Structural Dynamics-Us最新文献

{"title":"Non-thermal structural transformation of diamond driven by x-rays.","authors":"Philip Heimann,&nbsp;Nicholas J Hartley,&nbsp;Ichiro Inoue,&nbsp;Victor Tkachenko,&nbsp;Andre Antoine,&nbsp;Fabien Dorchies,&nbsp;Roger Falcone,&nbsp;Jérôme Gaudin,&nbsp;Hauke Höppner,&nbsp;Yuichi Inubushi,&nbsp;Konrad J Kapcia,&nbsp;Hae Ja Lee,&nbsp;Vladimir Lipp,&nbsp;Paloma Martinez,&nbsp;Nikita Medvedev,&nbsp;Franz Tavella,&nbsp;Sven Toleikis,&nbsp;Makina Yabashi,&nbsp;Toshinori Yabuuchi,&nbsp;Jumpei Yamada,&nbsp;Beata Ziaja","doi":"10.1063/4.0000193","DOIUrl":"https://doi.org/10.1063/4.0000193","url":null,"abstract":"<p><p>Intense x-ray pulses can cause the non-thermal structural transformation of diamond. At the SACLA XFEL facility, pump x-ray pulses triggered this phase transition, and probe x-ray pulses produced diffraction patterns. Time delays were observed from 0 to 250 fs, and the x-ray dose varied from 0.9 to 8.0 eV/atom. The intensity of the (111), (220), and (311) diffraction peaks decreased with time, indicating a disordering of the crystal lattice. From a Debye-Waller analysis, the rms atomic displacements perpendicular to the (111) planes were observed to be significantly larger than those perpendicular to the (220) or (311) planes. At a long time delay of 33 ms, graphite (002) diffraction indicates that graphitization did occur above a threshold dose of 1.2 eV/atom. These experimental results are in qualitative agreement with XTANT+ simulations using a hybrid model based on density-functional tight-binding molecular dynamics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10613085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414817","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":"Solution phase high repetition rate laser pump x-ray probe picosecond hard x-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource.","authors":"Marco Reinhard, Dean Skoien, Jacob A Spies, Angel T Garcia-Esparza, Benjamin D Matson, Jeff Corbett, Kai Tian, James Safranek, Eduardo Granados, Matthew Strader, Kelly J Gaffney, Roberto Alonso-Mori, Thomas Kroll, Dimosthenis Sokaras","doi":"10.1063/4.0000207","DOIUrl":"10.1063/4.0000207","url":null,"abstract":"<p><p>We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording data in an alternating on-off mode. The time-resolved x-ray measurements are enabled via gating the x-ray detectors with the 20 mA/70 ps camshaft bunch of SPEAR3, a mode available during the routine operations of the Stanford Synchrotron Radiation Lightsource. As a benchmark study, aiming to demonstrate the advantageous capabilities of this end-station, we have conducted picosecond Fe K-edge x-ray absorption spectroscopy on aqueous [Fe^II(phen)₃]²⁺, a prototypical spin crossover complex that undergoes light-induced excited spin state trapping forming an electronic excited state with a 0.6-0.7 ns lifetime. In addition, we report transient Fe Kβ main line and valence-to-core x-ray emission spectra, showing a unique detection sensitivity and an excellent agreement with model spectra and density functional theory calculations, respectively. Notably, the achieved signal-to-noise ratio, the overall performance, and the routine availability of the developed end-station have enabled a systematic time-resolved science program using the monochromatic beam at the Stanford Synchrotron Radiation Lightsource.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10613086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414818","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":"Electron population dynamics in resonant non-linear x-ray absorption in nickel at a free-electron laser.","authors":"Robin Y Engel,&nbsp;Oliver Alexander,&nbsp;Kaan Atak,&nbsp;Uwe Bovensiepen,&nbsp;Jens Buck,&nbsp;Robert Carley,&nbsp;Michele Cascella,&nbsp;Valentin Chardonnet,&nbsp;Gheorghe Sorin Chiuzbaian,&nbsp;Christian David,&nbsp;Florian Döring,&nbsp;Andrea Eschenlohr,&nbsp;Natalia Gerasimova,&nbsp;Frank de Groot,&nbsp;Loïc Le Guyader,&nbsp;Oliver S Humphries,&nbsp;Manuel Izquierdo,&nbsp;Emmanuelle Jal,&nbsp;Adam Kubec,&nbsp;Tim Laarmann,&nbsp;Charles-Henri Lambert,&nbsp;Jan Lüning,&nbsp;Jonathan P Marangos,&nbsp;Laurent Mercadier,&nbsp;Giuseppe Mercurio,&nbsp;Piter S Miedema,&nbsp;Katharina Ollefs,&nbsp;Bastian Pfau,&nbsp;Benedikt Rösner,&nbsp;Kai Rossnagel,&nbsp;Nico Rothenbach,&nbsp;Andreas Scherz,&nbsp;Justine Schlappa,&nbsp;Markus Scholz,&nbsp;Jan O Schunck,&nbsp;Kiana Setoodehnia,&nbsp;Christian Stamm,&nbsp;Simone Techert,&nbsp;Sam M Vinko,&nbsp;Heiko Wende,&nbsp;Alexander A Yaroslavtsev,&nbsp;Zhong Yin,&nbsp;Martin Beye","doi":"10.1063/4.0000206","DOIUrl":"10.1063/4.0000206","url":null,"abstract":"<p><p>Free-electron lasers provide bright, ultrashort, and monochromatic x-ray pulses, enabling novel spectroscopic measurements not only with femtosecond temporal resolution: The high fluence of their x-ray pulses can also easily enter the regime of the non-linear x-ray-matter interaction. Entering this regime necessitates a rigorous analysis