Structural Dynamics-Us最新文献

Helical spin dynamics in Cu₂OSeO₃ as measured with small-angle neutron scattering. 用小角中子散射测量Cu2OSeO3的螺旋自旋动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-18 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000305

Victor Ukleev, Priya R Baral, Robert Cubitt, Nina-Juliane Steinke, Arnaud Magrez, Oleg I Utesov

引用次数: 0

Structure and ultrafast dynamics of tri-nuclear Ag-/Tl-Pt₂POP₄ complexes in solution. 溶液中三核Ag-/Tl-Pt2POP4配合物的结构和超快动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-10 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000293

Philipp Lenzen, Kristoffer Haldrup, Asmus O Dohn, Frederik Beyer, Elisa Biasin, Morten Christensen, Bianca L Hansen, Tobias Harlang, Kasper Skov Kjær, Mads Goldschmidt Laursen, Peter Vester, Tim B van Driel, Matthieu Chollet, James M Glownia, Robert J Hartsock, Henrik T Lemke, Silke Nelson, Sanghoon Song, Kasper Steen Pedersen, Kelly J Gaffney, Klaus B Møller, Martin M Nielsen

{"title":"Structure and ultrafast dynamics of tri-nuclear Ag-/Tl-Pt2POP4 complexes in solution.","authors":"Philipp Lenzen, Kristoffer Haldrup, Asmus O Dohn, Frederik Beyer, Elisa Biasin, Morten Christensen, Bianca L Hansen, Tobias Harlang, Kasper Skov Kjær, Mads Goldschmidt Laursen, Peter Vester, Tim B van Driel, Matthieu Chollet, James M Glownia, Robert J Hartsock, Henrik T Lemke, Silke Nelson, Sanghoon Song, Kasper Steen Pedersen, Kelly J Gaffney, Klaus B Møller, Martin M Nielsen","doi":"10.1063/4.0000293","DOIUrl":"10.1063/4.0000293","url":null,"abstract":"The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt2(H2P2O5) <math> <mrow> <mrow><msubsup><mrow></mrow> <mn>4</mn> <mrow><mn>4</mn> <mo>-</mo></mrow> </msubsup> </mrow> </mrow> </math> ] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal-metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with <100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract <math><mo>∼</mo></math> 0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of <math><mo>∼</mo></math> 0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of <math><mo>∼</mo></math> 0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent (\"wave-packet\") oscillations along the metal-Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal-metal bonding behavior in both the ground and excited state for both complexes.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044902"},"PeriodicalIF":2.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643877","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

Unveiling hidden wavepacket dynamics in time-resolved x-ray scattering data via singular spectrum analysis. 通过奇异谱分析揭示时间分辨x射线散射数据中隐藏的波包动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-09 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000764

Jaeseok Kim, Hyunwoo Jeong, Jae Hyuk Lee, Rory Ma, Daewoong Nam, Minseok Kim, Dogeun Jang, Jong Goo Kim

{"title":"Unveiling hidden wavepacket dynamics in time-resolved x-ray scattering data via singular spectrum analysis.","authors":"Jaeseok Kim, Hyunwoo Jeong, Jae Hyuk Lee, Rory Ma, Daewoong Nam, Minseok Kim, Dogeun Jang, Jong Goo Kim","doi":"10.1063/4.0000764","DOIUrl":"10.1063/4.0000764","url":null,"abstract":"Time-resolved x-ray liquidography (TRXL) is a powerful technique for directly tracking ultrafast structural dynamics in real space. However, resolving the motion of vibrational wavepackets generated by femtosecond laser pulses remains challenging due to the limited temporal resolution and signal-to-noise ratio (SNR) of experimental data. This study addresses these challenges by introducing singular spectrum analysis (SSA) as an efficient method for extracting oscillatory signals associated with vibrational wavepackets from TRXL data. To evaluate its performance, we conducted a comparative study using simulated TRXL data, demonstrating that SSA outperforms conventional analysis methods such as the Fourier transform of temporal profiles and singular value decomposition, particularly under low SNR conditions. We further applied SSA to experimental TRXL data on the photodissociation of triiodide ( <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>3</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> ) in methanol, successfully isolating oscillatory signals arising from wavepacket dynamics in ground-state <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>3</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> and excited-state <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>2</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> , which had been challenging to resolve in previous TRXL studies. These results establish SSA as a highly effective tool for analyzing ultrafast structural dynamics in time-resolved experiments and open new opportunities for studying wavepacket dynamics in a wide range of photoinduced reactions.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044901"},"PeriodicalIF":2.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610048","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: Celebrating the work and achievements of Keith Moffat. 专题序言：庆祝基思·莫法特的工作和成就。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-01 DOI: 10.1063/4.0000771

Richard Neutze

引用次数: 0

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning. 从序列到蛋白质结构和构象动力学与人工智能/机器学习。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-24 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000765

Alexander M Ille, Emily Anas, Michael B Mathews, Stephen K Burley

{"title":"From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning.","authors":"Alexander M Ille, Emily Anas, Michael B Mathews, Stephen K Burley","doi":"10.1063/4.0000765","DOIUrl":"10.1063/4.0000765","url":null,"abstract":"The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"030902"},"PeriodicalIF":2.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12195464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498778","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

