Robert W. Henning, Irina Kosheleva, Vukica Šrajer, In-Sik Kim, Eric Zoellner, Rama Ranganathan
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
生物医学科学的一个主要目标是超越蛋白质和其他生物大分子的静态图像，研究其功能的内部动态。要了解这些分子是如何工作的，并设计出新的功能和功能调节器，就必须进行这一层次的研究。数十年前，基思-莫法特（Keith Moffat）对这一问题作出了富有远见的承诺，现在，结构生物学家群体已经拥有了一套 X 射线散射技术，可以在原子分辨率和与功能相关的运动的广泛时间尺度范围内观察生物大分子的分子内动力学。其中许多技术由 BioCARS 提供，这是一个在莫法特领导下建立的尖端同步辐射设施，位于阿贡国家实验室的先进光子源。BioCARS 能够进行时间分辨率从 100 ps 到几秒的分子动力学实验研究，并提供时间分辨 X 射线晶体学以及小角和广角 X 射线散射。结构变化可由多种方法引发--利用可调皮秒和纳秒激光脉冲进行紫外/可见光抽运、基底扩散以及电场和温度跃迁等全局扰动。动力学研究通常涉及对分子结构的微妙扰动，需要专门的计算技术来处理和解释数据。在这篇综述中，我们将介绍大分子动力学实验所面临的挑战，并介绍该设施目前的实验能力。正如莫法特多年前所设想的那样，BioCARS 现在的定位是推动科学界在理解蛋白质和其他复杂生物大分子方面取得根本性进展。
{"title":"BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules","authors":"Robert W. Henning, Irina Kosheleva, Vukica Šrajer, In-Sik Kim, Eric Zoellner, Rama Ranganathan","doi":"10.1063/4.0000238","DOIUrl":"https://doi.org/10.1063/4.0000238","url":null,"abstract":"A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139658481","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}
Hazem Daoud, Sreelaja Pulleri Vadhyar, Ehsan Nikbin, Cheng Lu, R. J. Dwayne Miller
Samples suitable for electron diffraction studies must satisfy certain characteristics such as having a thickness in the range of 10–100 nm. We report, to our knowledge, the first successful synthesis technique of nanometer-thin sheets of single-crystalline thymine suitable for electron diffraction and spectroscopy studies. This development provides a well-defined system to explore issues related to UV photochemistry of DNA and high intrinsic stability essential to maintaining integrity of genetic information. The crystals are grown using the evaporation technique, and the nanometer-thin sheets are obtained via microtoming. The sample is characterized via x-ray diffraction and is subsequently studied using electron diffraction via a transmission electron microscope. Thymine is found to be more radiation resistant than similar molecular moieties (e.g., carbamazepine) by a factor of 5. This raises interesting questions about the role of the fast relaxation processes of electron scattering-induced excited states, extending the concept of radiation hardening beyond photoexcited states. The high stability of thymine in particular opens the door for further studies of these ultrafast relaxation processes giving rise to the high stability of DNA to UV radiation.
适用于电子衍射研究的样品必须满足某些特征，例如厚度在 10-100 纳米之间。据我们所知，我们首次成功合成了适用于电子衍射和光谱研究的单晶胸腺嘧啶纳米薄片。这项研发提供了一个定义明确的系统，用于探索与 DNA 的紫外线光化学有关的问题，以及保持遗传信息完整性所必需的高内在稳定性。晶体是利用蒸发技术生长的，纳米薄片则是通过微成型技术获得的。样品通过 X 射线衍射进行表征，随后通过透射电子显微镜使用电子衍射进行研究。研究发现，胸腺嘧啶的抗辐射能力比同类分子（如卡马西平）强 5 倍。这就提出了电子散射引发的激发态快速弛豫过程的作用这一有趣的问题，将辐射硬化的概念扩展到了光激发态之外。尤其是胸腺嘧啶的高稳定性为进一步研究这些超快弛豫过程打开了大门，这些超快弛豫过程导致了 DNA 对紫外线辐射的高稳定性。
{"title":"Synthesis technique and electron beam damage study of nanometer-thin single-crystalline thymine","authors":"Hazem Daoud, Sreelaja Pulleri Vadhyar, Ehsan Nikbin, Cheng Lu, R. J. Dwayne Miller","doi":"10.1063/4.0000221","DOIUrl":"https://doi.org/10.1063/4.0000221","url":null,"abstract":"Samples suitable for electron diffraction studies must satisfy certain characteristics such as having a thickness in the range of 10–100 nm. We report, to our knowledge, the first successful synthesis technique of nanometer-thin sheets of single-crystalline thymine suitable for electron diffraction and spectroscopy studies. This development provides a well-defined system to explore issues related to UV photochemistry of DNA and high intrinsic stability essential to maintaining integrity of genetic information. The crystals are grown using the evaporation technique, and the nanometer-thin sheets are obtained via microtoming. The sample is characterized via x-ray diffraction and is subsequently studied using electron diffraction via a transmission electron microscope. Thymine is found to be more radiation resistant than similar molecular moieties (e.g., carbamazepine) by a factor of 5. This raises interesting questions about the role of the fast relaxation processes of electron scattering-induced excited states, extending the concept of radiation hardening beyond photoexcited states. The high stability of thymine in particular opens the door for further studies of these ultrafast relaxation processes giving rise to the high stability of DNA to UV radiation.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139658476","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}
Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.
