Structural Dynamics最新文献_第2页

Gigahertz streaking and compression of low-energy electron pulses 低能量电子脉冲的千兆赫条纹和压缩

Structural Dynamics Pub Date : 2024-04-01 DOI: 10.1063/4.0000235

Dennis Epp, Benjamin Schröder, Marcel Möller, Claus Ropers

引用次数: 0

The Cambridge Structural Database and structural dynamics 剑桥结构数据库和结构动力学

Structural Dynamics Pub Date : 2024-03-18 DOI: 10.1063/4.0000244

Hans-Beat Bürgi

{"title":"The Cambridge Structural Database and structural dynamics","authors":"Hans-Beat Bürgi","doi":"10.1063/4.0000244","DOIUrl":"https://doi.org/10.1063/4.0000244","url":null,"abstract":"With the availability of the computer readable information in the Cambridge Structural Database (CSD), wide ranging, largely automated comparisons of fragment, molecular, and crystal structures have become possible. They show that the distributions of interatomic distances, angles, and torsion angles for a given structural fragment occurring in different environments are highly correlated among themselves and with other observables such as spectroscopic signals, reaction and activation energies. The correlations often extend continuously over large ranges of parameter values. They are reminiscent of bond breaking and forming reactions, polyhedral rearrangements, and conformational changes. They map—qualitatively—the regions of the structural parameter space in which molecular dynamics take place, namely, the low energy regions of the respective (free) energy surfaces. The extension and continuous nature of the correlations provides an organizing principle of large groups of structural data and suggests a reconsideration of traditional definitions and descriptions of bonds, “nonbonded” and “noncovalent” interactions in terms of Lewis acids interacting with Lewis bases. These aspects are illustrated with selected examples of historic importance and with some later developments. It seems that the amount of information in the CSD (and other structural databases) and the knowledge on the nature of, and the correlations within, this body of information should allow one—in the near future—to make credible interpolations and possibly predictions of structures and their properties with machine learning methods.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140167390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural dynamics at surfaces by ultrafast reflection high-energy electron diffraction 通过超快反射高能电子衍射研究表面结构动力学

Structural Dynamics Pub Date : 2024-03-12 DOI: 10.1063/4.0000234

Michael Horn-von Hoegen

{"title":"Structural dynamics at surfaces by ultrafast reflection high-energy electron diffraction","authors":"Michael Horn-von Hoegen","doi":"10.1063/4.0000234","DOIUrl":"https://doi.org/10.1063/4.0000234","url":null,"abstract":"Many fundamental processes of structural changes at surfaces occur on a pico- or femtosecond timescale. In order to study such ultrafast processes, we have combined modern surface science techniques with fs-laser pulses in a pump–probe scheme. Grazing incidence of the electrons ensures surface sensitivity in ultrafast reflection high-energy electron diffraction (URHEED). Utilizing the Debye–Waller effect, we studied the nanoscale heat transport from an ultrathin film through a hetero-interface or the damping of vibrational excitations in monolayer adsorbate systems on the lower ps-timescale. By means of spot profile analysis, the different cooling rates of epitaxial Ge nanostructures of different size and strain state were determined. The excitation and relaxation dynamics of a driven phase transition far away from thermal equilibrium is demonstrated using the In-induced (8 × 2) reconstruction on Si(111). This Peierls-distorted surface charge density wave system exhibits a discontinuous phase transition of first order at 130 K from a (8 × 2) insulating ground state to (4 × 1) metallic excited state. Upon excitation by a fs-laser pulse, this structural phase transition is non-thermally driven in only 700 fs into the excited state. A small barrier of 40 meV hinders the immediate recovery of the ground state, and the system is found in a metastable supercooled state for up to few nanoseconds.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140115375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ultrafast electron diffuse scattering as a tool for studying phonon transport: Phonon hydrodynamics and second sound oscillations 超快电子漫散射作为研究声子传输的工具：声子流体力学和第二声振荡

Structural Dynamics Pub Date : 2024-03-12 DOI: 10.1063/4.0000224

Laurenz Kremeyer, Tristan L. Britt, Bradley J. Siwick, Samuel C. Huberman

{"title":"Ultrafast electron diffuse scattering as a tool for studying phonon transport: Phonon hydrodynamics and second sound oscillations","authors":"Laurenz Kremeyer, Tristan L. Britt, Bradley J. Siwick, Samuel C. Huberman","doi":"10.1063/4.0000224","DOIUrl":"https://doi.org/10.1063/4.0000224","url":null,"abstract":"Hydrodynamic phonon transport phenomena, like second sound, have been observed in liquid helium more than 50 years ago. More recently second sound has been observed in graphite at over 200 K using transient thermal grating (TG) techniques. In this work, we explore signatures of phonon hydrodynamic transport and second sound oscillations in ultrafast electron diffuse scattering patterns, which can provide time, momentum, and branch resolved information on the state-of-excitation of the phonon system beyond that available through TG experiments. We use the density functional theory and solve the Boltzmann transport equation to determine time-resolved non-equilibrium phonon populations and model phonon transport in graphite. This model also provides the information necessary to calculate the time evolution of one-phonon structure factors and diffuse scattering patterns during thermal transport covering ballistic, diffusive, and hydrodynamic regimes where the effect of a second sound oscillation on the phonon distribution is observed. Direct measurements of how the phonon distribution varies in time and space in various thermal transport regimes should yield new insights into the fundamental physics of the underlying processes.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"116 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140114779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses 用飞秒极紫外脉冲对 DyCo5 薄膜进行瞬态光栅光谱分析

