Structural Dynamics-Us最新文献

{"title":"Ultrafast internal dynamics of chiral domain walls probed by time-resolved x-ray resonant magnetic scattering.","authors":"Dmitriy Ksenzov, Flavio Capotondi, Nicolas Jaouen, Raphael Gruber, Vincent Cros, Mathias Kläui, Matteo Pancaldi, Emanuele Pedersoli, Nicolas Reyren, Christian Gutt","doi":"10.1063/4.0001223","DOIUrl":"10.1063/4.0001223","url":null,"abstract":"<p><p>We measure the picosecond dynamics of labyrinthine stripe domains with chiral Néel-type domain walls using time-resolved x-ray resonant magnetic scattering (XRMS). At the stripe-domain wavevector, the helicity-summed signal shows ultrafast demagnetization and recovery together with a weak oscillatory contribution attributed to laser-launched coherent surface phonons. In contrast, the dichroic signal, which is sensitive to the in-plane magnetization within the Néel domain walls, exhibits a pronounced oscillatory response. Interestingly, the observed frequency of domain wall dynamics decreases with increasing pump fluence. We associate this frequency decrease with a transient softening of the domain-wall restoring potential following optical excitation. This finding highlights that time-resolved XRMS isolates internal domain-wall dynamics and provides reciprocal-space access to wall-specific degrees of freedom in disordered stripe textures on picosecond time scales.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 5","pages":"054301"},"PeriodicalIF":2.9,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13671853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217184","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}

{"title":"Bayesian model comparison of type-I and type-II ultrafast demagnetization dynamics.","authors":"Hiroki Wadati, Tetsuro Ueno","doi":"10.1063/4.0001228","DOIUrl":"10.1063/4.0001228","url":null,"abstract":"<p><p>Ultrafast demagnetization dynamics are often phenomenologically classified into type-I and type-II responses according to their temporal evolution following femtosecond laser excitation. However, finite experimental temporal resolution and noise can substantially obscure the intrinsic dynamics and complicate this classification. In this work, we investigate the distinguishability of type-I and type-II demagnetization dynamics using Gaussian-convolved phenomenological models and Bayesian information criterion-based statistical model comparison. Synthetic datasets with varying temporal resolution and noise levels were first analyzed to evaluate the conditions under which the two classes can be reliably discriminated. We show that convolution with the instrumental response function significantly reduces the observable differences between the intrinsic responses, thereby producing broad regimes in which model discrimination becomes statistically inconclusive. The applicability of the framework is further demonstrated through analysis of representative experimental ultrafast demagnetization data from NiCo₂O₄ thin films. These results suggest that the apparent classification of ultrafast demagnetization dynamics can be highly sensitive to experimental resolution, noise level, and analysis methodology.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 5","pages":"054501"},"PeriodicalIF":2.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13619346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075937","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}

{"title":"Putrescine-bound structure and multi-temperature crystallography provide new insights into ligand binding and conformational heterogeneity in spermidine synthase.","authors":"Omowumi O Fagbohun, Molly A Canfield, Jonathan A Clinger","doi":"10.1063/4.0001217","DOIUrl":"10.1063/4.0001217","url":null,"abstract":"<p><p>Spermidine synthase (SPDS) is an important enzyme in the pathway for the biosynthesis of polyamines, and it synthesizes the polyamine spermidine from putrescine (PUT) and decarboxylated S-adenosylmethionine. This pathway is a promising target for antiproliferative therapies because of the functions of polyamines in cellular proliferation and differentiation. Higher polyamine levels are linked to cancer and cell proliferation. Previous structures of the enzyme were solved at cryogenic temperatures. Here, we report a new SPDS structure in complex with PUT (SPDS-PUT) and multitemperature crystallography of SPDS complexed with PUT and 5-deoxy-5-methylthioadenosine (MTA) at 100, 273, and 293 K to study its structure and dynamics. The results revealed that the occupancy of the active site is important for the extent of stabilization in the gatekeeping loop. The SPDS-PUT structure revealed putrescine binding in the absence of MTA, providing insight into its interactions within the active site and the conformational state of the gatekeeping loop. The binding of PUT alone was not enough to stabilize the gatekeeping loop, and greater stabilization of the loop occurred in the presence of MTA alone compared to PUT alone. The observed structural asymmetry between the gatekeeping loops of SPDS reflects differences in ligand binding between chains. These findings expand our understanding of the conformational landscape of SPDS.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 5","pages":"054701"},"PeriodicalIF":2.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13619349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149076105","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}

