Structural Dynamics-Us最新文献

Structure and spin of the low- and high-spin states of Fe²⁺(phen)₃ studied by x-ray scattering and emission spectroscopy. 利用 X 射线散射和发射光谱研究 Fe2+(phen)3 的低自旋态和高自旋态的结构和自旋。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-10-23 eCollection Date: 2024-09-01 DOI: 10.1063/4.0000254

Victoria Kabanova, Mathias Sander, Matteo Levantino, Qingyu Kong, Sophie Canton, Marius Retegan, Marco Cammarata, Philipp Lenzen, Latévi Max Daku Lawson, Michael Wulff

{"title":"Structure and spin of the low- and high-spin states of Fe2+(phen)3 studied by x-ray scattering and emission spectroscopy.","authors":"Victoria Kabanova, Mathias Sander, Matteo Levantino, Qingyu Kong, Sophie Canton, Marius Retegan, Marco Cammarata, Philipp Lenzen, Latévi Max Daku Lawson, Michael Wulff","doi":"10.1063/4.0000254","DOIUrl":"https://doi.org/10.1063/4.0000254","url":null,"abstract":"The structure and spin of photoexcited Fe2+(phen)3 in water are examined by x-ray scattering and x-ray emission spectroscopy with 100 ps time resolution. Excitation of the low-spin (LS) ground state (GS) to the charge transfer state 1MLCT* leads to the formation of a high-spin (HS) state that returns to the GS in 725 ps. Density functional theory (DFT) predicts a Fe-N bond elongation in HS by 0.19 Å in agreement with the scattering data. The angle between the ligands increases by 5.4° in HS, which allows the solvent to get 0.33 Å closer to Fe in spite of the expansion of the molecule. The rise in solvent temperature from the return of photoproducts to the GS is dominated by the formation dynamics of HS, 1MLCT* → HS, which is followed by a smaller rise from the HS → GS transition. The latter agrees with the 0.61 eV energy gap E(HS)-E(LS) calculated by DFT. However, the temperature rise from the 1MLCT → HS transition is greater than expected, by a factor of 2.1, which is explained by the re-excitation of nascent HS* by the 1.2 ps pump pulse. This hypothesis is supported by optical spectroscopy measurements showing that the 1.2 ps long pump pulse activates the HS* → 5MLCT* channel, which is followed by the ultrafast return to HS* via intersystem crossing. Finally, the spins of the photoproducts are monitored by the Kβ emission and the spectra confirm that the spins of LS and HS states are 0 and 2, respectively.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 5","pages":"054901"},"PeriodicalIF":2.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11501788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142511005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ultrafast energy-dispersive soft-x-ray diffraction in the water window with a laser-driven source. 利用激光驱动源在水窗中进行超快能量色散软 X 射线衍射。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-10-11 eCollection Date: 2024-09-01 DOI: 10.1063/4.0000270

Jasmin Jarecki, Martin Hennecke, Themistoklis Sidiropoulos, Matthias Schnuerer, Stefan Eisebitt, Daniel Schick

{"title":"Ultrafast energy-dispersive soft-x-ray diffraction in the water window with a laser-driven source.","authors":"Jasmin Jarecki, Martin Hennecke, Themistoklis Sidiropoulos, Matthias Schnuerer, Stefan Eisebitt, Daniel Schick","doi":"10.1063/4.0000270","DOIUrl":"https://doi.org/10.1063/4.0000270","url":null,"abstract":"Time-resolved soft-x-ray-diffraction experiments give access to microscopic processes in a broad range of solid-state materials by probing ultrafast dynamics of ordering phenomena. While laboratory-based high-harmonic generation (HHG) light sources provide the required photon energies, their limited photon flux is distributed over a wide spectral range, rendering typical monochromatic diffraction schemes challenging. Here, we present a scheme for energy-dispersive soft-x-ray diffraction with femtosecond temporal resolution and photon energies across the water window from 200 to 600 eV. The experiment utilizes the broadband nature of the HHG emission to efficiently probe large slices in reciprocal space. As a proof-of-concept, we study the laser-induced structural dynamics of a Mo/Si superlattice in an ultrafast, non-resonant soft-x-ray diffraction experiment. We extract the underlying strain dynamics from the measured shift of its first order superlattice Bragg peak in reciprocal space at photon energies around 500 eV via soft-x-ray scattering simulations.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 5","pages":"054303"},"PeriodicalIF":2.3,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11470808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Laue-DIALS: Open-source software for polychromatic x-ray diffraction data. Laue-DIALS：多色 X 射线衍射数据开源软件。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-10-02 eCollection Date: 2024-09-01 DOI: 10.1063/4.0000265