Structural Dynamics Pub Date : 2024-03-06 DOI: 10.1063/4.0000223

Victor Ukleev, Ludmila Leroy, Riccardo Mincigrucci, Dario Deangelis, Danny Fainozzi, Nupur Ninad Khatu, Ettore Paltanin, Laura Foglia, Filippo Bencivenga, Chen Luo, Florian Ruske, Florin Radu, Cristian Svetina, Urs Staub

{"title":"Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses","authors":"Victor Ukleev, Ludmila Leroy, Riccardo Mincigrucci, Dario Deangelis, Danny Fainozzi, Nupur Ninad Khatu, Ettore Paltanin, Laura Foglia, Filippo Bencivenga, Chen Luo, Florian Ruske, Florin Radu, Cristian Svetina, Urs Staub","doi":"10.1063/4.0000223","DOIUrl":"https://doi.org/10.1063/4.0000223","url":null,"abstract":"Surface acoustic waves (SAWs) are excited by femtosecond extreme ultraviolet (EUV) transient gratings (TGs) in a room-temperature ferrimagnetic DyCo5 alloy. TGs are generated by crossing a pair of EUV pulses from a free electron laser with the wavelength of 20.8 nm matching the Co M-edge, resulting in a SAW wavelength of Λ = 44 nm. Using the pump-probe transient grating scheme in reflection geometry, the excited SAWs could be followed in the time range of −10 to 100 ps in the thin film. Coherent generation of TGs by ultrafast EUV pulses allows to excite SAW in any material and to investigate their couplings to other dynamics, such as spin waves and orbital dynamics. In contrast, we encountered challenges in detecting electronic and magnetic signals, potentially due to the dominance of the larger SAW signal and the weakened reflection signal from underlying layers. A potential solution for the latter challenge involves employing soft x-ray probes, albeit introducing additional complexities associated with the required grazing incidence geometry.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140055920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Resonant multiphoton processes and excitation limits to structural dynamics 共振多光子过程和结构动力学的激发极限

Structural Dynamics Pub Date : 2024-03-01 DOI: 10.1063/4.0000239

William J. C. Francis, Harmanjot Grewal, Alexander A. C. Wainwright, Xuchun Yang, Massimo Olivucci, R. J. Dwayne Miller

{"title":"Resonant multiphoton processes and excitation limits to structural dynamics","authors":"William J. C. Francis, Harmanjot Grewal, Alexander A. C. Wainwright, Xuchun Yang, Massimo Olivucci, R. J. Dwayne Miller","doi":"10.1063/4.0000239","DOIUrl":"https://doi.org/10.1063/4.0000239","url":null,"abstract":"Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in the study of photoactive biological processes; the optical methods used to probe the structural dynamics of light activated protein functions have failed to ensure that the photoexcitation prepares a well-defined initial state relevant to the biological process of interest. Photoexcitation in nature occurs in the linear (one-photon per chromophore) regime; however, the extreme excitation conditions used experimentally give rise to biologically irrelevant multiphoton absorption. To evaluate and ensure the biological relevance of past and future experiments, a theoretical framework has been developed to determine the excitation conditions, which lead to resonant multiphoton absorption (RMPA) and thus define the excitation limit in general for the study of structural dynamics within the 1-photon excitation regime. Here, we apply the theoretical model to bacteriorhodopsin (bR) and show that RMPA occurs when excitation conditions exceed the linear saturation threshold, well below typical excitation conditions used in this class of experiments. This work provides the guidelines to ensure excitation in the linear 1-photon regime is relevant to biological and chemical processes.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"188 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140018402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-harmonic spectroscopy of impulsively aligned 1,3-cyclohexadiene: Signatures of attosecond charge migration 脉冲排列的 1,3-Cyclohexadiene 的高次谐波光谱：阿秒电荷迁移的特征

Structural Dynamics Pub Date : 2024-02-29 DOI: 10.1063/4.0000227

Andres Tehlar, Jakob T. Casanova, Andrey Dnestryan, Frank Jensen, Lars Bojer Madsen, Oleg I. Tolstikhin, Hans Jakob Wörner

