Structural dynamics (Melville, N.Y.)最新文献

{"title":"Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties.","authors":"Juncheng E,&nbsp;Y Kim,&nbsp;J Bielecki,&nbsp;M Sikorski,&nbsp;R de Wijn,&nbsp;C Fortmann-Grote,&nbsp;J Sztuk-Dambietz,&nbsp;J C P Koliyadu,&nbsp;R Letrun,&nbsp;H J Kirkwood,&nbsp;T Sato,&nbsp;R Bean,&nbsp;A P Mancuso,&nbsp;C Kim","doi":"10.1063/4.0000169","DOIUrl":"https://doi.org/10.1063/4.0000169","url":null,"abstract":"<p><p>The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"064101"},"PeriodicalIF":2.8,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9675053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40480826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy.","authors":"David Schwickert,&nbsp;Marco Ruberti,&nbsp;Přemysl Kolorenč,&nbsp;Andreas Przystawik,&nbsp;Slawomir Skruszewicz,&nbsp;Malte Sumfleth,&nbsp;Markus Braune,&nbsp;Lars Bocklage,&nbsp;Luis Carretero,&nbsp;Marie Kristin Czwalinna,&nbsp;Dian Diaman,&nbsp;Stefan Düsterer,&nbsp;Marion Kuhlmann,&nbsp;Steffen Palutke,&nbsp;Ralf Röhlsberger,&nbsp;Juliane Rönsch-Schulenburg,&nbsp;Sven Toleikis,&nbsp;Sergey Usenko,&nbsp;Jens Viefhaus,&nbsp;Anton Vorobiov,&nbsp;Michael Martins,&nbsp;Detlef Kip,&nbsp;Vitali Averbukh,&nbsp;Jon P Marangos,&nbsp;Tim Laarmann","doi":"10.1063/4.0000165","DOIUrl":"https://doi.org/10.1063/4.0000165","url":null,"abstract":"<p><p>In the present contribution, we use x-rays to monitor charge-induced chemical dynamics in the photoionized amino acid glycine with femtosecond time resolution. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay. Temporal modulation of the Auger electron signal correlated with specific ions is observed, which is governed by the initial electronic coherence and subsequent vibronic coupling to nuclear degrees of freedom. In the time-resolved x-ray absorption measurement, we monitor the time-frequency spectra of the resulting many-body quantum wave packets for a period of 175 fs along different reaction coordinates. Our experiment proves that by measuring specific fragments associated with the glycine dication as a function of the pump-probe delay, one can selectively probe electronic coherences at early times associated with a few distinguishable components of the broad electronic wave packet created initially by the pump pulse in the cation. The corresponding coherent superpositions formed by subsets of electronic eigenstates and evolving along parallel dynamical pathways show different phases and time periods in the range of <math><mrow><mo>(</mo> <mo>-</mo> <mn>0.3</mn> <mo>±</mo> <mn>0.1</mn> <mo>)</mo> <mi>π</mi> <mo>≤</mo> <mi>ϕ</mi> <mo>≤</mo> <mo>(</mo> <mn>0.1</mn> <mo>±</mo> <mn>0.2</mn> <mo>)</mo> <mi>π</mi></mrow> </math> and <math> <mrow> <msubsup><mrow><mn>18.2</mn></mrow> <mrow><mo>-</mo> <mn>1.4</mn></mrow> <mrow><mo>+</mo> <mn>1.7</mn></mrow> </msubsup> <mo>≤</mo> <mi>T</mi> <mo>≤</mo> <msubsup><mrow><mn>23.9</mn></mrow> <mrow><mo>-</mo> <mn>1.1</mn></mrow> <mrow><mo>+</mo> <mn>1.2</mn></mrow> </msubsup> </mrow> </math> fs. Furthermore, for long delays, the data allow us to pinpoint the driving vibrational modes of chemical dynamics mediating charge-induced bond cleavage along different reaction coordinates.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"064301"},"PeriodicalIF":2.8,"publicationDate":"2022-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9646253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40481439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays.","authors":"Sourav Banerjee,&nbsp;Zoltan Jurek,&nbsp;Malik Muhammad Abdullah,&nbsp;Robin Santra","doi":"10.1063/4.0000166","DOIUrl":"https://doi.org/10.1063/4.0000166","url":null,"abstract":"<p><p>The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"054101"},"PeriodicalIF":2.8,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9625838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40465527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Picosecond infrared laser driven sample delivery for simultaneous liquid-phase and gas-phase electron diffraction studies.","authors":"Zhipeng Huang,&nbsp;Meghanad Kayanattil,&nbsp;Stuart A Hayes,&nbsp;R