基于高次谐波发生和 X 射线自由电子激光器的新型超快 X 射线源正在为以优异的时间分辨率和原子位点特异性解析凝聚相系统中复杂的超快过程带来新的机遇。在这一视角中，我们介绍了利用时间分辨软 X 射线光谱解析有机半导体和有机光伏器件中电荷定位、转移和分离过程的技术。我们回顾了这些系统在超快软 X 射线光谱学方面的最新成果，并讨论了如何克服在热传导性差、非线性效应泵浦强度阈值低的光敏材料上进行时间分辨 X 射线实验所面临的技术挑战。
{"title":"Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices","authors":"Douglas Garratt, Mary Matthews, Jon Marangos","doi":"10.1063/4.0000214","DOIUrl":"https://doi.org/10.1063/4.0000214","url":null,"abstract":"Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139508951","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}
Alexander Neuhaus, Pascal Dreher, Florian Schütz, Helder Marchetto, Torsten Franz, Frank Meyer zu Heringdorf
Spectroscopic photoemission microscopy is a well-established method to investigate the electronic structure of surfaces. In modern photoemission microscopes, the electron optics allow imaging of the image plane, momentum plane, or dispersive plane, depending on the lens setting. Furthermore, apertures allow filtering of energy-, real-, and momentum space. Here, we describe how a standard spectroscopic and low-energy electron microscope can be equipped with an additional slit at the entrance of the already present hemispherical analyzer to enable an angle- and energy-resolved photoemission mode with micrometer spatial selectivity. We apply a photogrammetric calibration to correct for image distortions of the projective system behind the analyzer and present spectra recorded on Au(111) as a benchmark. Our approach makes data acquisition in energy–momentum space more efficient, which is a necessity for laser-based pump–probe photoemission microscopy with femtosecond time resolution.
{"title":"Angle-resolved photoelectron spectroscopy in a low-energy electron microscope","authors":"Alexander Neuhaus, Pascal Dreher, Florian Schütz, Helder Marchetto, Torsten Franz, Frank Meyer zu Heringdorf","doi":"10.1063/4.0000216","DOIUrl":"https://doi.org/10.1063/4.0000216","url":null,"abstract":"Spectroscopic photoemission microscopy is a well-established method to investigate the electronic structure of surfaces. In modern photoemission microscopes, the electron optics allow imaging of the image plane, momentum plane, or dispersive plane, depending on the lens setting. Furthermore, apertures allow filtering of energy-, real-, and momentum space. Here, we describe how a standard spectroscopic and low-energy electron microscope can be equipped with an additional slit at the entrance of the already present hemispherical analyzer to enable an angle- and energy-resolved photoemission mode with micrometer spatial selectivity. We apply a photogrammetric calibration to correct for image distortions of the projective system behind the analyzer and present spectra recorded on Au(111) as a benchmark. Our approach makes data acquisition in energy–momentum space more efficient, which is a necessity for laser-based pump–probe photoemission microscopy with femtosecond time resolution.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"120 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139068132","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}
Kristina S. Zinchenko, Fernando Ardana-Lamas, Valentina Utrio Lanfaloni, Nicholas Monahan, Issaka Seidu, Michael S. Schuurman, Simon P. Neville, Hans Jakob Wörner
The Jahn–Teller effect (JTE) is central to the understanding of the physical and chemical properties of a broad variety of molecules and materials. Whereas the manifestations of the JTE in stationary properties of matter are relatively well studied, the study of JTE-induced dynamics is still in its infancy, largely owing to its ultrafast and non-adiabatic nature. For example, the time scales reported for the distortion of CH4+ from the initial Td geometry to a nominal C2v relaxed structure range from 1.85 fs over 10 ± 2 fs to 20 ± 7 fs. Here, by combining element-specific attosecond transient-absorption spectroscopy and quantum-dynamics simulations, we show that the initial electronic relaxation occurs within 5 fs and that the subsequent nuclear dynamics are dominated by the Q2 scissoring and Q1 symmetric stretching modes, which dephase in 41 ± 10 fs and 13 ± 3 fs, respectively. Significant structural relaxation is found to take place only along the e-symmetry Q2 mode. These results demonstrate that CH4+ created by ionization of CH4 is best thought of as a highly fluxional species that possesses a long-time-averaged vibrational distribution centered around a D2d structure. The methods demonstrated in our work provide guidelines for the understanding of Jahn–Teller driven non-adiabatic dynamics in other more complex systems.