{"title":"High-harmonic spectroscopy of impulsively aligned 1,3-cyclohexadiene: Signatures of attosecond charge migration","authors":"Andres Tehlar, Jakob T. Casanova, Andrey Dnestryan, Frank Jensen, Lars Bojer Madsen, Oleg I. Tolstikhin, Hans Jakob Wörner","doi":"10.1063/4.0000227","DOIUrl":"https://doi.org/10.1063/4.0000227","url":null,"abstract":"High-harmonic spectroscopy is an all-optical technique with inherent attosecond temporal resolution that has been successfully employed to reconstruct charge migration, electron-tunneling dynamics, and conical-intersection dynamics. Here, we demonstrate the extension of two key components of high-harmonic spectroscopy, i.e., impulsive alignment and measurements with multiple driving wavelengths to 1,3-cyclohexadiene and benzene. In the case of 1,3-cyclohexadiene, we find that the temporal sequence of maximal and minimal emitted high-harmonic intensities as a function of the delay between the alignment and probe pulses inverts between 25 and 30 eV and again between 35 and 40 eV when an 800-nm driver is used, but no inversions are observed with a 1420-nm driver. This observation is explained by the wavelength-dependent interference of emission from multiple molecular orbitals (HOMO to HOMO-3), as demonstrated by calculations based on the weak-field asymptotic theory and accurate photorecombination matrix elements. These results indicate that attosecond charge migration takes place in the 1,3-cyclohexadiene cation and can potentially be reconstructed with the help of additional measurements. Our experiments also demonstrate a pathway toward studying photochemical reactions in the molecular frame of 1,3-cyclohexadiene.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140008425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microscopic nonlinear optical response: Analysis and calculations with the Floquet–Bloch formalism 微观非线性光学响应：用 Floquet-Bloch 公式进行分析和计算

Structural Dynamics Pub Date : 2024-02-23 DOI: 10.1063/4.0000220

Daria Popova-Gorelova, Robin Santra

引用次数: 0

Spatial–temporal characterization of photoemission in a streak-mode dynamic transmission electron microscope 条纹模式动态透射电子显微镜中光发射的时空特性分析

Structural Dynamics Pub Date : 2024-02-23 DOI: 10.1063/4.0000219

Samik Roy Moulik, Yingming Lai, Aida Amini, Patrick Soucy, Kenneth R. Beyerlein, Jinyang Liang

{"title":"Spatial–temporal characterization of photoemission in a streak-mode dynamic transmission electron microscope","authors":"Samik Roy Moulik, Yingming Lai, Aida Amini, Patrick Soucy, Kenneth R. Beyerlein, Jinyang Liang","doi":"10.1063/4.0000219","DOIUrl":"https://doi.org/10.1063/4.0000219","url":null,"abstract":"A long-standing motivation driving high-speed electron microscopy development is to capture phase transformations and material dynamics in real time with high spatial and temporal resolution. Current dynamic transmission electron microscopes (DTEMs) are limited to nanosecond temporal resolution and the ability to capture only a few frames of a transient event. With the motivation to overcome these limitations, we present our progress in developing a streak-mode DTEM (SM-DTEM) and demonstrate the recovery of picosecond images with high frame sequence depth. We first demonstrate that a zero-dimensional (0D) SM-DTEM can provide temporal information on any local region of interest with a 0.37 μm diameter, a 20-GHz sampling rate, and 1200 data points in the recorded trace. We use this method to characterize the temporal profile of the photoemitted electron pulse, finding that it deviates from the incident ultraviolet laser pulse and contains an unexpected peak near its onset. Then, we demonstrate a two-dimensional (2D) SM-DTEM, which uses compressed-sensing-based tomographic imaging to recover a full spatiotemporal photoemission profile over a 1.85-μm-diameter field of view with nanoscale spatial resolution, 370-ps inter-frame interval, and 140-frame sequence depth in a 50-ns time window. Finally, a perspective is given on the instrumental modifications necessary to further develop this promising technique with the goal of decreasing the time to capture a 2D SM-DTEM dataset.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"289 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139953702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography 蛋白质世界中的蓝与红：时间分辨晶体学揭示的光活性黄蛋白和植物色素

Structural Dynamics Pub Date : 2024-01-31 DOI: 10.1063/4.0000233

Marius Schmidt, Emina A. Stojković

{"title":"Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography","authors":"Marius Schmidt, Emina A. Stojković","doi":"10.1063/4.0000233","DOIUrl":"https://doi.org/10.1063/4.0000233","url":null,"abstract":"Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium, TR-SX has been inspired by the development of Free Electron Lasers for hard X-rays. Extremely intense, ultrashort x-ray pulses could probe micro and nanocrystals, but at the same time, they inflicted radiation damage that necessitated the replacement by a new crystal. Consequently, a large number of microcrystals are exposed to X-rays one by one in a serial fashion. With TR-SX methods, one of the largest obstacles of previous approaches, namely, the unsurmountable challenges associated with the investigation of non-cyclic (irreversible) reactions, can be overcome. This article describes successes and transformative contributions to the TRX field by Keith Moffat and his collaborators, highlighting two major projects on protein photoreceptors initiated in the Moffat lab at the turn of the millennium.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139658793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0