Structural Dynamics-Us最新文献_第4页

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models. ProteinReDiff：基于等变扩散的生成模型的复合体配体结合蛋白的重新设计。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-11-25 eCollection Date: 2024-11-01 DOI: 10.1063/4.0000271

Viet Thanh Duy Nguyen, Nhan D Nguyen, Truong Son Hy

引用次数: 0

Element-specific ultrafast lattice dynamics in FePt nanoparticles. 铁铂纳米粒子中特定元素的超快晶格动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-11-08 eCollection Date: 2024-11-01 DOI: 10.1063/4.0000260

Diego Turenne, Igor Vaskivskyi, Klaus Sokolowski-Tinten, Xijie J Wang, Alexander H Reid, Xiaozhe Shen, Ming-Fu Lin, Suji Park, Stephen Weathersby, Michael Kozina, Matthias C Hoffmann, Jian Wang, Jakub Sebesta, Yukiko K Takahashi, Oscar Grånäs, Peter M Oppeneer, Hermann A Dürr

{"title":"Element-specific ultrafast lattice dynamics in FePt nanoparticles.","authors":"Diego Turenne, Igor Vaskivskyi, Klaus Sokolowski-Tinten, Xijie J Wang, Alexander H Reid, Xiaozhe Shen, Ming-Fu Lin, Suji Park, Stephen Weathersby, Michael Kozina, Matthias C Hoffmann, Jian Wang, Jakub Sebesta, Yukiko K Takahashi, Oscar Grånäs, Peter M Oppeneer, Hermann A Dürr","doi":"10.1063/4.0000260","DOIUrl":"10.1063/4.0000260","url":null,"abstract":"Light-matter interaction at the nanoscale in magnetic alloys and heterostructures is a topic of intense research in view of potential applications in high-density magnetic recording. While the element-specific dynamics of electron spins is directly accessible to resonant x-ray pulses with femtosecond time structure, the possible element-specific atomic motion remains largely unexplored. We use ultrafast electron diffraction (UED) to probe the temporal evolution of lattice Bragg peaks of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. The diffraction interference between Fe and Pt sublattices enables us to demonstrate that the Fe mean square vibration amplitudes are significantly larger that those of Pt as expected from their different atomic mass. Both are found to increase as energy is transferred from the laser-excited electrons to the lattice. Contrary to this intuitive behavior, we observe a laser-induced lattice expansion that is larger for Pt than for Fe atoms during the first picosecond after laser excitation. This effect points to the strain-wave driven lattice expansion with the longitudinal acoustic Pt motion dominating that of Fe.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 6","pages":"064501"},"PeriodicalIF":2.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711669","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

Asymmetric conformation of the high-spin state of iron(II)-tris(2,2-bipyridine): Time-resolved x-ray absorption and ultraviolet circular dichroism. 三(2,2-联吡啶)铁(II)高自旋态的不对称构象：时间分辨 X 射线吸收和紫外圆二色性。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-11-08 eCollection Date: 2024-11-01 DOI: 10.1063/4.0000268

Nico Sanna, Costantino Zazza, Giovanni Chillemi, Elisabetta Pace, Francesco Cappelluti, Luigi Bencivenni, Malte Oppermann, Maurizio Benfatto, Majed Chergui

{"title":"Asymmetric conformation of the high-spin state of iron(II)-tris(2,2-bipyridine): Time-resolved x-ray absorption and ultraviolet circular dichroism.","authors":"Nico Sanna, Costantino Zazza, Giovanni Chillemi, Elisabetta Pace, Francesco Cappelluti, Luigi Bencivenni, Malte Oppermann, Maurizio Benfatto, Majed Chergui","doi":"10.1063/4.0000268","DOIUrl":"10.1063/4.0000268","url":null,"abstract":"We analyze the structures of the low-spin (LS) ground state and the high-spin (HS) lowest excited state of the iron-(II)-tris bipyridine complex ([Fe(bpy)3]2+) using density functional theory PBE methods, modeling the solvent interactions with conductor-like polarizable continuum model. These calculations are globally benchmarked against a wide range of experimental observables that include ultraviolet-visible linear absorption and circular dichroism (CD) spectra and Fe K-edge x-ray absorption near edge spectra (XANES). The calculations confirm the already established D3 geometry of the LS state, as well as a departure from this geometry for the HS state, with the appearance of inequivalent Fe-N bond elongations. The simulated structures nicely reproduce the above-mentioned experimental observables. We also calculate the vibrational modes of the LS and HS states. For the former, they reproduce well the vibrational frequencies from published infrared and Raman data, while for the latter, they predict very well the low-frequency vibrational coherences, attributed to Fe-N stretch modes, which were reported in ultrafast spectroscopic experiments. We further present calculations of the high-frequency region, which agree with recent ultrafast transient infrared spectroscopy studies. This work offers a common basis to the structural information encoded in the excited state CD and the Fe K XANES of the HS state tying together different structural IR, UV-visible, and x-ray observables.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 6","pages":"064101"},"PeriodicalIF":2.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740987","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

Scaling and merging time-resolved pink-beam diffraction with variational inference. 变分推理的时间分辨粉束衍射标度与合并。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-11-06 eCollection Date: 2024-11-01 DOI: 10.1063/4.0000269

Kara A Zielinski, Cole Dolamore, Harrison K Wang, Robert W Henning, Mark A Wilson, Lois Pollack, Vukica Srajer, Doeke R Hekstra, Kevin M Dalton

{"title":"Scaling and merging time-resolved pink-beam diffraction with variational inference.","authors":"Kara A Zielinski, Cole Dolamore, Harrison K Wang, Robert W Henning, Mark A Wilson, Lois Pollack, Vukica Srajer, Doeke R Hekstra, Kevin M Dalton","doi":"10.1063/4.0000269","DOIUrl":"10.1063/4.0000269","url":null,"abstract":"Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners. Recent work demonstrated this challenge can be addressed when merging redundant observations by a statistical technique known as variational inference (VI). However, the variational approach to time-resolved data analysis requires identification of successful hyperparameters in order to optimally extract signal. In this case study, we present a successful application of VI to time-resolved changes in an enzyme, DJ-1, upon mixing with a substrate molecule, methylglyoxal. We present a strategy to extract high signal-to-noise changes in electron density from these data. Furthermore, we conduct an ablation study, in which we systematically remove one hyperparameter at a time to demonstrate the impact of each hyperparameter choice on the success of our model. We expect this case study will serve as a practical example for how others may deploy VI in order to analyze their time-resolved diffraction data.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 6","pages":"064301"},"PeriodicalIF":2.3,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773935","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

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