{"title":"Few-femtosecond electronic and structural rearrangements of CH4+ driven by the Jahn–Teller effect","authors":"Kristina S. Zinchenko, Fernando Ardana-Lamas, Valentina Utrio Lanfaloni, Nicholas Monahan, Issaka Seidu, Michael S. Schuurman, Simon P. Neville, Hans Jakob Wörner","doi":"10.1063/4.0000217","DOIUrl":"https://doi.org/10.1063/4.0000217","url":null,"abstract":"The Jahn–Teller effect (JTE) is central to the understanding of the physical and chemical properties of a broad variety of molecules and materials. Whereas the manifestations of the JTE in stationary properties of matter are relatively well studied, the study of JTE-induced dynamics is still in its infancy, largely owing to its ultrafast and non-adiabatic nature. For example, the time scales reported for the distortion of CH4+ from the initial Td geometry to a nominal C2v relaxed structure range from 1.85 fs over 10 ± 2 fs to 20 ± 7 fs. Here, by combining element-specific attosecond transient-absorption spectroscopy and quantum-dynamics simulations, we show that the initial electronic relaxation occurs within 5 fs and that the subsequent nuclear dynamics are dominated by the Q2 scissoring and Q1 symmetric stretching modes, which dephase in 41 ± 10 fs and 13 ± 3 fs, respectively. Significant structural relaxation is found to take place only along the e-symmetry Q2 mode. These results demonstrate that CH4+ created by ionization of CH4 is best thought of as a highly fluxional species that possesses a long-time-averaged vibrational distribution centered around a D2d structure. The methods demonstrated in our work provide guidelines for the understanding of Jahn–Teller driven non-adiabatic dynamics in other more complex systems.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687773","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}
A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical, experimental and software development. This work was added to the broad research and development program of synchrotron radiation at the UK's SRS. This whole program led to knowledge transfer from the UK's SRS to the ESRF as well as for neutron Laue protein crystallography to the reactor spallation sources and later to spallation neutron sources.
{"title":"Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments","authors":"John R. Helliwell","doi":"10.1063/4.0000225","DOIUrl":"https://doi.org/10.1063/4.0000225","url":null,"abstract":"A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical, experimental and software development. This work was added to the broad research and development program of synchrotron radiation at the UK's SRS. This whole program led to knowledge transfer from the UK's SRS to the ESRF as well as for neutron Laue protein crystallography to the reactor spallation sources and later to spallation neutron sources.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687478","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}
Photoelectron circular dichroism (PECD), the forward–backward asymmetry of the photoelectron angular distribution when ionizing randomly oriented chiral molecules with circularly polarized light, is an established method to investigate chiral properties of molecules in their electronic ground state. Here, we develop a computational strategy for predicting time-resolved PECD (TRPECD) of chemical reactions and demonstrate the method on the photodissociation of 1-iodo-2-methylbutane. Our approach combines multi-configurational quantum-chemical calculations of the relevant potential-energy surfaces of the neutral and singly ionized molecule with ab initio molecular-dynamics (AIMD) calculations. The PECD parameters along the AIMD trajectories are calculated with the aid of electron-molecule scattering calculations based on the Schwinger variational principle implemented in ePolyScat. Our calculations have been performed for two probe wavelengths (133 and 160 nm) accessible through low-order harmonic generation in gases. Our results show that the TRPECD is a highly sensitive probe of photochemical reaction dynamics. Most interestingly, the TRPECD is found to change sign multiple times along the photodissociation coordinate, in agreement with recent experiments on CHBrFI [Svoboda et al., “Femtosecond photoelectron circular dichroism of chemical reactions,” Sci. Adv. 8, eabq2811 (2022)]. The computational protocol introduced in the present work is general and readily applicable to other chiral photochemical processes.
