Structural Dynamics-Us最新文献

SISYPHOS: An automatic procedure for the serial refinement of single-crystal diffraction data in Olex2. 在Olex2中对单晶衍射数据进行串行细化的自动程序。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-10-03 eCollection Date: 2025-09-01 DOI: 10.1063/4.0000784

Florian Meurer, Florian Kleemiss, Birgit Hischa, Daniel Brüx, Ann-Cathrin Koch, Michael Bodensteiner

引用次数: 0

Validation of 3D cryoEM single-particle reconstruction correctness and handedness with Ewald's sphere correction. 用Ewald球校正验证三维低温电镜单粒子重建的正确性和手性。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1063/4.0000777

R Bromberg, Y Guo, D Borek, Z Otwinowski

{"title":"Validation of 3D cryoEM single-particle reconstruction correctness and handedness with Ewald's sphere correction.","authors":"R Bromberg, Y Guo, D Borek, Z Otwinowski","doi":"10.1063/4.0000777","DOIUrl":"10.1063/4.0000777","url":null,"abstract":"The correct description of quantum scattering places the observed scattering contributions on the Ewald's sphere and its Friedel mate copy. In electron microscopy, due to the large radius of the Ewald's sphere, these scattering contributions are typically merged during data analysis. We present an approach that separates and factorizes those contributions into real and imaginary components of the image. When an inverted solution is calculated, the map derived from the real component of the image generates an inverted solution, while the map derived from the imaginary component of the image generates an inverted and sign-flipped solution. Therefore, the sign of correlation between reconstructions derived from the real and imaginary components provides the automatic determination of handedness and additional validation for the quality of 3D reconstructions. The factorization and its implementation are robust enough to be routinely used in single-particle reconstructions, even at resolutions below the limit where the curvature of the Ewald's sphere affects the overall signal-to-noise ratio.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054301"},"PeriodicalIF":2.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12488216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214087","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

Spin dynamics in elemental Ni and Ni₈₅Co₁₅ thin films probed by high harmonic generated photons around the M _2,3 edges. 用m2,3边附近的高谐波光子探测单质Ni和Ni85Co15薄膜的自旋动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-09-11 eCollection Date: 2025-09-01 DOI: 10.1063/4.0000769

Juliette Dubois, Emmanuelle Jal, Carlos Rodriguez Cortez, Marcel Hennes, Renaud Delaunay, Guillaume Lambert, Boris Vodungbo

{"title":"Spin dynamics in elemental Ni and Ni85Co15 thin films probed by high harmonic generated photons around the M 2,3 edges.","authors":"Juliette Dubois, Emmanuelle Jal, Carlos Rodriguez Cortez, Marcel Hennes, Renaud Delaunay, Guillaume Lambert, Boris Vodungbo","doi":"10.1063/4.0000769","DOIUrl":"10.1063/4.0000769","url":null,"abstract":"We compared ultrafast spin dynamics in laser-excited Ni85Co15 alloy and pure Ni thin films exhibiting magnetic weak stripe domains using x-ray resonant magnetic scattering. By relying on extreme ultraviolet pulses obtained via high-harmonic generation, we simultaneously probed our samples using four energies around the Co and Ni <math> <mrow> <mrow> <msub><mrow><mi>M</mi></mrow> <mrow><mn>2</mn> <mo>,</mo> <mn>3</mn></mrow> </msub> </mrow> </mrow> </math> edges. Our results show a significant laser-induced reduction of the intensity of the magnetic scattering peaks on fs timescales and clearly highlight that this effect depends sensitively on the probing wavelength: different quenching amplitudes and characteristic timescales are found when changing the probing energy. More particularly, in our alloyed thin film, we observe a delay of about 17 fs in the scattered intensity dynamics between probing energies close to the Ni and Co edges, respectively. This delay is not observed in the pure Ni sample and is therefore most likely induced by the presence of Co in the thin film, reflecting the different ultrafast magnetic responses of the two 3d metals in these alloys.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054501"},"PeriodicalIF":2.3,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12440127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082033","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

