Glassy dynamics of landscape evolution.
Ontology highlight
ABSTRACT:
SUBMITTER: Ferdowsi B
PROVIDER: S-EPMC5948954 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Supercooled liquids undergo complicated structural relaxation processes, which have been a long-standing problem in both experimental and theoretical aspects of condensed matter physics. In particular, past experiments widely observed for many types of molecular liquids that relaxation dynamics separated into two distinct processes at low temperatures. One of the possible interpretations is that this separation originates from the two-scale hierarchical topography of the potential energy landscape; however, it has never been verified. Molecular dynamics simulations are a promising approach to tackle this issue, but we must overcome laborious difficulties. First, we must handle a model of molecular liquids that is computationally demanding compared to simple spherical models, which have been intensively studied but show only a slower process: α relaxation. Second, we must reach a sufficiently low-temperature regime where the two processes become well-separated. Here, we handle an asymmetric dimer system that exhibits a faster process: Johari-Goldstein β relaxation. Then, we employ the parallel tempering method to access the low-temperature regime. These laborious efforts enable us to investigate the potential energy landscape in detail and unveil the first direct evidence of the topographic hierarchy that induces the β relaxation. We also successfully characterize the microscopic motions of particles during each relaxation process. Finally, we study the correlation between low-frequency modes and two relaxation processes. Our results establish a fundamental and comprehensive understanding of experimentally observed relaxation dynamics in supercooled liquids.
| S-EPMC10083593 | biostudies-literature
Project description:The cytoskeleton is a highly interconnected meshwork of strongly coupled subsystems providing mechanical stability as well as dynamic functions to cells. To elucidate the underlying biophysical principles, it is central to investigate not only one distinct functional subsystem but rather their interplay as composite biopolymeric structures. Two of the key cytoskeletal elements are actin and vimentin filaments. Here, we show that composite networks reconstituted from actin and vimentin can be described by a superposition of two non-interacting scaffolds. Arising effects are demonstrated in a scale-spanning frame connecting single filament dynamics to macro-rheological network properties. The acquired results of the linear and non-linear bulk mechanics can be captured within an inelastic glassy wormlike chain model. In contrast to previous studies, we find no emergent effects in these composite networks. Thus, our study paves the way to predict the mechanics of the cytoskeleton based on the properties of its single structural components.
| S-EPMC6183213 | biostudies-literature
Project description:Grain boundary (GB) microstructure and dynamics dictate the macroscopic properties of polycrystalline materials. Although GBs have been investigated extensively in conventional materials, it is only recently that molecular dynamics simulations have shown that GBs exhibit features similar to those of glass-forming liquids. However, current simulation techniques to probe GBs are limited to temperatures and driving forces much higher than those typically encountered in atomic experiments. Further, the short spatial and temporal scales in atomic systems preclude direct experimental access to GB dynamics. Here, we have used confocal microscopy to investigate the dynamics of high misorientation angle GBs in a three-dimensional colloidal polycrystal, with single-particle resolution, in the zero-driving force limit. We show quantitatively that glassy behavior is inherent to GBs as exemplified by the slowing down of particle dynamics due to transient cages formed by their nearest neighbors, non-Gaussian probability distribution of particle displacements and string-like cooperative rearrangements of particles. Remarkably, geometric confinement of the GB region by adjacent crystallites decreases with the misorientation angle and results in an increase in the size of cooperatively rearranging regions and hence the fragility of the glassy GBs.
| S-EPMC3136284 | biostudies-literature
Project description:When classical systems fail to explore their entire configurational space, intriguing macroscopic phenomena like aging and glass formation may emerge. Also closed quanto-mechanical systems may stop wandering freely around the whole Hilbert space, even if they are initially prepared into a macroscopically large combination of eigenstates. Here, we report numerical evidences that the dynamics of strongly interacting lattice bosons driven sufficiently far from equilibrium can be trapped into extremely long-lived inhomogeneous metastable states. The slowing down of incoherent density excitations above a threshold energy, much reminiscent of a dynamical arrest on the verge of a glass transition, is identified as the key feature of this phenomenon. We argue that the resulting long-lived inhomogeneities are responsible for the lack of thermalization observed in large systems. Such a rich phenomenology could be experimentally uncovered upon probing the out-of-equilibrium dynamics of conveniently prepared quantum states of trapped cold atoms which we hereby suggest.
