Structural Dynamics-Us最新文献

The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon.

X-ray free electron laser experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely spaced sets of coherent x-ray pulses to be compared after scattering from a dynamic system at different times. This enables the study of fluctuations in many-body quantum systems at the level of the ultrafast pulse durations, but this method has been limited to a select number of examples and required complex and advanced analytical tools. By applying a new methodology to this problem, we have made qualitative advances in three separate areas that will likely also find application to new fields. As compared to the "droplet-type" models, which typically are used to estimate the photon distributions on pixelated detectors to obtain the coherent x-ray speckle patterns, our algorithm achieves an order of magnitude speedup on CPU hardware and two orders of magnitude improvement on GPU hardware. We also find that it retains accuracy in low-contrast conditions, which is the typical regime for many experiments in structural dynamics. Finally, it can predict photon distributions in high average-intensity applications, a regime which up until now has not been accessible. Our artificial intelligence-assisted algorithm will enable a wider adoption of x-ray coherence spectroscopies, by both automating previously challenging analyses and enabling new experiments that were not otherwise feasible without the developments described in this work.

Ultrafast electron diffraction (UED) from aligned molecules in the gas phase has successfully retrieved structures of both linear and symmetric top molecules. Alignment of asymmetric tops has been recorded with UED but no structural information was retrieved. We present here the extraction of two-dimensional structural information from simple transformations of experimental diffraction patterns of aligned molecules as a proof-of-principle for the recovery of the full structure. We align 4-fluorobenzotrifluoride with a linearly polarized laser and show that we can distinguish between atomic pairs with equal distances that are parallel and perpendicular to the aligned axis. We additionally show with numerical simulations that by cooling the molecules to a rotational temperature of 1 K, more distances and angles can be resolved through direct transformations.

Here, we report on a new approach based on laser driven molecular beams that provides simultaneously nanoscale liquid droplets and gas-phase sample delivery for femtosecond electron diffraction studies. The method relies on Picosecond InfraRed Laser (PIRL) excitation of vibrational modes to strongly drive phase transitions under energy confinement by a mechanism referred to as Desorption by Impulsive Vibrational Excitation (DIVE). This approach is demonstrated using glycerol as the medium with selective excitation of the OH stretch region for energy deposition. The resulting plume was imaged with both an ultrafast electron gun and a pulsed bright-field optical microscope to characterize the sample source simultaneously under the same conditions with time synchronization equivalent to sub-micrometer spatial resolution in imaging the plume dynamics. The ablation front gives the expected isolated gas phase, whereas the trailing edge of the plume is found to consist of nanoscale liquid droplets to thin films depending on the excitation conditions. Thus, it is possible by adjusting the timing to go continuously from probing gas phase to solution phase dynamics in a single experiment with 100% hit rates and very low sample consumption (<100 nl per diffraction image). This approach will be particularly interesting for biomolecules that are susceptible to denaturation in turbulent flow, whereas PIRL-DIVE has been shown to inject molecules as large as proteins into the gas phase fully intact. This method opens the door as a general approach to atomically resolving solution phase chemistry as well as conformational dynamics of large molecular systems and allow separation of the solvent coordinate on the dynamics of interest.

The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D₂O) and fully deuterated PEG/hydrogenated water (d-PEG/H₂O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D₂O show the dynamics of PEG, and that of d-PEG/H₂O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H₂O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.

The structural organization of natural pigment-protein complexes provides a specific environment for the chromophore groups. Yet, proteins are inherently dynamic and conformationally mobile. In this work, we demonstrate the heterogeneity of chromophores of C-phycocyanin (C-PC) from Arthrospira platensis. Part of the population of trimeric C-PC is subject to spontaneous disturbances of protein-protein interactions resulting in increased conformational mobility of the chromophores. Upon fluorescence excitation in the visible range, the spectral signatures of these poorly populated states are masked by bulk chromophore states, but the former could be clearly discriminated when the fluorescence is excited by near-infrared quanta. Such selective excitation of conformationally mobile C-PC chromophores is due to the structure of their S₁ level, which is characterized by a significantly broadened spectral line. We demonstrate that the anti-Stokes C-PC fluorescence is the result of single-photon absorption. By combining spectral and structural methods, we characterize four distinct states of C-PC chromophores emitting at 620, 650, 665, and 720 nm and assigned the fast component in the anti-Stokes fluorescence decay kinetics in the range of 690-750 nm to the chromophores with increased conformational mobility. Our data suggest that the spectral and temporal characteristics of the anti-Stokes fluorescence can be used to study protein dynamics and develop methods to visualize local environment parameters such as temperature.