{"title":"John L. Markley, a legacy of service in structural biology.","authors":"Jeffrey C Hoch, Stephen K Burley, Genji Kurisu, Kyle L Morris, Sameer Velankar","doi":"10.1063/4.0001229","DOIUrl":"10.1063/4.0001229","url":null,"abstract":"<p><p>John L. Markley was an early pioneer of the application of nuclear magnetic resonance (NMR) spectroscopy to investigate the structure, dynamics, and function of biological macromolecules by NMR. A recurring theme of his career is the development of standards and shared resources that have enabled the biological NMR community to coherently and collectively advance the disciplines of structural biology and metabolomics. Spanning development standards for atom nomenclature, founding shared NMR resources at Purdue and UW-Madison, and founding the Biological Magnetic Resonance Data Bank (BMRB) and shepherding BMRB membership in the Worldwide Protein Data Bank, this appreciation revisits the many and lasting contributions by our friend and colleague John Markley in support of the global structural biology community.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 5","pages":"050901"},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13553183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148913849","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}

{"title":"Slowly exchanging bound states of SARS-CoV-2 3CL^pro-inhibitor complexes revealed by ¹⁹F NMR.","authors":"Anna De Falco, Ben Shurina, Rebecca Greene-Cramer, Theresa A Ramelot, Gaetano T Montelione","doi":"10.1063/4.0001210","DOIUrl":"https://doi.org/10.1063/4.0001210","url":null,"abstract":"<p><p>The SARS-CoV-2 virus causes COVID-19, and several of its gene products have been successfully targeted for antiviral drug development, including the 3C-like protease (3CL^pro). The substrate-binding site of 3CL^pro exhibits significant conformational plasticity. While available X-ray crystal structures reveal substantial loop variability and molecular dynamics simulations indicate that conformational heterogeneity persists in ligand-bound complexes, the slow-timescale thermodynamic and kinetic landscape of these complexes in solution remains incompletely defined. Using ¹⁹F NMR spectroscopy, we characterize a slow-exchange conformational equilibrium in both the covalent nirmatrelvir (NMV) and noncovalent ensitrelvir (ENS) complexes of 3CL^pro. For the wild-type 3CL^pro-NMV complex at 298 K, joint dual-field line shape and exchange spectroscopy analysis resolves a millisecond-timescale exchange between two distinct states (population ratio ∼ 65:35; <i>k_ex</i>  ≈ 52 s^-1; ΔG^‡ ≈ 15 kcal mol^-1). Co-existing bound states also persist in both the noncovalent NMV-[C145A] mutant (minor state population, <i>p_B</i>  ≈ 18%) and wild-type ENS (<i>p_B</i>  ≈ 38%) complexes, demonstrating that this slow-exchange heterogeneity is an intrinsic property of the ligated protease rather than a consequence of covalent attachment. These dynamics are not readily explained by available crystal structures or conventional microsecond molecular dynamics simulations, suggesting that in solution the inhibited enzyme samples alternative, energetically accessible conformations that are not fully represented in the crystal lattice. This study highlights the utility of solution-state ¹⁹F NMR for quantifying low-energy conformational states relevant to drug-target energetics and inhibitor design.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044701"},"PeriodicalIF":2.9,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13493197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148799684","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}

