The notion of heterogeneous dynamics in glasses, that is, the spatial and temporal variations of structural relaxation rates, explains many of the puzzling features of glass dynamics. The nature and the dynamics of these heterogeneities, however, have been very controversial. Single rhodamine B molecules in poly(vinyl acetate) at the glass transition reorient through sudden jumps. With a statistical search for the most likely break points in the logarithm of the ratio of the two perpendicular fluorescence polarizations, we determine the times of these angular jumps. We interpret these jumps as an indication for individual glass rearrangements in the vicinity of the probe molecule. Time-series analysis of the resulting sequence of waiting times between jumps shows that dynamic heterogeneities in the matrix exist, but are short lived. From the correlation of the logarithm of the waiting time between subsequent jumps, we determine an upper limit for the lifetime of heterogeneities in the sample. The correlation time of τ(het) = 32 s is three times shorter than the orientational correlation time of the probe molecule, τ(orient) = 90 s, in the sample at this temperature, but 13 times longer than the structural relaxation time, τ(α) = 2.5 s, estimated for this sample from dielectric experiments. We present a model for glass dynamics in which each rearrangement in one region causes a random change in the barrier height for subsequent rearrangements in a neighboring region. This model, which equates the dynamics of the heterogeneities with the dynamics of the glass itself and thus implies a factor of one between heterogeneity lifetime and structural relaxation time, successfully reproduces the statistics of the experimentally observed waiting time sequences.
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Adv Biotechnol (Singap)
December 2023
Bone Marrow Transplantation Center, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
Ribosome profiling has revolutionized our understanding of gene expression regulation by providing a snapshot of global translation in vivo. This powerful technique enables the investigation of the dynamics of translation initiation, elongation, and termination, and has provided insights into the regulation of protein synthesis under various conditions. Despite its widespread adoption, challenges persist in obtaining high-quality ribosome profiling data.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
Water dynamics are investigated in binary osmolyte-water mixtures, exhibiting a microscopic heterogeneity driven by molecular aggregation, on the basis of molecular dynamics (MD) simulation studies. The protecting osmolyte TMAO molecules in solution are evenly dispersed without the formation of noticeable osmolyte aggregates, while the denaturant TMU molecules aggregate readily, generating microscopic heterogeneity in the spatial distribution of component molecules in TMU-water mixtures. A combined study of MD simulation with graph theoretical analysis and spatial inhomogeneity measurement with -values in the two osmolyte solutions revealed that the translational and rotational motions of water in the microheterogeneous environment of TMU-water mixtures are less hindered than those in the homogeneous media of TMAO-water mixtures.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
State Key Laboratory of Molecular Reaction Dynamics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Directly probing the heterogeneous conformations of intracellular proteins within their native cellular environment remains a significant challenge in mass spectrometry (MS). Here, we establish an in-cell MS and ultraviolet photodissociation (UVPD) strategy that directly ejects proteins from living cells into a mass spectrometer, followed by 193 nm UVPD for structural analysis. Applying this approach to calmodulin (CaM), we reveal that it adopts more extended conformations within living cells compared with purified samples , highlighting the unique influence of intracellular environments on protein folding.
View Article and Find Full Text PDFRev Sci Instrum
January 2025
Institute for Physical Chemistry, University of Göttingen, 37077 Göttingen, Germany.
Surface science instruments require excellent vacuum to ensure surface cleanliness; they also require control of sample temperature, both to clean the surface of contaminants and to control reaction rates at the surface, for example, for molecular beam epitaxy and studies of heterogeneous catalysis. Standard approaches to sample heating within high vacuum chambers involve passing current through filaments of refractory metals, which then heat the sample by convective, radiative, or electron bombardment induced heat transfer. Such hot filament methods lead to outgassing of molecules from neighboring materials that are inadvertently heated; they also produce electrons and ions that may interfere with other aspects of the surface science experiment.
View Article and Find Full Text PDFJ Exp Biol
January 2025
Centre de Recherches sur la Cognition Animale, CNRS, Université Paul Sabatier, Toulouse 31062 cedex 09, France.
Solitary foraging insects like desert ants rely heavily on vision for navigation. While ants can learn visual scenes, it is unclear what cues they use to decide if a scene is worth exploring at the first place. To investigate this, we recorded the motor behavior of Cataglyphis velox ants navigating in a virtual reality set-up (VR) and measured their lateral oscillations in response to various unfamiliar visual scenes under both closed-loop and open-loop conditions.
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