Rick A Hewitt, Kevin M Dalton, Derek A Mendez, Harrison K Wang, Margaret A Klureza, Dennis E Brookner, Jack B Greisman, David McDonagh, Vukica Šrajer, Nicholas K Sauter, Aaron S Brewster, Doeke R Hekstra

{"title":"Laue-DIALS: Open-source software for polychromatic x-ray diffraction data.","authors":"Rick A Hewitt, Kevin M Dalton, Derek A Mendez, Harrison K Wang, Margaret A Klureza, Dennis E Brookner, Jack B Greisman, David McDonagh, Vukica Šrajer, Nicholas K Sauter, Aaron S Brewster, Doeke R Hekstra","doi":"10.1063/4.0000265","DOIUrl":"10.1063/4.0000265","url":null,"abstract":"Most x-ray sources are inherently polychromatic. Polychromatic (\"pink\") x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure-ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 5","pages":"054701"},"PeriodicalIF":2.3,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11462730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatiotemporal determination of photoinduced strain in a Weyl semimetal. 韦尔半金属中光诱导应变的时空测定。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-09-30 eCollection Date: 2024-09-01 DOI: 10.1063/4.0000263

Jianyu Wu, Amit Kumar Prasad, Alexander Balatsky, Jonas Weissenrieder

{"title":"Spatiotemporal determination of photoinduced strain in a Weyl semimetal.","authors":"Jianyu Wu, Amit Kumar Prasad, Alexander Balatsky, Jonas Weissenrieder","doi":"10.1063/4.0000263","DOIUrl":"10.1063/4.0000263","url":null,"abstract":"The application of dynamic strain holds the potential to manipulate topological invariants in topological quantum materials. This study investigates dynamic structural deformation and strain modulation in the Weyl semimetal WTe2, focusing on the microscopic regions with static strain defects. The interplay of static strain fields, at local line defects, with dynamic strain induced from photo-excited coherent acoustic phonons results in the formation of local standing waves at the defect sites. The dynamic structural distortion is precisely determined utilizing ultrafast electron microscopy with nanometer spatial and gigahertz temporal resolutions. Numerical simulations are employed to interpret the experimental results and explain the mechanism for how the local strain fields are transiently modulated through light-matter interaction. This research provides the experimental foundation for investigating predicted phenomena such as the mixed axial-torsional anomaly, acoustogalvanic effect, and axial magnetoelectric effects in Weyl semimetals, and paves the road to manipulate quantum invariants through transient strain fields in quantum materials.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 5","pages":"054301"},"PeriodicalIF":2.3,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11462575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-repetition-rate ultrafast electron diffraction with direct electron detection. 具有直接电子探测功能的高重复率超快电子衍射。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-09-27 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000256

F R Diaz, M Mero, K Amini

{"title":"High-repetition-rate ultrafast electron diffraction with direct electron detection.","authors":"F R Diaz, M Mero, K Amini","doi":"10.1063/4.0000256","DOIUrl":"https://doi.org/10.1063/4.0000256","url":null,"abstract":"Ultrafast electron diffraction (UED) instruments typically operate at kHz or lower repetition rates and rely on indirect detection of electrons. However, these experiments encounter limitations because they are required to use electron beams containing a relatively large number of electrons (≫100 electrons/pulse), leading to severe space-charge effects. Consequently, electron pulses with long durations and large transverse diameters are used to interrogate the sample. Here, we introduce a novel UED instrument operating at a high repetition rate and employing direct electron detection. We operate significantly below the severe space-charge regime by using electron beams containing 1-140 electrons per pulse at 30 kHz. We demonstrate the ability to detect time-resolved signals from thin film solid samples with a difference contrast signal, <math><mi>Δ</mi> <mi>I</mi> <mo>/</mo> <mrow> <msub><mrow><mi>I</mi></mrow> <mrow><mn>0</mn></mrow> </msub> </mrow> </math> , and an instrument response function as low as 10-5 and 184-fs (FWHM), respectively, without temporal compression. Overall, our findings underscore the importance of increasing the repetition rate of UED experiments and adopting a direct electron detection scheme, which will be particularly impactful for gas-phase UED. Our newly developed scheme enables more efficient and sensitive investigations of ultrafast dynamics in photoexcited samples using ultrashort electron beams.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 5","pages":"054302"},"PeriodicalIF":2.3,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11438501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Laser-induced electron diffraction: Imaging of a single gas-phase molecular structure with one of its own electrons. 激光诱导电子衍射：利用单个气相分子结构自身的一个电子进行成像。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-08-30 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000237

