Pub Date : 2021-08-23eCollection Date: 2021-07-01DOI: 10.1063/4.0000127
Ruslan Khubbutdinov, Natalia Gerasimova, Giuseppe Mercurio, Dameli Assalauova, Jerome Carnis, Luca Gelisio, Loïc Le Guyader, Alexandr Ignatenko, Young Yong Kim, Benjamin E Van Kuiken, Ruslan P Kurta, Dmitry Lapkin, Martin Teichmann, Alexander Yaroslavtsev, Oleg Gorobtsov, Alexey P Menushenkov, Matthias Scholz, Andreas Scherz, Ivan A Vartanyants
Second-order intensity interferometry was employed to study the spatial and temporal properties of the European X-ray Free-Electron Laser (EuXFEL). Measurements were performed at the soft x-ray Self-Amplified Spontaneous Emission (SASE3) undulator beamline at a photon energy of 1.2 keV in the Self-Amplified Spontaneous Emission (SASE) mode. Two high-power regimes of the SASE3 undulator settings, i.e., linear and quadratic undulator tapering at saturation, were studied in detail and compared with the linear gain regime. The statistical analysis showed an exceptionally high degree of spatial coherence up to 90% for the linear undulator tapering. Analysis of the measured data in spectral and spatial domains provided an average pulse duration of about 10 fs in our measurements. The obtained results will be valuable for the experiments requiring and exploiting short pulse duration and utilizing high coherence properties of the EuXFEL.
{"title":"High spatial coherence and short pulse duration revealed by the Hanbury Brown and Twiss interferometry at the European XFEL.","authors":"Ruslan Khubbutdinov, Natalia Gerasimova, Giuseppe Mercurio, Dameli Assalauova, Jerome Carnis, Luca Gelisio, Loïc Le Guyader, Alexandr Ignatenko, Young Yong Kim, Benjamin E Van Kuiken, Ruslan P Kurta, Dmitry Lapkin, Martin Teichmann, Alexander Yaroslavtsev, Oleg Gorobtsov, Alexey P Menushenkov, Matthias Scholz, Andreas Scherz, Ivan A Vartanyants","doi":"10.1063/4.0000127","DOIUrl":"https://doi.org/10.1063/4.0000127","url":null,"abstract":"<p><p>Second-order intensity interferometry was employed to study the spatial and temporal properties of the European X-ray Free-Electron Laser (EuXFEL). Measurements were performed at the soft x-ray Self-Amplified Spontaneous Emission (SASE3) undulator beamline at a photon energy of 1.2 keV in the Self-Amplified Spontaneous Emission (SASE) mode. Two high-power regimes of the SASE3 undulator settings, i.e., linear and quadratic undulator tapering at saturation, were studied in detail and compared with the linear gain regime. The statistical analysis showed an exceptionally high degree of spatial coherence up to 90% for the linear undulator tapering. Analysis of the measured data in spectral and spatial domains provided an average pulse duration of about 10 fs in our measurements. The obtained results will be valuable for the experiments requiring and exploiting short pulse duration and utilizing high coherence properties of the EuXFEL.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8384452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39379941","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}
Pub Date : 2021-08-05eCollection Date: 2021-07-01DOI: 10.1063/4.0000108
Somnath Jana, Shreyas Muralidhar, Johan Åkerman, Christian Schüßler-Langeheine, Niko Pontius
We study the optical-pump induced ultrafast transient change of x-ray absorption at L3 absorption resonances of the transition metals Ni and Fe in the Fe0.5Ni0.5 alloy. We find the effect for both elements to occur simultaneously on a femtosecond timescale. This effect may hence be used as a handy cross correlation scheme, providing a time-zero reference for ultrafast optical-pump soft x-ray-probe measurement. The method benefits from a relatively simple experimental setup as the sample itself acts as time-reference tool. In particular, this technique works with low flux ultrafast soft x-ray sources. The measurements are compared to the cross correlation method introduced in an earlier publication.