Benchmarking crystal structure refinement: A systematic study on Hirshfeld atom refinement. 基准晶体结构细化：赫斯菲尔德原子细化的系统研究。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-09-09 eCollection Date: 2025-09-01 DOI: 10.1063/4.0000774

Daniel Brüx, Florian Meurer, Florian Kleemiss

{"title":"Benchmarking crystal structure refinement: A systematic study on Hirshfeld atom refinement.","authors":"Daniel Brüx, Florian Meurer, Florian Kleemiss","doi":"10.1063/4.0000774","DOIUrl":"10.1063/4.0000774","url":null,"abstract":"This study systematically investigates the influence of various parameters of the wavefunction calculation during Hirshfeld atom refinement (HAR). We aim to address the lack of consensus in the literature and conflicting information on a generally recommended procedure. A set of amino acid test structures, known for their immense biochemical importance and unimpeachable experimental data quality, was employed to ensure reliable results, unbiased by the question of insufficient diffraction data quality. A comprehensive permutation of refinement parameters was conducted to avoid overlooking potential influences, resulting in 2496 structure refinements per amino acid. Applying a solvent model systematically improved refinement results compared to gas-phase calculations. Additionally, it was observed that the pure Hartree-Fock method outperforms all tested density functional theory methods across all structures in this test set of polar-organic molecules. These findings underscore the importance of carefully considering the level of theory applied in HAR and offer an overview of the performance of various methods and parameters.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054101"},"PeriodicalIF":2.3,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12422757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145041940","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

Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography. 低温电子断层扫描用超快脉冲有源相板的研制进展。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-26 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000770

Daniel X Du, Adam C Bartnik, Cameron J R Duncan, Usama Choudhry, Tanya Tabachnik, Chaim Sallah, Ebrahim Najafi, Ding-Shyue Yang, Jared M Maxson, Anthony W P Fitzpatrick

{"title":"Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography.","authors":"Daniel X Du, Adam C Bartnik, Cameron J R Duncan, Usama Choudhry, Tanya Tabachnik, Chaim Sallah, Ebrahim Najafi, Ding-Shyue Yang, Jared M Maxson, Anthony W P Fitzpatrick","doi":"10.1063/4.0000770","DOIUrl":"10.1063/4.0000770","url":null,"abstract":"Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy excels in determining protein structures purified from recombinant or endogenous sources due to an abundance of particles, weak contrast issues are accentuated in cryo-ET by low copy numbers in crowded cellular milieux. Continuous laser phase plates offer improved contrast in cryo-ET; however, their implementation demands exceptionally high-peak optical intensities. Instead, a novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Furthermore, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way toward exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexes in situ, thus advancing the field of cell biology.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044302"},"PeriodicalIF":2.3,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12396848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975048","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

Molecular chameleons adaptability in target binding. 分子变色龙在靶结合中的适应性。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-13 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000757

Guanhong Bu, Måns Eriksson, Emma Rova Danelius

{"title":"Molecular chameleons adaptability in target binding.","authors":"Guanhong Bu, Måns Eriksson, Emma Rova Danelius","doi":"10.1063/4.0000757","DOIUrl":"10.1063/4.0000757","url":null,"abstract":"Estimates show that up to 85% of the human therapeutic proteomes are undruggable by traditional small molecules. Macrocycles, a class of molecular leads, often extend beyond the traditional drug space and offer the potential to modulate challenging targets within this 85%. These modalities exhibit significant conformational flexibility and often function as molecular chameleons, enabling them to adapt to environments with varying polarities while ensuring good oral bioavailability. In this study, we explore the conformational adaptability in target binding of the three known molecular chameleons, paritaprevir, grazoprevir, and simeprevir, by docking their experimental crystal structures, solution conformations, and target-bound structures into multiple protein targets, including human drug transporters associated with drug-drug interactions and COVID-19 related proteins. Our findings reveal that the macrocyclic core conformational class, or \"chameleonic group,\" determines the overall pharmacophore conformations and influences the conformational changes required for binding to various proteins. These insights provide a pathway toward rationalizing drug optimizations for molecular chameleons as well as offering specific guidance for improving Hepatitis C virus nonstructural protein 3/4A inhibitors, including providing a starting point for their COVID-19 repurposing and cancer therapy.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044701"},"PeriodicalIF":2.3,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12352931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876126","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