J Dwayne Miller","doi":"10.1063/4.0000159","DOIUrl":"https://doi.org/10.1063/4.0000159","url":null,"abstract":"<p><p>Here, we report on a new approach based on laser driven molecular beams that provides simultaneously nanoscale liquid droplets and gas-phase sample delivery for femtosecond electron diffraction studies. The method relies on Picosecond InfraRed Laser (PIRL) excitation of vibrational modes to strongly drive phase transitions under energy confinement by a mechanism referred to as Desorption by Impulsive Vibrational Excitation (DIVE). This approach is demonstrated using glycerol as the medium with selective excitation of the OH stretch region for energy deposition. The resulting plume was imaged with both an ultrafast electron gun and a pulsed bright-field optical microscope to characterize the sample source simultaneously under the same conditions with time synchronization equivalent to sub-micrometer spatial resolution in imaging the plume dynamics. The ablation front gives the expected isolated gas phase, whereas the trailing edge of the plume is found to consist of nanoscale liquid droplets to thin films depending on the excitation conditions. Thus, it is possible by adjusting the timing to go continuously from probing gas phase to solution phase dynamics in a single experiment with 100% hit rates and very low sample consumption (<100 nl per diffraction image). This approach will be particularly interesting for biomolecules that are susceptible to denaturation in turbulent flow, whereas PIRL-DIVE has been shown to inject molecules as large as proteins into the gas phase fully intact. This method opens the door as a general approach to atomically resolving solution phase chemistry as well as conformational dynamics of large molecular systems and allow separation of the solvent coordinate on the dynamics of interest.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"054301"},"PeriodicalIF":2.8,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9482465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40370767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores.","authors":"Georgy V Tsoraev,&nbsp;Elena A Protasova,&nbsp;Elizaveta A Klimanova,&nbsp;Yury L Ryzhykau,&nbsp;Alexander I Kuklin,&nbsp;Yury S Semenov,&nbsp;Baosheng Ge,&nbsp;Wenjun Li,&nbsp;Song Qin,&nbsp;Thomas Friedrich,&nbsp;Nikolai N Sluchanko,&nbsp;Eugene G Maksimov","doi":"10.1063/4.0000164","DOIUrl":"https://doi.org/10.1063/4.0000164","url":null,"abstract":"<p><p>The structural organization of natural pigment-protein complexes provides a specific environment for the chromophore groups. Yet, proteins are inherently dynamic and conformationally mobile. In this work, we demonstrate the heterogeneity of chromophores of C-phycocyanin (C-PC) from <i>Arthrospira platensis</i>. Part of the population of trimeric C-PC is subject to spontaneous disturbances of protein-protein interactions resulting in increased conformational mobility of the chromophores. Upon fluorescence excitation in the visible range, the spectral signatures of these poorly populated states are masked by bulk chromophore states, but the former could be clearly discriminated when the fluorescence is excited by near-infrared quanta. Such selective excitation of conformationally mobile C-PC chromophores is due to the structure of their S₁ level, which is characterized by a significantly broadened spectral line. We demonstrate that the anti-Stokes C-PC fluorescence is the result of single-photon absorption. By combining spectral and structural methods, we characterize four distinct states of C-PC chromophores emitting at 620, 650, 665, and 720 nm and assigned the fast component in the anti-Stokes fluorescence decay kinetics in the range of 690-750 nm to the chromophores with increased conformational mobility. Our data suggest that the spectral and temporal characteristics of the anti-Stokes fluorescence can be used to study protein dynamics and develop methods to visualize local environment parameters such as temperature.