Structural Dynamics-Us最新文献

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data. 通过重采样时间分辨序列 X 射线晶体学数据评估蛋白质构象变化

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-07-24 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000258

Adams Vallejos, Gergely Katona, Richard Neutze

{"title":"Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.","authors":"Adams Vallejos, Gergely Katona, Richard Neutze","doi":"10.1063/4.0000258","DOIUrl":"10.1063/4.0000258","url":null,"abstract":"With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11272219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761869","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

Preface to Special Topic: The Advent of Ultrafast X-Ray Absorption Spectroscopy. 专题序言：超快 X 射线吸收光谱学的到来。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-06-21 eCollection Date: 2024-05-01 DOI: 10.1063/4.0000259

Emiliano Principi

引用次数: 0

A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. 时间分辨 X 射线和电子散射探测结构动态的比较综述。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-05-01 DOI: 10.1063/4.0000249

Yunbeom Lee, Key Young Oang, Doyeong Kim, Hyotcherl Ihee

{"title":"A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics.","authors":"Yunbeom Lee, Key Young Oang, Doyeong Kim, Hyotcherl Ihee","doi":"10.1063/4.0000249","DOIUrl":"https://doi.org/10.1063/4.0000249","url":null,"abstract":"The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872246","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-energy-resolution off-resonant spectroscopy with self-seeded x-ray free-electron laser pulses. 利用自种子 X 射线自由电子激光脉冲进行高能分辨率非共振光谱分析。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-03-26 eCollection Date: 2024-03-01 DOI: 10.1063/4.0000243

Jang Hyeob Sohn, Gyeongbo Kang, Tae-Kyu Choi, Gyusang Lee, Changhoo Lee, Sae Hwan Chun, Jaeku Park, Dongbin Shin, Byoung-Ick Cho

{"title":"High-energy-resolution off-resonant spectroscopy with self-seeded x-ray free-electron laser pulses.","authors":"Jang Hyeob Sohn, Gyeongbo Kang, Tae-Kyu Choi, Gyusang Lee, Changhoo Lee, Sae Hwan Chun, Jaeku Park, Dongbin Shin, Byoung-Ick Cho","doi":"10.1063/4.0000243","DOIUrl":"10.1063/4.0000243","url":null,"abstract":"This paper presents the implementation of high-energy-resolution off-resonant spectroscopy (HEROS) measurements using self-seeded x-ray free-electron laser (XFEL) pulses. This study systematically investigated XFEL conditions, including photon energy and accumulated shot numbers, to optimize the measurement efficiency for copper foil samples near the K-edge. The x-ray absorption spectra reconstructed using HEROS were compared with those derived from fluorescence-yield measurements. The HEROS-based spectra exhibited consistent line shapes independent of the sample thickness. The potential application of HEROS to high-temperature copper was also explored. HEROS offers distinct advantages including scan-free measurement of x-ray absorption spectra with reduced core-hole lifetime broadening and self-absorption effects. Using self-seeded XFEL pulses, HEROS facilitates single-shot-based pump-probe measurements to investigate the ultrafast dynamics in various materials and diverse conditions.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10972604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307505","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

Vector-based feedback of continuous wave radiofrequency compression cavity for ultrafast electron diffraction. 基于矢量反馈的连续波射频压缩腔用于超快电子衍射。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2024-03-25 eCollection Date: 2024-03-01 DOI: 10.1063/4.0000231

Thomas M Sutter, Joshua S H Lee, Atharva V Kulkarni, Pietro Musumeci, Anshul Kogar

引用次数: 0