Modeling electron dynamics in silicon driven by high-intensity femtosecond x-rays. 由高强度飞秒x射线驱动的硅中的电子动力学建模。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-01 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000299

Sebastian Cardoch, Nicusor Timneanu

{"title":"Modeling electron dynamics in silicon driven by high-intensity femtosecond x-rays.","authors":"Sebastian Cardoch, Nicusor Timneanu","doi":"10.1063/4.0000299","DOIUrl":"10.1063/4.0000299","url":null,"abstract":"High-intensity femtosecond-duration x-rays from free electron lasers have enabled innovative imaging techniques that employ smaller crystal sizes than conventional crystallography. Developments aimed at increasing x-ray pulse intensities bring opportunities and constraints due to ultra-fast changes to atomic scattering form factors from electron dynamics. Experiments on silicon by Inoue et al. [Inoue et al., Phys. Rev. Lett. 131, 163201 (2023)] illustrate this by measuring diffraction efficiencies with increasing x-ray pulse intensities. Results at the highest experimental x-ray pulse intensity have been theoretically studied [Inoue et al., Phys. Rev. Lett. 131, 163201 (2023); Ziaja et al., Atoms 11, 154 (2023)] but not fully reproduced, which raises questions about the mechanisms behind these changes. Using collisional radiative simulations and relativistic configuration-averaged atomic data, we compute the ionization dynamics and diffraction efficiency of silicon and find good agreement within the experimental uncertainty. We incorporate the effects of ionization potential depression by removing energy levels close to the ionization threshold over selected charge states. We identify the main electron impact mechanisms present in our simulations. We bridge the gap between high and low intensity and find regimes where electronic damage affects the efficiency of high- and low-momentum transfer. We computationally examine the effects of free electron degeneracy and find that it does not influence ionization dynamics. Finally, we consider how a non-thermal electron distribution may modify our results. This investigation gives insight into the mechanisms and helps guide future experiments that utilize intense x-ray pulses to achieve high-resolution structural determination.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044101"},"PeriodicalIF":2.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12317780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144776676","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

Accelerating structural dynamics through integrated research informatics. 通过综合研究信息学加速结构动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-30 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000759

Ben Eisenbraun, Alex Ho, Peter A Meyer, Piotr Sliz

{"title":"Accelerating structural dynamics through integrated research informatics.","authors":"Ben Eisenbraun, Alex Ho, Peter A Meyer, Piotr Sliz","doi":"10.1063/4.0000759","DOIUrl":"10.1063/4.0000759","url":null,"abstract":"Structural dynamics research requires robust computational methods, reliable software, accessible data, and scalable infrastructure. Managing these components is complex and directly affects reproducibility and efficiency. The SBGrid Consortium addresses these challenges through a three-pillar approach that encompasses Software, Data, and Infrastructure, designed to foster a consistent and rigorous computational environment. At the core is the SBGrid software collection (>620 curated applications), supported by the Capsules Software Execution Environment, which ensures conflict-free, version-controlled execution. The SBGrid Data Bank supports open science by enabling the publication of primary experimental data. SBCloud, a fully managed cloud computing platform, provides scalable, on-demand infrastructure optimized for structural biology workloads. Together, they reduce computational friction, enabling researchers to focus on interpreting time-resolved data, modeling structural transitions, and managing large simulation datasets for advancing structural dynamics. This integrated platform delivers a reliable and accessible foundation for computationally intensive research across diverse scientific fields sharing common computational methods.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"041101"},"PeriodicalIF":2.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761828","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

The 2024 challenges in structural biology summit. 2024结构生物学峰会的挑战。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-22 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000752

Brent L Nannenga, Tamir Gonen

引用次数: 0

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