{"title":"Theoretical study of time-resolved photoelectron circular dichroism in the photodissociation of a chiral molecule","authors":"Marit R. Fiechter, Vít Svoboda, Hans Jakob Wörner","doi":"10.1063/4.0000213","DOIUrl":"https://doi.org/10.1063/4.0000213","url":null,"abstract":"Photoelectron circular dichroism (PECD), the forward–backward asymmetry of the photoelectron angular distribution when ionizing randomly oriented chiral molecules with circularly polarized light, is an established method to investigate chiral properties of molecules in their electronic ground state. Here, we develop a computational strategy for predicting time-resolved PECD (TRPECD) of chemical reactions and demonstrate the method on the photodissociation of 1-iodo-2-methylbutane. Our approach combines multi-configurational quantum-chemical calculations of the relevant potential-energy surfaces of the neutral and singly ionized molecule with ab initio molecular-dynamics (AIMD) calculations. The PECD parameters along the AIMD trajectories are calculated with the aid of electron-molecule scattering calculations based on the Schwinger variational principle implemented in ePolyScat. Our calculations have been performed for two probe wavelengths (133 and 160 nm) accessible through low-order harmonic generation in gases. Our results show that the TRPECD is a highly sensitive probe of photochemical reaction dynamics. Most interestingly, the TRPECD is found to change sign multiple times along the photodissociation coordinate, in agreement with recent experiments on CHBrFI [Svoboda et al., “Femtosecond photoelectron circular dichroism of chemical reactions,” Sci. Adv. 8, eabq2811 (2022)]. The computational protocol introduced in the present work is general and readily applicable to other chiral photochemical processes.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687580","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}
Yongzhao Zhang, Jun Li, Wentao Wang, Huanfang Tian, Wenli Gao, Jianqi Li, Shuaishuai Sun, Huaixin Yang
Ultrafast electron diffraction has been proven to be a powerful tool for the study of coherent acoustic phonons owing to its high sensitivity to crystal structures. However, this sensitivity leads to complicated behavior of the diffraction intensity, which complicates the analysis process of phonons, especially higher harmonics. Here, we theoretically analyze the effects of photoinduced coherent transverse and longitudinal acoustic phonons on electron diffraction to provide a guide for the exploitation and modulation of coherent phonons. The simulation of the electron diffraction was performed in 30-nm films with different optical penetration depths based on the atomic displacements obtained by solving the wave equation. The simulation results exhibit a complex relationship between the frequencies of the phonons and diffraction signals, which highly depends on the laser penetration depth, sample thickness, and temporal stress distribution. In addition, an intensity decomposition method is proposed to account for the in-phase oscillation and high harmonics caused by inhomogeneous excitation. These results can provide new perspectives and insights for a comprehensive and accurate understanding of the lattice response under coherent phonons.
{"title":"Simulation of ultrafast electron diffraction intensity under coherent acoustic phonons","authors":"Yongzhao Zhang, Jun Li, Wentao Wang, Huanfang Tian, Wenli Gao, Jianqi Li, Shuaishuai Sun, Huaixin Yang","doi":"10.1063/4.0000199","DOIUrl":"https://doi.org/10.1063/4.0000199","url":null,"abstract":"Ultrafast electron diffraction has been proven to be a powerful tool for the study of coherent acoustic phonons owing to its high sensitivity to crystal structures. However, this sensitivity leads to complicated behavior of the diffraction intensity, which complicates the analysis process of phonons, especially higher harmonics. Here, we theoretically analyze the effects of photoinduced coherent transverse and longitudinal acoustic phonons on electron diffraction to provide a guide for the exploitation and modulation of coherent phonons. The simulation of the electron diffraction was performed in 30-nm films with different optical penetration depths based on the atomic displacements obtained by solving the wave equation. The simulation results exhibit a complex relationship between the frequencies of the phonons and diffraction signals, which highly depends on the laser penetration depth, sample thickness, and temporal stress distribution. In addition, an intensity decomposition method is proposed to account for the in-phase oscillation and high harmonics caused by inhomogeneous excitation. These results can provide new perspectives and insights for a comprehensive and accurate understanding of the lattice response under coherent phonons.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"57 1-2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135715084","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}
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