{"title":"Simultaneous two-color absorption dynamics in the van der Waals ferromagnet Fe₃GeTe₂.","authors":"Nele Stetzuhn, Emmanuelle Jal, Juliette Dubois, Boris Vodungbo, Flavio Capotondi, Emanuele Pedersoli, Matteo Pancaldi, Luca Gianessi, Claudio Masciovecchio, Ivaylo Nikolov, Giovanni Perosa, Dario De Angelis, Marco Malvestuto, Iuliia Bykova, Benedikt Rösner, Christian David, Jan Lüning, Angelo Giglia, Nicola Mahne, Deepika Gill, Sangeeta Sharma, Kirill I Bolotin, Clemens von Korff Schmising, Stefan Eisebitt","doi":"10.1063/4.0001216","DOIUrl":"10.1063/4.0001216","url":null,"abstract":"<p><p>For the integration of two-dimensional materials in future devices, a fundamental understanding of their response to external stimuli is needed. Toward this goal, we have investigated the electron and spin dynamics in the metallic van der Waals material Fe₃GeTe₂ (FGT) in its paramagnetic state after ultrafast optical excitation. To this end, we have employed a zone plate streaking technique with probing energies in the extreme ultraviolet range, tuned to the Fe M_2,3 and Te N_4,5 absorption edges. This approach provides insights into energy-dependent charge dynamics with a sensitivity to transient absorption changes on the order of <math><mrow><mo>∼</mo> <mrow> <msup><mrow><mn>10</mn></mrow> <mrow><mo>-</mo> <mn>4</mn></mrow> </msup> </mrow> </mrow> </math> . We find a slow carrier relaxation time at both elemental edges-up to <math><mrow><mo>(</mo> <mn>2.2</mn> <mo>±</mo> <mn>0.6</mn> <mo>)</mo> <mtext> ps</mtext></mrow> </math> in Te and exceeding several picoseconds in Fe-which is surprising for a metal. To elucidate the complex time-resolved response, we also employ static x-ray absorption spectroscopy at the corresponding elemental edges, in which we find a double feature at the Fe M_2,3 edge. We attribute this to different Fe sites in the pristine material and an oxidized surface layer, and we propose that the time-resolved absorption dynamics show a mixture of signals stemming from the different species. Additionally, we conducted time-resolved x-ray magnetic circular dichroism measurements in FGT at room temperature. We do not find clear evidence of the previously observed light-induced ferromagnetic order above <math> <mrow> <mrow> <msub><mrow><mi>T</mi></mrow> <mi>C</mi></msub> </mrow> </mrow> </math> . Our study lays the groundwork for a deeper understanding of charge and spin dynamics in FGT after optical excitation as part of a roadmap for 2D spintronics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044501"},"PeriodicalIF":2.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13437137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148674325","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}

{"title":"Structural heterogeneity of iron-sulfur cluster scaffold protein IscU: Metamorphic or partially folded?","authors":"Jongbum Na, Minchan Jeong, Jin Hae Kim","doi":"10.1063/4.0001219","DOIUrl":"10.1063/4.0001219","url":null,"abstract":"<p><p>The scaffold protein IscU plays a central role in iron-sulfur (Fe-S) cluster assembly and transfer. Despite extensive structural and biochemical research, the conformational nature of IscU remains unclear. IscU has been proposed as a metamorphic protein that interconverts between structured (S) and disordered (D) states. However, its conformational heterogeneity has often been interpreted as a consequence of intrinsic marginal stability, with the D-state described as an unfolded and functionally irrelevant state. These contrasting views highlight the fundamental challenge in defining the structural identity of IscU. In this review, we provide a comprehensive overview of the structural heterogeneity of IscU and examine how intrinsic and extrinsic factors shape the conformational equilibrium between the S- and D-states. Furthermore, we consider how these conflicting interpretations could be reconciled within an ensemble-based framework. In addition, we highlight promising approaches for characterizing the structurally elusive D-state, including high-pressure nuclear magnetic resonance, single-molecule Förster resonance energy transfer, native ion mobility mass spectrometry, and artificial intelligence-based structural analysis, all of which provide new opportunities for probing low-populated and transient conformational states. Collectively, these perspectives suggest that the functional behavior of IscU is closely linked to its conformational heterogeneity and that a conformational landscape view may provide a more integrated understanding of its role in Fe-S cluster biosynthesis.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"041301"},"PeriodicalIF":2.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13423590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632320","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}