我们研究了在 Fe0.5Ni0.5 合金中过渡金属 Ni 和 Fe 的 L 3 吸收共振处,光泵诱导 X 射线吸收的超快瞬态变化。我们发现这两种元素的效应在飞秒时间尺度上同时发生。因此,这种效应可作为一种方便的交叉相关方案,为超快光泵软 X 射线探针测量提供时间零点参考。这种方法的优点是实验装置相对简单,因为样品本身就是时间参考工具。这项技术尤其适用于低通量超快软 X 射线源。测量结果与早期出版物中介绍的交叉相关方法进行了比较。
{"title":"Using the photoinduced <i>L</i> <sub>3</sub> resonance shift in Fe and Ni as time reference for ultrafast experiments at low flux soft x-ray sources.","authors":"Somnath Jana, Shreyas Muralidhar, Johan Åkerman, Christian Schüßler-Langeheine, Niko Pontius","doi":"10.1063/4.0000108","DOIUrl":"10.1063/4.0000108","url":null,"abstract":"<p><p>We study the optical-pump induced ultrafast transient change of x-ray absorption at <i>L</i> <sub>3</sub> absorption resonances of the transition metals Ni and Fe in the Fe<sub>0.5</sub>Ni<sub>0.5</sub> alloy. We find the effect for both elements to occur simultaneously on a femtosecond timescale. This effect may hence be used as a handy cross correlation scheme, providing a time-zero reference for ultrafast optical-pump soft x-ray-probe measurement. The method benefits from a relatively simple experimental setup as the sample itself acts as time-reference tool. In particular, this technique works with low flux ultrafast soft x-ray sources. The measurements are compared to the cross correlation method introduced in an earlier publication.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39316206","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}
Pub Date : 2021-07-29eCollection Date: 2021-07-01DOI: 10.1063/4.0000105
Phay J Ho, Christopher Knight, Linda Young
We theoretically investigate the fluorescence intensity correlation (FIC) of Ar clusters and Mo-doped iron oxide nanoparticles subjected to intense, femtosecond, and sub-femtosecond x-ray free-electron laser pulses for high-resolution and elemental contrast imaging. We present the FIC of and emission in Ar clusters and discuss the impact of sample damage on retrieving high-resolution structural information and compare the obtained structural information with those from the coherent diffractive imaging (CDI) approach. We found that, while sub-femtosecond pulses will substantially benefit the CDI approach, few-femtosecond pulses may be sufficient for achieving high-resolution information with the FIC. Furthermore, we show that the fluorescence intensity correlation computed from the fluorescence of the Mo atoms in Mo-doped iron oxide nanoparticles can be used to image dopant distributions in the nonresonant regime.
{"title":"Fluorescence intensity correlation imaging with high spatial resolution and elemental contrast using intense x-ray pulses.","authors":"Phay J Ho, Christopher Knight, Linda Young","doi":"10.1063/4.0000105","DOIUrl":"https://doi.org/10.1063/4.0000105","url":null,"abstract":"<p><p>We theoretically investigate the fluorescence intensity correlation (FIC) of Ar clusters and Mo-doped iron oxide nanoparticles subjected to intense, femtosecond, and sub-femtosecond x-ray free-electron laser pulses for high-resolution and elemental contrast imaging. We present the FIC of <math><mrow><mi>K</mi> <mi>α</mi></mrow> </math> and <math><mrow><mi>K</mi> <msup><mi>α</mi> <mi>h</mi></msup> </mrow> </math> emission in Ar clusters and discuss the impact of sample damage on retrieving high-resolution structural information and compare the obtained structural information with those from the coherent diffractive imaging (CDI) approach. We found that, while sub-femtosecond pulses will substantially benefit the CDI approach, few-femtosecond pulses may be sufficient for achieving high-resolution information with the FIC. Furthermore, we show that the fluorescence intensity correlation computed from the fluorescence of the Mo atoms in Mo-doped iron oxide nanoparticles can be used to image dopant distributions in the nonresonant regime.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39292220","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}
Pub Date : 2021-07-23eCollection Date: 2021-07-01DOI: 10.1063/4.0000113
Lingrong Zhao, Jun Wu, Zhe Wang, Heng Tang, Xiao Zou, Tao Jiang, Pengfei Zhu, Dao Xiang, Jie Zhang
We demonstrate a noninvasive time-sorting method for ultrafast electron diffraction (UED) experiments with radio frequency (rf)-compressed electron beams. We show that electron beam energy and arrival time at the sample after the rf compression are strongly correlated, such that the arrival time jitter may be corrected through the measurement of the beam energy. The method requires minimal change to the infrastructure of most of the UED machines and is applicable to both keV and MeV UED. In our experiment with ∼3 MeV beam, the timing jitter after the rf compression is corrected with a 35-fs root mean square (rms) accuracy, limited by the energy stability. For keV UED with a high energy stability, sub-10 fs accuracy in time-sorting should be readily achievable. This time-sorting technique allows us to retrieve the 2.5 THz oscillation related to coherent A1g phonon in the laser-excited Bismuth film and extends the temporal resolution of UED to a regime far beyond the 100-200 fs rms jitter limitation.