Advances in structural science: Education, outreach, and research applications. 结构科学的进展：教育、推广和研究应用。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-20 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000304

Charles Bou-Nader, Jamaine Davis, Louise N Dawe, David S Goodsell, James Kaduk, Bart Kahr, Helen Maynard-Casely, Brandon Q Mercado, Beata E Mierzwa, Olayinka Olatunji-Ojo, Allen Oliver, Christine Zardecki, Shao-Liang Zheng

引用次数: 0

Advanced glycation end product (AGE) crosslinking of a bacterial protein: Are AGE-modifications going undetected in our studies? 细菌蛋白的晚期糖基化终产物（AGE）交联：AGE修饰在我们的研究中未被检测到吗？

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-12 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000754

Bonnie J Cuthbert, Steven J Jensen, Christopher S Hayes, Celia W Goulding

{"title":"Advanced glycation end product (AGE) crosslinking of a bacterial protein: Are AGE-modifications going undetected in our studies?","authors":"Bonnie J Cuthbert, Steven J Jensen, Christopher S Hayes, Celia W Goulding","doi":"10.1063/4.0000754","DOIUrl":"10.1063/4.0000754","url":null,"abstract":"The small reactive molecules, glyoxal (GO) and methylglyoxal (MGO), are common byproducts of metabolic processes. GO and MGO are known to modify proteins, DNA, and lipids, resulting in advance glycation end products (AGEs). AGEs are linked to numerous human diseases but are found across all three domains of life due to the widespread presence of GO and MGO. Recent structural studies have revealed that an antibacterial phospholipase toxin contains a methylglyoxal-derived imidazolium crosslink (MODIC). Unlike AGEs that are associated with human diseases and protein dysfunction, crosslinking is required for the toxin's enzymatic activity, indicating that MODIC acts as a bona fide post-translational modification to promote function. The MODIC-modified toxin represents the first structure in the protein data bank with an AGE-modification. However, because GO and MGO are present in all cells, AGE-modifications are likely more prevalent than currently reported but have gone undetected. We used the toxin's MODIC structural motif to query the protein data bank for other modified proteins. This search recovered the colicin Ia pore-forming toxin. Using the deposited crystal structure and structural data for colicin Ia, we were able to model glyoxal-derived imidazolium crosslink or MODIC modifications into the electron density map, suggesting that GO/MGO modifications may indeed be more common in bacterial proteins.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"031001"},"PeriodicalIF":2.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303374","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

Statistically elucidated responses from low-signal contrast mechanisms in ultrafast electron microscopy. 超快电子显微镜下低信号对比机制的统计分析。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-12 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000751

Spencer A Reisbick, Alexandre Pofelski, Myung-Geun Han, Chuhang Liu, Eric Montgomery, Chunguang Jing, Kayla Callaway, John Cumings, June W Lau, Yimei Zhu

{"title":"Statistically elucidated responses from low-signal contrast mechanisms in ultrafast electron microscopy.","authors":"Spencer A Reisbick, Alexandre Pofelski, Myung-Geun Han, Chuhang Liu, Eric Montgomery, Chunguang Jing, Kayla Callaway, John Cumings, June W Lau, Yimei Zhu","doi":"10.1063/4.0000751","DOIUrl":"10.1063/4.0000751","url":null,"abstract":"The emergence of ultrafast electron microscopy (UEM) has enabled the discovery of strongly correlated dynamic mechanisms, including electron-phonon coupling, structural phase transitions, thermal transport, and electromagnetic deflection. Most UEM systems operate stroboscopically, meaning that the technique is susceptible to artifacts, mistakes, and misinterpretation of the data due to extensive experimental effort. In contrast to the ultrafast designation, data acquisition is extraordinarily slow because the electron beam has significantly reduced signal compared to traditional transmission electron microscopy due to pulsing the electron beam. Consequently, the sample may drift, tilt, or undergo irreversible structural changes that are independent of the time-resolved dynamics throughout the experimental time frame. Furthermore, these datasets require significant user interpretation that can be problematic when proper controls are not implemented thoroughly. Here, we demonstrate a new algorithm designed to separate ultrafast structural dynamics from long-term artifacts using a LiNbO3 sample experiencing electrically driven surface acoustic wave propagation. Additionally, we provide examples of the impact of user bias when analyzing the data and provide a methodology, which enables the extraction of time-resolved responses when the image signal is extraordinarily low. Overall, the goal of this publication is to provide methods that validate the experimental results and reduce researcher biases during UEM data interpretation.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034302"},"PeriodicalIF":2.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303375","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

"Everything's a sample": Characterizing everyday materials using x-ray powder diffraction. “一切都是样品”：用x射线粉末衍射表征日常材料。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-02 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000756

James A Kaduk

引用次数: 0

Applications of visualization technology in the structural sciences. 可视化技术在结构科学中的应用。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-05-27 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000753

Edward T Eng, Nichole R Valdez

{"title":"Applications of visualization technology in the structural sciences.","authors":"Edward T Eng, Nichole R Valdez","doi":"10.1063/4.0000753","DOIUrl":"10.1063/4.0000753","url":null,"abstract":"The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data-particularly from cryo-electron microscopy and x-ray crystallography-are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"030901"},"PeriodicalIF":2.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12119125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175406","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