| S-EPMC3272662 | biostudies-literature
Project description:Fingerprints of the three-dimensional organization of genomes have emerged using advances in Hi-C and imaging techniques. However, genome dynamics is poorly understood. Here, we create the chromosome copolymer model (CCM) by representing chromosomes as a copolymer with two epigenetic loci types corresponding to euchromatin and heterochromatin. Using novel clustering techniques, we establish quantitatively that the simulated contact maps and topologically associating domains (TADs) for chromosomes 5 and 10 and those inferred from Hi-C experiments are in good agreement. Chromatin exhibits glassy dynamics with coherent motion on micron scale. The broad distribution of the diffusion exponents of the individual loci, which quantitatively agrees with experiments, is suggestive of highly heterogeneous dynamics. This is reflected in the cell-to-cell variations in the contact maps. Chromosome organization is hierarchical, involving the formation of chromosome droplets (CDs) on genomic scale, coinciding with the TAD size, followed by coalescence of the CDs, reminiscent of Ostwald ripening.
| S-EPMC6082855 | biostudies-other
Project description:We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.
| S-EPMC3607545 | biostudies-literature
Project description:One of the greatest challenges in contemporary condensed matter physics is to ascertain whether the formation of glasses from liquids is fundamentally thermodynamic or dynamic in origin. Although the thermodynamic paradigm has dominated theoretical research for decades, the purely kinetic perspective of the dynamical facilitation (DF) theory has attained prominence in recent times. In particular, recent experiments and simulations have highlighted the importance of facilitation using simple model systems composed of spherical particles. However, an overwhelming majority of liquids possess anisotropy in particle shape and interactions, and it is therefore imperative to examine facilitation in complex glass formers. Here, we apply the DF theory to systems with orientational degrees of freedom as well as anisotropic attractive interactions. By analyzing data from experiments on colloidal ellipsoids, we show that facilitation plays a pivotal role in translational as well as orientational relaxation. Furthermore, we demonstrate that the introduction of attractive interactions leads to spatial decoupling of translational and rotational facilitation, which subsequently results in the decoupling of dynamical heterogeneities. Most strikingly, the DF theory can predict the existence of reentrant glass transitions based on the statistics of localized dynamical events, called excitations, whose duration is substantially smaller than the structural relaxation time. Our findings pave the way for systematically testing the DF approach in complex glass formers and also establish the significance of facilitation in governing structural relaxation in supercooled liquids.
| S-EPMC4217396 | biostudies-literature
Project description:The two-dimensional freezing transition is very different from its three-dimensional counterpart. In contrast, the glass transition is usually assumed to have similar characteristics in two and three dimensions. Using computer simulations, here we show that glassy dynamics in supercooled two- and three-dimensional fluids are fundamentally different. Specifically, transient localization of particles on approaching the glass transition is absent in two dimensions, whereas it is very pronounced in three dimensions. Moreover, the temperature dependence of the relaxation time of orientational correlations is decoupled from that of the translational relaxation time in two dimensions but not in three dimensions. Last, the relationships between the characteristic size of dynamically heterogeneous regions and the relaxation time are very different in two and three dimensions. These results strongly suggest that the glass transition in two dimensions is different than in three dimensions.
| S-EPMC4490572 | biostudies-literature
Project description:By employing molecular dynamics simulations, we explore the dynamics of NPs in semiflexible ring polymer nanocomposite melts. A novel glass transition is observed for NPs in semiflexible ring polymer melts as the bending energy (Kb) of ring polymers increases. For NPs in flexible ring polymer melts (Kb = 0), NPs move in the classic diffusive behavior. However, for NPs in semiflexible ring polymer melts with large bending energy, NPs diffuse very slowly and exhibit the glassy state in which the NPs are all irreversibly caged be the neighbouring semiflexible ring polymers. This glass transition occurs well above the classical glass transition temperature at which microscopic mobility is lost, and the topological interactions of semiflexible ring polymers play an important role in this non-classical glass transition. This investigation can help us understand the nature of the glass transition in polymer systems.
| S-EPMC5349566 | biostudies-literature
Project description:The emergence of glassy dynamics and the glass transition in dense disordered systems is still not fully understood theoretically. Mode-coupling theory (MCT) has shown to be effective in describing some of the non-trivial features of glass formation, but it cannot explain the full glassy phenomenology due to the strong approximations on which it is based. Generalized mode-coupling theory (GMCT) is a hierarchical extension of the theory, which is able to outclass MCT by carefully describing the dynamics of higher-order correlations in its generalized framework. Unfortunately, the theory has so far only been developed for single-component systems and as a result works poorly for highly polydisperse materials. In this paper, we solve this problem by developing GMCT for multi-component systems. We use it to predict the glassy dynamics of the binary Kob-Andersen Lennard-Jones mixture, as well as its purely repulsive Weeks-Chandler-Andersen analogue. Our results show that each additional level of the GMCT hierarchy gradually improves the predictive power of GMCT beyond its previous limit. This implies that our theory is able to harvest more information from the static correlations, thus being able to better understand the role of attraction in supercooled liquids from a first-principles perspective.
| S-EPMC8260512 | biostudies-literature