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Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses
摘要： X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.
关键词： plasma electron screening,radiation damage,ion caging,structural dynamics,protein nanocrystals,X-ray free-electron lasers
更新于2025-09-23 15:21:01
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Compressed Ultrafast Electron Diffraction Imaging Through Electronic Encoding
摘要： Ultrafast electron di?raction (UED) with high temporal and spatial resolutions is a powerful tool to observe transient structural changes in materials on an atomic scale. This technique is based on a pump-probe method using ultrashort laser and electron pulses. Therefore, UED requires that the measured transients be highly repeatable. Moreover, the relative time jitter between laser and electron pulses signi?cantly a?ects the UED temporal resolution. To overcome the UED technical limitations, we propose a technique called compressed ultrafast electron di?raction imaging (CUEDI). In this technique, we encode time-evolving electron di?raction patterns with random codes on an electron encoder. Then, the encoded electron di?raction pattern is measured by a detector after a temporal shearing operation. Finally, the evolution process of the electron di?raction pattern is reconstructed using a compressed sensing algorithm. We con?rm the feasibility of our proposed scheme by numerically simulating the polycrystalline gold melting process based on the experimental data measured with the pump-probe method. Because CUEDI employs a continuous or long electron pulse, the relative time jitter between laser and electron pulses can be eliminated. Additionally, CUEDI measures transients with a single shot, which allows irreversible processes to be directly observed.
关键词： compressed sensing,structural dynamics,single-shot measurement,Ultrafast electron di?raction
更新于2025-09-23 15:21:01
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Ultrafast Structural Dynamics of Nanoparticles in Intense Laser Fields
摘要： Femtosecond laser pulses have opened new frontiers for the study of ultrafast phase transitions and nonequilibrium states of matter. In this Letter, we report on structural dynamics in atomic clusters pumped with intense near-infrared (NIR) pulses into a nanoplasma state. Employing wide-angle scattering with intense femtosecond x-ray pulses from a free-electron laser source, we find that highly excited xenon nanoparticles retain their crystalline bulk structure and density in the inner core long after the driving NIR pulse. The observed emergence of structural disorder in the nanoplasma is consistent with a propagation from the surface to the inner core of the clusters.
关键词： x-ray scattering,nanoparticles,nanoplasma,intense laser fields,ultrafast structural dynamics
更新于2025-09-11 14:15:04
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[Advances in Experimental Medicine and Biology] Glycobiophysics Volume 1104 || Synchrotron-Radiation Vacuum-Ultraviolet Circular-Dichroism Spectroscopy for Characterizing the Structure of Saccharides
摘要： Circular-dichroism (CD) spectroscopy is a powerful tool for analyzing the structures of chiral molecules and biomolecules. The development of CD instruments using synchrotron radiation has greatly expanded the utility of this method by extending the spectra to the vacuum-ultraviolet (VUV) region below 190 nm and thereby yielding information that is unobtainable by conventional CD instruments. This technique is especially advantageous for monitoring the structure of saccharides that contain hydroxy and acetal groups with high-energy transitions in the VUV region. Combining VUVCD spectra with theoretical calculations provides new insight into the contributions of anomeric hydroxy groups and rotational isomers of hydroxymethyl groups to the dynamics, intramolecular hydrogen bonds, and hydration of saccharides in aqueous solution.
关键词： Glycoprotein,Hydration,Circular dichroism,Synchrotron radiation,Time-dependent density functional theory,Molecular dynamics simulation,Saccharide,Intramolecular hydrogen bond,Solution structure,Structural dynamics,Vacuum ultraviolet,Glycosaminoglycan
更新于2025-09-10 09:29:36
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Structural Dynamics of Dimethyl Sulfoxide Aqueous Solutions Investigated by Ultrafast Infrared Spectroscopy: Using Thiocyanate Anion as a Local Vibrational Probe
摘要： The microscopic structure of dimethyl sulfoxide (DMSO) aqueous solutions was investigated by FTIR spectroscopy and ultrafast IR spectroscopy. The structural dynamics of the binary mixtures were reflected by using thiocyanate anion (SCN-) as a local vibrational probe. FTIR spectra of SCN- anion showed the hydrogen bond networks of water are affected by the presence of DMSO molecules, and the peak position and bandwidth of SCN- anions are red-shifted and narrowed accordingly due to the weak hydration in the binary mixture. The vibrational lifetime of the SCN- anion showed almost linear enhancement with the increase of DMSO, which can be explained by the weak interaction between SCN- and the hydrophobic groups in DMSO molecule. However, the rotational dynamics of SCN- are slowing down significantly and showed a maximum response at XDMSO (mole fraction) of 0.35, which is mainly caused by the confinement of SCN- anions positioned in the vicinity of the complex structure formed between DMSO and water molecules. The concentration dependent rotational dynamics of water molecules and SCN- anions are having similar behavior, indicated that the complex structure can be formed between water and DMSO molecules due to the strong interaction. The result also demonstrates that the structural inhomogeneity in aqueous solution can be unraveled by monitoring the vibrational relaxation dynamics of SCN- anion serving as the local vibrational probe.
关键词： structural dynamics,thiocyanate anion,FTIR spectroscopy,Dimethyl sulfoxide,ultrafast IR spectroscopy,aqueous solutions,vibrational probe
更新于2025-09-10 09:29:36
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Competing optical instruments for the estimation of Full Field FRFs
摘要： Thanks to the progress of optical measurement systems, known to use non-contact transducers (with their own peculiarities, application domains and drawbacks), nowadays addressing complex testing problems, especially direct dynamic measurements and modal analyses on lightweight structural components, is becoming even more common than in the recent past. Furthermore, obtaining vibration patterns with optical gears, in broad frequency bands with high spatial resolution, is easier than before, for the advantage of many advanced applications in vibration engineering, testing and product development.
关键词： Full Field Operative Deflection Shapes,Full Field Frequency Response Functions,Dynamic ESPI,Full field vibration measurements,Surface structural dynamics,Optical metrology,Hi-Speed DIC,SLDV
更新于2025-09-09 09:28:46