K Chirvi, J Biegert

引用次数: 0

Deconvolution of dynamic heterogeneity in protein structure. 蛋白质结构动态异质性的解卷积。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-08-19 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000261

Zhong Ren, Xiaojing Yang

{"title":"Deconvolution of dynamic heterogeneity in protein structure.","authors":"Zhong Ren, Xiaojing Yang","doi":"10.1063/4.0000261","DOIUrl":"10.1063/4.0000261","url":null,"abstract":"Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 4","pages":"041302"},"PeriodicalIF":2.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of crystal orientation in attosecond photoinjection dynamics of germanium. 晶体取向在锗的阿秒级光注入动力学中的作用。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-08-19 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000253

Nicola Di Palo, Lyudmyla Adamska, Simone Bonetti, Giacomo Inzani, Matteo Talarico, Marta Arias Velasco, Gian Luca Dolso, Rocío Borrego-Varillas, Mauro Nisoli, Stefano Pittalis, Carlo Andrea Rozzi, Matteo Lucchini

{"title":"Role of crystal orientation in attosecond photoinjection dynamics of germanium.","authors":"Nicola Di Palo, Lyudmyla Adamska, Simone Bonetti, Giacomo Inzani, Matteo Talarico, Marta Arias Velasco, Gian Luca Dolso, Rocío Borrego-Varillas, Mauro Nisoli, Stefano Pittalis, Carlo Andrea Rozzi, Matteo Lucchini","doi":"10.1063/4.0000253","DOIUrl":"10.1063/4.0000253","url":null,"abstract":"Understanding photoinjection in semiconductors-a fundamental physical process-represents the first step toward devising new opto-electronic devices, capable of operating on unprecedented time scales. Fostered by the development of few-femtosecond, intense infrared pulses, and attosecond spectroscopy techniques, ultrafast charge injection in solids has been the subject of intense theoretical and experimental investigation. Recent results have shown that while under certain conditions photoinjection can be ascribed to a single, well-defined phenomenon, in a realistic multi-band semiconductor like Ge, several competing mechanisms determine the sub-cycle interaction of an intense light field with the atomic and electronic structure of matter. In this latter case, it is yet unclear how the complex balance between the different physical mechanisms is altered by the chosen interaction geometry, dictated by the relative orientation between the crystal lattice and the laser electric field direction. In this work, we investigate ultrafast photoinjection in a Ge monocrystalline sample with attosecond temporal resolution under two distinct orientations. Our combined theoretical and experimental effort suggests that the physical mechanisms determining carrier excitation in Ge are largely robust against crystal rotation. Nevertheless, the different alignment between the laser field and the crystal unit cell causes non-negligible changes in the momentum distribution of the excited carriers and their injection yield. Further experiments are needed to clarify whether the crystal orientation can be used to tune the photoinjection of carriers in a semiconductor at these extreme time scales.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 4","pages":"044303"},"PeriodicalIF":2.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11341128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention. CrysFormer：通过帕特森图谱、深度学习和部分结构关注确定蛋白质结构。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-08-14 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000252

Tom Pan, Chen Dun, Shikai Jin, Mitchell D Miller, Anastasios Kyrillidis, George N Phillips

{"title":"CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention.","authors":"Tom Pan, Chen Dun, Shikai Jin, Mitchell D Miller, Anastasios Kyrillidis, George N Phillips","doi":"10.1063/4.0000252","DOIUrl":"10.1063/4.0000252","url":null,"abstract":"Determining the atomic-level structure of a protein has been a decades-long challenge. However, recent advances in transformers and related neural network architectures have enabled researchers to significantly improve solutions to this problem. These methods use large datasets of sequence information and corresponding known protein template structures, if available. Yet, such methods only focus on sequence information. Other available prior knowledge could also be utilized, such as constructs derived from x-ray crystallography experiments and the known structures of the most common conformations of amino acid residues, which we refer to as partial structures. To the best of our knowledge, we propose the first transformer-based model that directly utilizes experimental protein crystallographic data and partial structure information to calculate electron density maps of proteins. In particular, we use Patterson maps, which can be directly obtained from x-ray crystallography experimental data, thus bypassing the well-known crystallographic phase problem. We demonstrate that our method, CrysFormer, achieves precise predictions on two synthetic datasets of peptide fragments in crystalline forms, one with two residues per unit cell and the other with fifteen. These predictions can then be used to generate accurate atomic models using established crystallographic refinement programs.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 4","pages":"044701"},"PeriodicalIF":2.3,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11326852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Introduction to the Special Issue Tribute to Olga Kennard (1924-2023). 向奥尔加-肯纳德（1924-2023 年）致敬特刊导言。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-07-30 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000264

John R Helliwell

引用次数: 0