{"title":"Noninvasive time-sorting in radio frequency-compressed ultrafast electron diffraction.","authors":"Lingrong Zhao, Jun Wu, Zhe Wang, Heng Tang, Xiao Zou, Tao Jiang, Pengfei Zhu, Dao Xiang, Jie Zhang","doi":"10.1063/4.0000113","DOIUrl":"10.1063/4.0000113","url":null,"abstract":"<p><p>We demonstrate a noninvasive time-sorting method for ultrafast electron diffraction (UED) experiments with radio frequency (rf)-compressed electron beams. We show that electron beam energy and arrival time at the sample after the rf compression are strongly correlated, such that the arrival time jitter may be corrected through the measurement of the beam energy. The method requires minimal change to the infrastructure of most of the UED machines and is applicable to both keV and MeV UED. In our experiment with ∼3 MeV beam, the timing jitter after the rf compression is corrected with a 35-fs root mean square (rms) accuracy, limited by the <math><mrow><mn>3</mn> <mo>×</mo> <msup><mrow><mn>10</mn></mrow> <mrow><mo>-</mo> <mn>4</mn></mrow> </msup> </mrow> </math> energy stability. For keV UED with a high energy stability, sub-10 fs accuracy in time-sorting should be readily achievable. This time-sorting technique allows us to retrieve the 2.5 THz oscillation related to coherent A<sub>1<i>g</i></sub> phonon in the laser-excited Bismuth film and extends the temporal resolution of UED to a regime far beyond the 100-200 fs rms jitter limitation.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39266002","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}
Pub Date : 2021-07-20eCollection Date: 2021-07-01DOI: 10.1063/4.0000125
Joseph Tanski, Christine Zardecki, Andrey Yakovenko, Cassandra Eagle
{"title":"Transactions from the 70th Annual Meeting of the American Crystallographic Association: Structural Science-New Ways to Teach the Next Generation.","authors":"Joseph Tanski, Christine Zardecki, Andrey Yakovenko, Cassandra Eagle","doi":"10.1063/4.0000125","DOIUrl":"https://doi.org/10.1063/4.0000125","url":null,"abstract":"","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39265542","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}
In recent years, real-time observations of molecules have been required to understand their behavior and function. To date, we have reported two different time-resolved observation methods: diffracted x-ray tracking and diffracted x-ray blinking (DXB). The former monitors the motion of diffracted spots derived from nanocrystals labeled onto target molecules, and the latter measures the fluctuation of the diffraction intensity that is highly correlated with the target molecular motion. However, these reports use a synchrotron x-ray source because of its high average flux, resulting in a high time resolution. Here, we used a laboratory x-ray source and DXB to measure the internal molecular dynamics of three different systems. The samples studied were bovine serum albumin (BSA) pinned onto a substrate, antifreeze protein (AFP) crystallized as a single crystal, and poly{2-(perfluorooctyl)ethyl acrylate} (PC8FA) polymer between polyimide sheets. It was found that not only BSA but also AFP and PC8FA molecules move in the systems. In addition, the molecular motion of AFP molecules was observed to increase with decreasing temperature. The rotational diffusion coefficients (DR) of BSA, AFP, and PC8FA were estimated to be 0.73 pm2/s, 0.65 pm2/s, and 3.29 pm2/s, respectively. Surprisingly, the DR of the PC8FA polymer was found to be the highest among the three samples. This is the first report that measures the molecular motion of a single protein crystal and polymer by using DXB with a laboratory x-ray source. This technique can be applied to any kind of crystal and crystalline polymer and provides atomic-order molecular information.