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"054701"},"PeriodicalIF":2.8,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9440762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40353241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mode-selective ballistic pathway to a metastable electronic phase.","authors":"Hannes Böckmann,&nbsp;Jan Gerrit Horstmann,&nbsp;Abdus Samad Razzaq,&nbsp;Stefan Wippermann,&nbsp;Claus Ropers","doi":"10.1063/4.0000162","DOIUrl":"https://doi.org/10.1063/4.0000162","url":null,"abstract":"<p><p>Exploiting vibrational excitation for the dynamic control of material properties is an attractive goal with wide-ranging technological potential. Most metal-to-insulator transitions are mediated by few structural modes and are, thus, ideal candidates for selective driving toward a desired electronic phase. Such targeted navigation within a generally multi-dimensional potential energy landscape requires microscopic insight into the non-equilibrium pathway. However, the exact role of coherent inertial motion across the transition state has remained elusive. Here, we demonstrate mode-selective control over the metal-to-insulator phase transition of atomic indium wires on the Si(111) surface, monitored by ultrafast low-energy electron diffraction. We use tailored pulse sequences to individually enhance or suppress key phonon modes and thereby steer the collective atomic motion within the potential energy surface underlying the structural transformation. <i>Ab initio</i> molecular dynamics simulations demonstrate the ballistic character of the structural transition along the deformation vectors of the Peierls amplitude modes. Our work illustrates that coherent excitation of collective modes via exciton-phonon interactions evades entropic barriers and enables the dynamic control of materials functionality.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"045102"},"PeriodicalIF":2.8,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9385219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40714637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low-temperature nanoscale heat transport in a gadolinium iron garnet heterostructure probed by ultrafast x-ray diffraction.","authors":"Deepankar Sri Gyan,&nbsp;Danny Mannix,&nbsp;Dina Carbone,&nbsp;James L Sumpter,&nbsp;Stephan Geprägs,&nbsp;Maxim Dietlein,&nbsp;Rudolf Gross,&nbsp;Andrius Jurgilaitis,&nbsp;Van-Thai Pham,&nbsp;Hélène Coudert-Alteirac,&nbsp;Jörgen Larsson,&nbsp;Daniel Haskel,&nbsp;Jörg Strempfer,&nbsp;Paul G Evans","doi":"10.1063/4.0000154","DOIUrl":"https://doi.org/10.1063/4.0000154","url":null,"abstract":"<p><p>Time-resolved x-ray diffraction has been used to measure the low-temperature thermal transport properties of a Pt/Gd₃Fe₅O₁₂//Gd₃Ga₅O₁₂ metal/oxide heterostructure relevant to applications in spin caloritronics. A pulsed femtosecond optical signal produces a rapid temperature rise in the Pt layer, followed by heat transport into the Gd₃Fe₅O₁₂ (GdIG) thin film and the Gd₃Ga₅O₁₂ (GGG) substrate. The time dependence of x-ray diffraction from the GdIG layer was tracked using an accelerator-based femtosecond x-ray source. The ultrafast diffraction measurements probed the intensity of the GdIG (1 -1 2) x-ray reflection in a grazing-incidence x-ray diffraction geometry. The comparison of the variation of the diffracted x-ray intensity with a model including heat transport and the temperature dependence of the GdIG lattice parameter allows the thermal conductance of the Pt/GdIG and GdIG//GGG interfaces to be determined. Complementary synchrotron x-ray diffraction studies of the low-temperature thermal expansion properties of the GdIG layer provide a precise calibration of the temperature dependence of the GdIG lattice parameter. The interfacial thermal conductance of the Pt/GdIG and GdIG//GGG interfaces determined from the time-resolved diffraction study is of the same order of magnitude as previous reports for metal/oxide and epitaxial dielectric interfaces. The thermal parameters of the Pt/GdIG//GGG heterostructure will aid in the design and implementation of thermal transport devices and nanostructures.