{"title":"Prospects for direct electron detectors in ultrafast electron diffraction and scattering experiments.","authors":"Laurenz Kremeyer, David Cai, Malik Lahlou, Sebastian Hammer, Raphael Schwenzer, Bradley J Siwick","doi":"10.1063/4.0001206","DOIUrl":"10.1063/4.0001206","url":null,"abstract":"<p><p>Ultrafast electron diffraction and phonon-diffuse scattering [UED(S)] experiments make use of photo-induced changes to electron scattering intensity across 2D detectors to report on a very wide range of dynamic structural phenomena in molecules and materials. Hybrid pixel counting detectors (HPCDs) are a promising technology for improved sensitivity and signal-to-noise in UED(S) experiments, as they offer near-zero readout noise and dark counts with the possibility of new acquisition modalities (e.g., shot-to-shot normalization) due to their high frame rates. However, it is well known that HPCDs suffer from count losses at high electron fluxes even in CW beam applications. How this translates to ultrashort electron pulse exposures has yet to be determined and is critical to understanding the application of this technology to ultrafast electron scattering experiments. Here, we show that count losses are significantly exacerbated in ultrafast (pulsed) experiments and that HPCDs require unconventional data handling and saturate above <math><mrow><mo>≈</mo> <mn>2</mn></mrow> </math> electrons per pixel per pulse. This count-rate limitation presents a severe constraint on electron bunch charge when interrogating single crystal samples. Normalization strategies to optimize signal-to-noise in UED(S) and a complete model for measurement uncertainties using HPCDs are developed and tested using a large dataset. Finally, we suggest ways HPCDs could be better adapted to ultrashort pulsed beam experiments.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044302"},"PeriodicalIF":2.9,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13391233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148563391","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}

{"title":"Coherent phonon-driven band renormalizations in 1<i>T'</i>-MoTe₂.","authors":"Carl E Jensen, Christoph Emeis, Stephan Jauernik, Petra Hein, Fabio Caruso, Michael Bauer","doi":"10.1063/4.0001209","DOIUrl":"10.1063/4.0001209","url":null,"abstract":"<p><p>Here, we investigate phonon mode- and electron band-selective electron-phonon couplings in centrosymmetric 1<i>T</i>'-MoTe₂ using time- and angle-resolved photoemission spectroscopy combined with frequency-domain analysis. Femtosecond near-infrared pulses excite coherent <math> <mrow> <mrow> <msub><mrow><mi>A</mi></mrow> <mi>g</mi></msub> </mrow> </mrow> </math> -symmetric phonon modes at 2.34, 3.34, and 3.86 THz, which manifest as oscillatory modulations in photoemission intensity and binding energy across the valence bands. Pixel-wise Fourier analysis using recently developed methodologies reveals pronounced band selectivity with distinct coupling strengths for different electronic states and phonon modes, enabling the evaluation of band-renormalization amplitudes in the range of few meV. <i>Ab initio</i> calculations qualitatively reproduce the experimentally observed coupling patterns and relative trends, demonstrating the capability of combined experimental and theoretical approaches to resolve ultrafast electron-phonon interactions in quantum materials.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044301"},"PeriodicalIF":2.9,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13364501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148438573","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}

{"title":"¹³C NMR as a foundation for machine learning models of polysaccharides.","authors":"Stephanann M Costello, Zeina C Sleiman, John N Glushka, Breeanna R Urbanowicz, Arthur S Edison","doi":"10.1063/4.0001213","DOIUrl":"10.1063/4.0001213","url":null,"abstract":"<p><p>Polysaccharide structural assignment via nuclear magnetic resonance (NMR) spectroscopy remains an analytical challenge due to spectral overlap because of limited chemical shift dispersion. This challenge is exacerbated by the wide-spread use of proton (¹H) detection. Progress has also been hindered by the dispersed nature of carbohydrate databases and the restricted applicability of most prediction tools, which provide limited atom-specific residue discrimination in larger polymers. These limitations hamper the efficient characterization of glycosyltransferase (GT) activity, which depends on defining donor-acceptor substrate pairs and accurately identifying corresponding products. Here, we demonstrate the utility of high field ¹³C-detected NMR for the assignment of two homohexamers. Laminarihexaose and xylohexaose were analyzed using 2D heteronuclear correlation and correlation via long-range coupling (COLOC) experiments to evaluate whether complete residue level assignments could be achieved. The COLOC experiment revealed long range correlations that were not resolved using heteronuclear multiple bond correlation, and the 1D ¹³C spectra provided exceptional resolution, including distinct shoulders corresponding to residue specific chemical shift differences previously assumed to be indistinguishable. These findings suggest that high field ¹³C NMR can provide the nuanced atom level information required to train machine learning models for predicting chemical shift assignments of large, complex, and highly degenerate polysaccharides. Such models offer a promising framework for rapid structural identification of GT reaction products, enabling progress of high throughput characterization of plant derived polysaccharides central to renewable biomaterial development.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034302"},"PeriodicalIF":2.9,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333771","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}