector geometry that reduces significantly the background signal due to backscattered electrons resulting in an enhanced imaging performance of the detector. Utilizing DEPFET (DEpleted P-channel Field Effect Transistor) technology and the novel ideas for the optimized detector geometry, a unique direct hit electron detector is currently being produced.
Carrier and lattice dynamics of laser excited CdTe was studied by time-resolved reflectivity for excitation fluences spanning about three orders of magnitude, from 0.064 to 6.14 mJ cm(-2). At fluences below 1 mJ cm(-2) the transient reflectivity is dominated by the dynamics of hybrid phonon-plasmon modes. At fluences above 1 mJ cm(-2) the time-dependent reflectivity curves show a complex interplay between band-gap renormalization, band filling, carrier dynamics and recombination. A framework that accounts for such complex dynamics is presented and used to model the time-dependent reflectivity data. This model suggests that the excess energy of the laser-excited hot carriers is reduced much more efficiently by emitting hybrid phonon-plasmon modes rather than bare longitudinal optical phonons.
The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.
Gijs van der Schot, Martin Svenda, Filipe R.N.C. Maia, Max F. Hantke, Daniel P. DePonte, M. Marvin Seibert, Andrew Aquila, Joachim Schulz, Richard A. Kirian, Mengning Liang, Francesco Stellato, Sadia Bari, Bianca Iwan, Jakob Andreasson, Nicusor Timneanu, Johan Bielecki, Daniel Westphal, Francisca Nunes de Almeida, Duško Odić, Dirk Hasse, Gunilla H. Carlsson, Daniel S.D. Larsson, Anton Barty, Andrew V. Martin, Sebastian Schorb, Christoph Bostedt, John D. Bozek, Sebastian Carron, Ken Ferguson, Daniel Rolles, Artem Rudenko, Sascha W. Epp, Lutz Foucar, Benedikt Rudek, Benjamin Erk, Robert Hartmann, Nils Kimmel, Peter Holl, Lars Englert, N. Duane Loh, Henry N. Chapman, Inger Andersson, Janos Hajdu & Tomas Ekeberg