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"045101"},"PeriodicalIF":2.8,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9337877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40681111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Observation of photo-induced plasmon-phonon coupling in PbTe via ultrafast x-ray scattering.","authors":"M P Jiang,&nbsp;S Fahy,&nbsp;A Hauber,&nbsp;É D Murray,&nbsp;I Savić,&nbsp;C Bray,&nbsp;J N Clark,&nbsp;T Henighan,&nbsp;M Kozina,&nbsp;A M Lindenberg,&nbsp;P Zalden,&nbsp;M Chollet,&nbsp;J M Glownia,&nbsp;M C Hoffmann,&nbsp;T Sato,&nbsp;D Zhu,&nbsp;O Delaire,&nbsp;A F May,&nbsp;B C Sales,&nbsp;R Merlin,&nbsp;M Trigo,&nbsp;D A Reis","doi":"10.1063/4.0000133","DOIUrl":"https://doi.org/10.1063/4.0000133","url":null,"abstract":"<p><p>We report the observation of photo-induced plasmon-phonon coupled modes in the group IV-VI semiconductor PbTe using ultrafast x-ray diffuse scattering at the Linac Coherent Light Source. We measure the near-zone-center excited-state dispersion of the heavily screened longitudinal optical (LO) phonon branch as extracted from differential changes in x-ray diffuse scattering intensity following above bandgap photoexcitation. We suggest that upon photoexcitation, the LO phonon-plasmon coupled (LOPC) modes themselves become coupled to longitudinal acoustic modes that drive electron band shifts via acoustic deformation potentials and possibly to low-energy single-particle excitations within the plasma and that these couplings give rise to displacement-correlations that oscillate in time with a period given effectively by the heavily screened LOPC frequency.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"024301"},"PeriodicalIF":2.8,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40308673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Underdamped longitudinal soft modes in ionic crystallites-lattice and charge motions observed by ultrafast x-ray diffraction.","authors":"Isabel Gonzalez-Vallejo,&nbsp;Azize Koç,&nbsp;Klaus Reimann,&nbsp;Michael Woerner,&nbsp;Thomas Elsaesser","doi":"10.1063/4.0000143","DOIUrl":"https://doi.org/10.1063/4.0000143","url":null,"abstract":"<p><p>Soft modes in crystals are lattice vibrations with frequencies that decrease and eventually vanish as the temperature approaches a critical point, e.g., a structural change due to a phase transition. In ionic para- or ferroelectric materials, the frequency decrease is connected with a diverging electric susceptibility and, for infrared active modes, a strong increase in oscillator strength. The traditional picture describes soft modes as overdamped transverse optical phonons of a hybrid vibrational-electronic character. In this context, potassium dihydrogen phosphate (KH₂PO₄, KDP) has been studied for decades as a prototypical material with, however, inconclusive results regarding the soft modes in its para- and ferroelectric phase. There are conflicting assignments of soft-mode frequencies and damping parameters. We report the first observation of a longitudinal underdamped soft mode in paraelectric KDP. Upon impulsive femtosecond Raman excitation of coherent low-frequency phonons in the electronic ground state of KDP crystallites, transient powder diffraction patterns are recorded with femtosecond hard x-ray pulses. Electron density maps derived from the x-ray data reveal oscillatory charge relocations over interatomic distances, much larger than the sub-picometer nuclear displacements, a direct hallmark of soft-mode behavior. The strongly underdamped character of the soft mode manifests in charge oscillations persisting for more than 10 ps. The soft-mode frequency decreases from 0.55 THz at <i>T </i>=<i> </i>295 K to 0.39 THz at <i>T </i>=<i> </i>175 K. An analysis of the Raman excitation conditions in crystallites and the weak damping demonstrate a longitudinal character. Our results extend soft-mode physics well beyond the traditional picture and pave the way for an atomic-level characterization of soft modes.</p>","PeriodicalId":520783,"journal":{"name":"Structural dynamics (Melville, N.Y.)","volume":" ","pages":"024501"},"PeriodicalIF":2.8,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40309605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}