{"title":"Laboratory diffracted x-ray blinking to monitor picometer motions of protein molecules and application to crystalline materials.","authors":"Tatsuya Arai, Rena Inamasu, Hiroki Yamaguchi, Daisuke Sasaki, Ayana Sato-Tomita, Hiroshi Sekiguchi, Kazuhiro Mio, Sakae Tsuda, Masahiro Kuramochi, Yuji C Sasaki","doi":"10.1063/4.0000112","DOIUrl":"https://doi.org/10.1063/4.0000112","url":null,"abstract":"<p><p>In recent years, real-time observations of molecules have been required to understand their behavior and function. To date, we have reported two different time-resolved observation methods: diffracted x-ray tracking and diffracted x-ray blinking (DXB). The former monitors the motion of diffracted spots derived from nanocrystals labeled onto target molecules, and the latter measures the fluctuation of the diffraction intensity that is highly correlated with the target molecular motion. However, these reports use a synchrotron x-ray source because of its high average flux, resulting in a high time resolution. Here, we used a laboratory x-ray source and DXB to measure the internal molecular dynamics of three different systems. The samples studied were bovine serum albumin (BSA) pinned onto a substrate, antifreeze protein (AFP) crystallized as a single crystal, and poly{2-(perfluorooctyl)ethyl acrylate} (PC<sub>8</sub>FA) polymer between polyimide sheets. It was found that not only BSA but also AFP and PC<sub>8</sub>FA molecules move in the systems. In addition, the molecular motion of AFP molecules was observed to increase with decreasing temperature. The rotational diffusion coefficients (D<sub>R</sub>) of BSA, AFP, and PC<sub>8</sub>FA were estimated to be 0.73 pm<sup>2</sup>/s, 0.65 pm<sup>2</sup>/s, and 3.29 pm<sup>2</sup>/s, respectively. Surprisingly, the D<sub>R</sub> of the PC<sub>8</sub>FA polymer was found to be the highest among the three samples. This is the first report that measures the molecular motion of a single protein crystal and polymer by using DXB with a laboratory x-ray source. This technique can be applied to any kind of crystal and crystalline polymer and provides atomic-order molecular information.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39181542","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}
Pub Date : 2021-07-08eCollection Date: 2021-07-01DOI: 10.1063/4.0000099
Felix Brausse, Mario Borgwardt, Johannes Mahl, Matthew Fraund, Friedrich Roth, Monika Blum, Wolfgang Eberhardt, Oliver Gessner
We present a novel technique to monitor dynamics in interfacial systems through temporal correlations in x-ray photoelectron spectroscopy (XPS) signals. To date, the vast majority of time-resolved x-ray spectroscopy techniques rely on pump-probe schemes, in which the sample is excited out of equilibrium by a pump pulse, and the subsequent dynamics are monitored by probe pulses arriving at a series of well-defined delays relative to the excitation. By definition, this approach is restricted to processes that can either directly or indirectly be initiated by light. It cannot access spontaneous dynamics or the microscopic fluctuations of ensembles in chemical or thermal equilibrium. Enabling this capability requires measurements to be performed in real (laboratory) time with high temporal resolution and, ultimately, without the need for a well-defined trigger event. The time-correlation XPS technique presented here is a first step toward this goal. The correlation-based technique is implemented by extending an existing optical-laser pump/multiple x-ray probe setup by the capability to record the kinetic energy and absolute time of arrival of every detected photoelectron. The method is benchmarked by monitoring energy-dependent, periodic signal modulations in a prototypical time-resolved XPS experiment on photoinduced surface-photovoltage dynamics in silicon, using both conventional pump-probe data acquisition, and the new technique based on laboratory time. The two measurements lead to the same result. The findings provide a critical milestone toward the overarching goal of studying equilibrium dynamics at surfaces and interfaces through time correlation-based XPS measurements.
{"title":"Real-time interfacial electron dynamics revealed through temporal correlations in x-ray photoelectron spectroscopy.","authors":"Felix Brausse, Mario Borgwardt, Johannes Mahl, Matthew Fraund, Friedrich Roth, Monika Blum, Wolfgang Eberhardt, Oliver Gessner","doi":"10.1063/4.0000099","DOIUrl":"https://doi.org/10.1063/4.0000099","url":null,"abstract":"<p><p>We present a novel technique to monitor dynamics in interfacial systems through temporal correlations in x-ray photoelectron spectroscopy (XPS) signals. To date, the vast majority of time-resolved x-ray spectroscopy techniques rely on pump-probe schemes, in which the sample is excited out of equilibrium by a pump pulse, and the subsequent dynamics are monitored by probe pulses arriving at a series of well-defined delays relative to the excitation. By definition, this approach is restricted to processes that can either directly or indirectly be initiated by light. It cannot access spontaneous dynamics or the microscopic fluctuations of ensembles in chemical or thermal equilibrium. Enabling this capability requires measurements to be performed in real (laboratory) time with high temporal