and reliable prediction of the relevant non-linear processes for future experiment designs. Here, we show non-linear changes in the <math><mrow><msub><mi>L</mi><mn>3</mn></msub></mrow></math>-edge absorption of metallic nickel thin films, measured with fluences up to 60 J/cm². We present a simple but predictive rate model that quantitatively describes spectral changes based on the evolution of electronic populations within the pulse duration. Despite its simplicity, the model reaches good agreement with experimental results over more than three orders of magnitude in fluence, while providing a straightforward understanding of the interplay of physical processes driving the non-linear changes. Our findings provide important insights for the design and evaluation of future high-fluence free-electron laser experiments and contribute to the understanding of non-linear electron dynamics in x-ray absorption processes in solids at the femtosecond timescale.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41242005","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":"Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser.","authors":"R Guillemin,&nbsp;L Inhester,&nbsp;M Ilchen,&nbsp;T Mazza,&nbsp;R Boll,&nbsp;Th Weber,&nbsp;S Eckart,&nbsp;P Grychtol,&nbsp;N Rennhack,&nbsp;T Marchenko,&nbsp;N Velasquez,&nbsp;O Travnikova,&nbsp;I Ismail,&nbsp;J Niskanen,&nbsp;E Kukk,&nbsp;F Trinter,&nbsp;M Gisselbrecht,&nbsp;R Feifel,&nbsp;G Sansone,&nbsp;D Rolles,&nbsp;M Martins,&nbsp;M Meyer,&nbsp;M Simon,&nbsp;R Santra,&nbsp;T Pfeifer,&nbsp;T Jahnke,&nbsp;M N Piancastelli","doi":"10.1063/4.0000197","DOIUrl":"10.1063/4.0000197","url":null,"abstract":"<p><p>Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in H₂O²⁺, D₂O²⁺, and HDO²⁺, such as asymmetric bond elongation and bond-angle opening, leading to two-body or three-body fragmentation on a timescale of a few femtoseconds. A method to disentangle the sequences of events taking place upon the consecutive absorption of two x-ray photons is described. The obtained deep look into structural properties and dynamics of dissociating water isotopologues provides essential insights into the underlying mechanisms.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10550338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41159729","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":"RF acceleration of ultracold electron bunches.","authors":"D F J Nijhof,&nbsp;T C H de Raadt,&nbsp;J V Huijts,&nbsp;J G H Franssen,&nbsp;P H A Mutsaers,&nbsp;O J Luiten","doi":"10.1063/4.0000200","DOIUrl":"10.1063/4.0000200","url":null,"abstract":"<p><p>The ultrafast and ultracold electron source, based on laser cooling and trapping of atomic gas and its subsequent near-threshold two-step photoionization, is capable of generating electron bunches with a high transverse brightness at energies of roughly 10 keV. This paper investigates the possibility of increasing the range of applications of this source by accelerating the bunch using radio frequency electromagnetic fields. Bunch energies up to 35 keV are measured by analyzing the diffraction patterns generated from a mono-crystalline gold sample. It is found that the normalized transverse emittance is largely preserved during acceleration.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10550337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41143102","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":"Nonequilibrium warm dense matter investigated with laser-plasma-based XANES down to the femtosecond.","authors":"F Dorchies,&nbsp;K Ta Phuoc,&nbsp;L Lecherbourg","doi":"10.1063/4.0000202","DOIUrl":"10.1063/4.0000202","url":null,"abstract":"<p><p>The use of laser-plasma-based x-ray sources is discussed, with a view to carrying out time-resolved x-ray absorption spectroscopy measurements, down to the femtosecond timescale. A review of recent experiments performed by our team is presented. They concern the study of the nonequilibrium transition of metals from solid to the warm dense regime, which imposes specific constraints (the sample being destroyed after each shot). Particular attention is paid to the description of experimental devices and methodologies. Two main types of x-ray sources are compared, respectively, based on the emission of a hot plasma, and on the betatron radiation from relativistic electrons accelerated by laser.