Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adam-Gibbs model in the density scaling regime and its implications for the configurational entropy scaling.

ABSTRACT: To solve a long-standing problem of condensed matter physics with determining a proper description of the thermodynamic evolution of the time scale of molecular dynamics near the glass transition, we have extended the well-known Adam-Gibbs model to describe the temperature-volume dependence of structural relaxation times, τα(T, V). We also employ the thermodynamic scaling idea reflected in the density scaling power law, τα = f(T(-1)V(-γ)), recently acknowledged as a valid unifying concept in the glass transition physics, to differentiate between physically relevant and irrelevant attempts at formulating the temperature-volume representations of the Adam-Gibbs model. As a consequence, we determine a straightforward relation between the structural relaxation time τα and the configurational entropy SC, giving evidence that also SC(T, V) = g(T(-1)V(-γ)) with the exponent γ that enables to scale τα(T, V). This important findings have meaningful implications for the connection between thermodynamics and molecular dynamics near the glass transition, because it implies that τα can be scaled with SC.

SUBMITTER: Masiewicz E

PROVIDER: S-EPMC4568462 | biostudies-other | 2015

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Activation volume of selected liquid crystals in the density scaling regime.

Project description:In this paper, we demonstrate and thoroughly analyze the activation volumetric properties of selected liquid crystals in the nematic and crystalline E phases in comparison with those reported for glass-forming liquids. In the analysis, we have employed and evaluated two entropic models (based on either total or configurational entropies) to describe the longitudinal relaxation times of the liquid crystals in the density scaling regime. In this study, we have also exploited two equations of state: volumetric and activation volumetric ones. As a result, we have established that the activation volumetric properties of the selected liquid crystals are quite opposite to such typical properties of glass-forming materials, i.e., the activation volume decreases and the isothermal bulk modulus increases when a liquid crystal is isothermally compressed. Using the model based on the configurational entropy, we suggest that the increasing pressure dependences of the activation volume in isothermal conditions and the negative curvature of the pressure dependences of isothermal longitudinal relaxation times can be related to the formation of antiparallel doublets in the examined liquid crystals. A similar pressure effect on relaxation dynamics may be also observed for other material groups in case of systems, the molecules of which form some supramolecular structures.

| S-EPMC5299607 | biostudies-literature

The Zero-Density Limit of the Residual Entropy Scaling of Transport Properties.

Project description:The modified residual entropy scaling approach has been shown to be a successful means of scaling dense phase transport properties. In this work, we investigate the dilute-gas limit of this scaling. This limit is considered for model potentials and highly accurate results from calculations with ab initio pair potentials for small molecules. These results demonstrate that with this approach, the scaled transport properties of noble gases can be collapsed without any empirical parameters to nearly their mutual uncertainties and that the scaled transport properties of polyatomic molecules are qualitatively similar, and for sufficiently high temperatures they agree with "universal" values proposed by Rosenfeld in 1999. There are significant quantitative differences between the model potentials and real fluids in these scaled coordinates, but this study provides a thorough coverage of model fluids and simple real fluids, providing the basis for further study. In the supporting information we provide the collected calculations with ab initio pair potentials from the literature, as well as code in the Python language implementing all aspects of our analysis.

| S-EPMC7448542 | biostudies-literature

Asymptotic entropy of the Gibbs state of complex networks.

Project description:In this work we study the entropy of the Gibbs state corresponding to a graph. The Gibbs state is obtained from the Laplacian, normalized Laplacian or adjacency matrices associated with a graph. We calculated the entropy of the Gibbs state for a few classes of graphs and studied their behavior with changing graph order and temperature. We illustrate our analytical results with numerical simulations for Erdős-Rényi, Watts-Strogatz, Barabási-Albert and Chung-Lu graph models and a few real-world graphs. Our results show that the behavior of Gibbs entropy as a function of the temperature differs for a choice of real networks when compared to the random Erdős-Rényi graphs.

| S-EPMC7801599 | biostudies-literature

The vortex gas scaling regime of baroclinic turbulence.

Project description:The mean state of the atmosphere and ocean is set through a balance between external forcing (radiation, winds, heat and freshwater fluxes) and the emergent turbulence, which transfers energy to dissipative structures. The forcing gives rise to jets in the atmosphere and currents in the ocean, which spontaneously develop turbulent eddies through the baroclinic instability. A critical step in the development of a theory of climate is to properly include the eddy-induced turbulent transport of properties like heat, moisture, and carbon. In the linear stages, baroclinic instability generates flow structures at the Rossby deformation radius, a length scale of order 1,000 km in the atmosphere and 100 km in the ocean, smaller than the planetary scale and the typical extent of ocean basins, respectively. There is, therefore, a separation of scales between the large-scale gradient of properties like temperature and the smaller eddies that advect it randomly, inducing effective diffusion. Numerical solutions show that such scale separation remains in the strongly nonlinear turbulent regime, provided there is sufficient drag at the bottom of the atmosphere and ocean. We compute the scaling laws governing the eddy-driven transport associated with baroclinic turbulence. First, we provide a theoretical underpinning for empirical scaling laws reported in previous studies, for different formulations of the bottom drag law. Second, these scaling laws are shown to provide an important first step toward an accurate local closure to predict the impact of baroclinic turbulence in setting the large-scale temperature profiles in the atmosphere and ocean.

| S-EPMC7060697 | biostudies-literature

Entropy-scaling search of massive biological data.