resolution and, ultimately, without the need for a well-defined trigger event. The time-correlation XPS technique presented here is a first step toward this goal. The correlation-based technique is implemented by extending an existing optical-laser pump/multiple x-ray probe setup by the capability to record the kinetic energy and absolute time of arrival of every detected photoelectron. The method is benchmarked by monitoring energy-dependent, periodic signal modulations in a prototypical time-resolved XPS experiment on photoinduced surface-photovoltage dynamics in silicon, using both conventional pump-probe data acquisition, and the new technique based on laboratory time. The two measurements lead to the same result. The findings provide a critical milestone toward the overarching goal of studying equilibrium dynamics at surfaces and interfaces through time correlation-based XPS measurements.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39181541","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}
Pub Date : 2021-07-08eCollection Date: 2021-07-01DOI: 10.1063/4.0000087
Zhen Su, Medhanjali Dasgupta, Frédéric Poitevin, Irimpan I Mathews, Henry van den Bedem, Michael E Wall, Chun Hong Yoon, Mark A Wilson
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
{"title":"Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.","authors":"Zhen Su, Medhanjali Dasgupta, Frédéric Poitevin, Irimpan I Mathews, Henry van den Bedem, Michael E Wall, Chun Hong Yoon, Mark A Wilson","doi":"10.1063/4.0000087","DOIUrl":"https://doi.org/10.1063/4.0000087","url":null,"abstract":"<p><p>Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000087","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39181543","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}
Pub Date : 2021-06-30eCollection Date: 2021-05-01DOI: 10.1063/4.0000096
Carlo Kleine, Maria Ekimova, Marc-Oliver Winghart, Sebastian Eckert, Oliver Reichel, Heike Löchel, Jürgen Probst, Christoph Braig, Christian Seifert, Alexei Erko, Andrey Sokolov, Marc J J Vrakking, Erik T J Nibbering, Arnaud Rouzée
We present a novel soft x-ray spectrometer for ultrafast absorption spectroscopy utilizing table-top femtosecond high-order harmonic sources. Where most commercially available spectrometers rely on spherical variable line space gratings with a typical efficiency on the order of 3% in the first diffractive order, this spectrometer, based on a Hettrick-Underwood design, includes a reflective zone plate as a dispersive element. An improved efficiency of 12% at the N K-edge is achieved, accompanied by a resolving power of 890. The high performance of the soft x-ray spectrometer is further demonstrated by comparing nitrogen K-edge absorption spectra from calcium nitrate in aqueous solution obtained with our high-order harmonic source to previous measurements performed at the electron storage ring facility BESSY II.
我们介绍了一种利用台式飞秒高阶谐波源进行超快吸收光谱分析的新型软 X 射线光谱仪。大多数市售光谱仪依靠球形可变线空间光栅,其第一衍射阶的典型效率约为3%,而该光谱仪基于Hettrick-Underwood设计,包括一个反射区板作为色散元件。N K 边的效率提高了 12%,分辨力达到 890。通过比较利用我们的高阶谐波源获得的水溶液中硝酸钙的氮K边吸收光谱与之前在电子储存环设施BESSY II上进行的测量结果,进一步证明了软X射线光谱仪的高性能。
{"title":"Highly efficient soft x-ray spectrometer for transient absorption spectroscopy with broadband table-top high harmonic sources.","authors":"Carlo Kleine, Maria Ekimova, Marc-Oliver Winghart, Sebastian Eckert, Oliver Reichel, Heike Löchel, Jürgen Probst, Christoph Braig, Christian Seifert, Alexei Erko, Andrey Sokolov, Marc J J Vrakking, Erik T J Nibbering, Arnaud Rouzée","doi":"10.1063/4.0000096","DOIUrl":"10.1063/4.0000096","url":null,"abstract":"<p><p>We present a novel soft x-ray spectrometer for ultrafast absorption spectroscopy utilizing table-top femtosecond high-order harmonic sources. Where most commercially available spectrometers rely on spherical variable line space gratings with a typical efficiency on the order of 3% in the first diffractive order, this spectrometer, based on a Hettrick-Underwood design, includes a reflective zone plate as a dispersive element. An improved efficiency of 12% at the N K-edge is achieved, accompanied by a resolving power of 890. The high performance of the soft x-ray spectrometer is further demonstrated by comparing nitrogen K-edge absorption spectra from calcium nitrate in aqueous solution obtained with our high-order harmonic source to previous measurements performed at the electron storage ring facility BESSY II.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163007","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}
Pub Date : 2021-06-30eCollection Date: 2021-05-01DOI: 10.1063/4.0000098
Saminathan Ramakrishnan, Jason R Stagno, Valentin Magidson, William F Heinz, Yun-Xing Wang
Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 μm2) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.
{"title":"Dependence of phase transition uniformity on crystal sizes characterized using birefringence.","authors":"Saminathan Ramakrishnan, Jason R Stagno, Valentin Magidson, William F Heinz, Yun-Xing Wang","doi":"10.1063/4.0000098","DOIUrl":"10.1063/4.0000098","url":null,"abstract":"<p><p>Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 <i>μ</i>m<sup>2</sup>) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/4.0000098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163006","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}