Exploiting vibrational excitation for the dynamic control of material properties is an attractive goal with wide-ranging technological potential. Most metal-to-insulator transitions are mediated by few structural modes and are, thus, ideal candidates for selective driving toward a desired electronic phase. Such targeted navigation within a generally multi-dimensional potential energy landscape requires microscopic insight into the non-equilibrium pathway. However, the exact role of coherent inertial motion across the transition state has remained elusive. Here, we demonstrate mode-selective control over the metal-to-insulator phase transition of atomic indium wires on the Si(111) surface, monitored by ultrafast low-energy electron diffraction. We use tailored pulse sequences to individually enhance or suppress key phonon modes and thereby steer the collective atomic motion within the potential energy surface underlying the structural transformation. Ab initio molecular dynamics simulations demonstrate the ballistic character of the structural transition along the deformation vectors of the Peierls amplitude modes. Our work illustrates that coherent excitation of collective modes via exciton-phonon interactions evades entropic barriers and enables the dynamic control of materials functionality.

Time-resolved x-ray diffraction has been used to measure the low-temperature thermal transport properties of a Pt/Gd₃Fe₅O₁₂//Gd₃Ga₅O₁₂ metal/oxide heterostructure relevant to applications in spin caloritronics. A pulsed femtosecond optical signal produces a rapid temperature rise in the Pt layer, followed by heat transport into the Gd₃Fe₅O₁₂ (GdIG) thin film and the Gd₃Ga₅O₁₂ (GGG) substrate. The time dependence of x-ray diffraction from the GdIG layer was tracked using an accelerator-based femtosecond x-ray source. The ultrafast diffraction measurements probed the intensity of the GdIG (1 -1 2) x-ray reflection in a grazing-incidence x-ray diffraction geometry. The comparison of the variation of the diffracted x-ray intensity with a model including heat transport and the temperature dependence of the GdIG lattice parameter allows the thermal conductance of the Pt/GdIG and GdIG//GGG interfaces to be determined. Complementary synchrotron x-ray diffraction studies of the low-temperature thermal expansion properties of the GdIG layer provide a precise calibration of the temperature dependence of the GdIG lattice parameter. The interfacial thermal conductance of the Pt/GdIG and GdIG//GGG interfaces determined from the time-resolved diffraction study is of the same order of magnitude as previous reports for metal/oxide and epitaxial dielectric interfaces. The thermal parameters of the Pt/GdIG//GGG heterostructure will aid in the design and implementation of thermal transport devices and nanostructures.

We report the first nitrogen 1s Auger-Meitner electron spectrum from a liquid ammonia microjet at a temperature of ∼223 K (-50 °C) and compare it with the simultaneously measured spectrum for gas-phase ammonia. The spectra from both phases are interpreted with the assistance of high-level electronic structure and ab initio molecular dynamics calculations. In addition to the regular Auger-Meitner-electron features, we observe electron emission at kinetic energies of 374-388 eV, above the leading Auger-Meitner peak (3a₁ ²). Based on the electronic structure calculations, we assign this peak to a shake-up satellite in the gas phase, i.e., Auger-Meitner emission from an intermediate state with additional valence excitation present. The high-energy contribution is significantly enhanced in the liquid phase. We consider various mechanisms contributing to this feature. First, in analogy with other hydrogen-bonded liquids (noticeably water), the high-energy signal may be a signature for an ultrafast proton transfer taking place before the electronic decay (proton transfer mediated charge separation). The ab initio dynamical calculations show, however, that such a process is much slower than electronic decay and is, thus, very unlikely. Next, we consider a non-local version of the Auger-Meitner decay, the Intermolecular Coulombic Decay. The electronic structure calculations support an important contribution of this purely electronic mechanism. Finally, we discuss a non-local enhancement of the shake-up processes.

Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted intensities are affected by partiality. To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of equivalent reflections within each bin. This binning and averaging often involve a loss of information. Here, we propose an alternative approach, which we call low-pass spectral analysis (LPSA). In this method, the data are projected onto the subspace defined by a set of trigonometric functions, with frequencies up to a certain cutoff. This approach attenuates undesirable high-frequency features and facilitates retrieving the underlying dynamics. A time-lagged embedding step can be included prior to subspace projection to improve the stability of the results with respect to the parameters involved. Subsequent modal decomposition allows to produce a low-rank description of the system's evolution. Using a synthetic time-evolving model with incomplete and partial observations, we analyze the LPSA results in terms of quality of the retrieved signal, as a function of the parameters involved. We compare the performance of LPSA to that of a range of other sophisticated data analysis techniques. We show that LPSA allows to achieve excellent dynamics reconstruction at modest computational cost. Finally, we demonstrate the superiority of dynamics retrieval by LPSA compared to time binning and merging, which is, to date, the most commonly used method to extract dynamical information from TR-SFX data.