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10505070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10360906","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":"Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser.","authors":"Seonmyeong Kim,&nbsp;Matlabjon Sattorov,&nbsp;Dongpyo Hong,&nbsp;Heon Kang,&nbsp;Jaehun Park,&nbsp;Jae Hyuk Lee,&nbsp;Rory Ma,&nbsp;Andrew V Martin,&nbsp;Carl Caleman,&nbsp;Jonas A Sellberg,&nbsp;Prasanta Kumar Datta,&nbsp;Sang Yoon Park,&nbsp;Gun-Sik Park","doi":"10.1063/4.0000185","DOIUrl":"10.1063/4.0000185","url":null,"abstract":"<p><p>The direct observation of the structure of micrometer-sized vapor-deposited ice is performed at Pohang Accelerator Laboratory x-ray free electron laser (PAL-XFEL). The formation of micrometer-sized ice crystals and their structure is important in various fields, including atmospheric science, cryobiology, and astrophysics, but understanding the structure of micrometer-sized ice crystals remains challenging due to the lack of direct observation. Using intense x-ray diffraction from PAL-XFEL, we could observe the structure of micrometer-sized vapor-deposited ice below 150 K with a thickness of 2-50 <i>μ</i>m grown in an ultrahigh vacuum chamber. The structure of the ice grown comprises cubic and hexagonal sequences that are randomly arranged to produce a stacking-disordered ice. We observed that ice with a high cubicity of more than 80% was transformed to partially oriented hexagonal ice when the thickness of the ice deposition grew beyond 5 <i>μ</i>m. This suggests that precise temperature control and clean deposition conditions allow <i>μ</i>m-thick ice films with high cubicity to be grown on hydrophilic Si₃N₄ membranes. The low influence of impurities could enable <i>in situ</i> diffraction experiments of ice nucleation and growth from interfacial layers to bulk ice.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990493","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":"Microcalorimetry reveals multi-state thermal denaturation of <i>G. stearothermophilus</i> tryptophanyl-tRNA synthetase.","authors":"Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V Dokholyan, Charles W Carter","doi":"10.1063/4.0000181","DOIUrl":"10.1063/4.0000181","url":null,"abstract":"<p><p>Mechanistic studies of <i>Geobacillus stearothermophilus</i> tryptophanyl-tRNA synthetase (TrpRS) afford an unusually detailed description-the escapement mechanism-for the distinct steps coupling catalysis to domain motion, efficiently converting the free energy of ATP hydrolysis into biologically useful alternative forms of information and work. Further elucidation of the escapement mechanism requires understanding thermodynamic linkages between domain configuration and conformational stability. To that end, we compare experimental thermal melting of fully liganded and apo TrpRS with a computational simulation of the melting of its fully liganded form. The simulation also provides important structural cameos at successively higher temperatures, enabling more confident interpretation. Experimental and simulated melting both proceed through a succession of three transitions at successively higher temperature. The low-temperature transition occurs at approximately the growth temperature of the organism and so may be functionally relevant but remains too subtle to characterize structurally. Structural metrics from the simulation imply that the two higher-temperature transitions entail forming a molten globular state followed by unfolding of secondary structures. Ligands that stabilize the enzyme in a pre-transition (PreTS) state compress the temperature range over which these transitions occur and sharpen the transitions to the molten globule and fully denatured states, while broadening the low-temperature transition. The experimental enthalpy changes provide a key parameter necessary to convert changes in melting temperature of combinatorial mutants into mutationally induced conformational free energy changes. The TrpRS urzyme, an excerpted model representing an early ancestral form, containing virtually the entire catalytic apparatus, remains largely intact at the highest simulated temperatures.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9840276","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":"Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.","authors":"Yang Shen,&nbsp;Ad Bax","doi":"10.1063/4.0000192","DOIUrl":"https://doi.org/10.1063/4.0000192","url":null,"abstract":"<p><p>The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, M^pro, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9877711","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":"Practical considerations for the analysis of time-resolved x-ray data.","authors":"Marius Schmidt","doi":"10.1063/4.0000196","DOIUrl":"https://doi.org/10.1063/4.0000196","url":null,"abstract":"<p><p>The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available. Techniques to collect and process data from XFELs spread to synchrotron light sources. Although time-scales and data collection modalities can differ substantially between these types of light sources, the analysis of the resulting x-ray data proceeds essentially along the same pathway. At the base of a successful time-resolved experiment is a difference electron density (DED) map that contains chemically meaningful signal. If such a difference map cannot be obtained, the experiment has failed. Here, a practical approach is presented to calculate DED maps and use them to determine structural models.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10049456","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}