Project description:Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the data set is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains-high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND (3700x BLASTX)), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve 'compressive omics,' and the general theory can be readily applied to data science problems outside of biology. Source code: http://gems.csail.mit.edu.

| S-EPMC4591002 | biostudies-literature

Excess-entropy scaling in supercooled binary mixtures.

Project description:Transport coefficients, such as viscosity or diffusion coefficient, show significant dependence on density or temperature near the glass transition. Although several theories have been proposed for explaining this dynamical slowdown, the origin remains to date elusive. We apply here an excess-entropy scaling strategy using molecular dynamics computer simulations and find a quasiuniversal, almost composition-independent, relation for binary mixtures, extending eight orders of magnitude in viscosity or diffusion coefficient. Metallic alloys are also well captured by this relation. The excess-entropy scaling predicts a quasiuniversal breakdown of the Stokes-Einstein relation between viscosity and diffusion coefficient in the supercooled regime. Additionally, we find evidence that quasiuniversality extends beyond binary mixtures, and that the origin is difficult to explain using existing arguments for single-component quasiuniversality.

| S-EPMC7453028 | biostudies-literature

Direct measurement of weakly nonequilibrium system entropy is consistent with Gibbs-Shannon form.

Project description:Stochastic thermodynamics extends classical thermodynamics to small systems in contact with one or more heat baths. It can account for the effects of thermal fluctuations and describe systems far from thermodynamic equilibrium. A basic assumption is that the expression for Shannon entropy is the appropriate description for the entropy of a nonequilibrium system in such a setting. Here we measure experimentally this function in a system that is in local but not global equilibrium. Our system is a micron-scale colloidal particle in water, in a virtual double-well potential created by a feedback trap. We measure the work to erase a fraction of a bit of information and show that it is bounded by the Shannon entropy for a two-state system. Further, by measuring directly the reversibility of slow protocols, we can distinguish unambiguously between protocols that can and cannot reach the expected thermodynamic bounds.

| S-EPMC5651767 | biostudies-literature

A high-density crowd state judgment model based on entropy theory.

Project description:A high-density crowd state is prone to cause large-scale crowd stampede accidents that seriously threaten the people's security and property. The key to preventing crowd congestion is to accurately predict the location and time of crowd events, particularly when there is a high density of people. In this paper, the entropy theory is used to characterize the state of a crowded system. The theoretical entropy Sr and the actual entropy S of the crowd system are obtained according to the area occupied by the different crowd state The maximum entropy value and the actual entropy value under different conditions of the system are compared to judge the state of crowded extent. The results show that the model is practical and effective. According to the situation of the crowd, different management and evacuation measures are considered to prevent the occurrence of crowd accidents.

| S-EPMC8412320 | biostudies-literature

The isothermal Boltzmann-Gibbs entropy reduction affects survival of the fruit fly Drosophila melanogaster.

Project description:To the best of our knowledge, this is the first experimental evidence of the effect of isothermal changes in entropy on a living organism. In greater detail, the effect of the reduction of the total Boltzmann-Gibbs entropy (S) of the aquatic environment on the survival rate and body mass of the fruit fly Drosophila melanogaster was investigated. The tests were carried out in standard thermodynamic states at room temperature of 296.15 K and ambient atmospheric pressure of 1 bar. Two variants of entropy reduction (ΔS) were tested for ΔS = 28.49 and 51.14 J K-1 mol-1 compared to the blind and control samples. The entropy level was experimentally changed, using the quantum system for isothermal entropy reduction. This system is based on quantum bound entanglement of phonons and the phenomenon of phonon resonance (interference of phonon modes) in condensed matter (Silicon dioxide (SiO2) and single crystals of Silicon (Si0), Aluminum (Al0) plates ("chips"), glass, and water). All studied organisms were of the same age (1 day). Mortality was observed daily until the natural death of the organisms. The investigations showed that changes in the Boltzmann-Gibbs entropy affected the survival and body mass of the fruit flies. On the one hand, the reduction in entropy under isothermal conditions in the aquatic environment for ΔS = 28.49 J K-1 mol-1 resulted in an extension of the lifespan and an increase in the body mass of female fruit flies. On the other hand, the almost twofold reduction in this entropy for ΔS = 51.14 J K-1 mol-1 shortened the lives of the males. Thus, the lifespan and body mass of flies turned out to be a specific reaction of metabolism related to changes in the entropy of the aquatic environment.

| S-EPMC10465501 | biostudies-literature

Scaling Law for Irreversible Entropy Production in Critical Systems.

Project description:We examine the Jarzynski equality for a quenching process across the critical point of second-order phase transitions, where absolute irreversibility and the effect of finite-sampling of the initial equilibrium distribution arise in a single setup with equal significance. We consider the Ising model as a prototypical example for spontaneous symmetry breaking and take into account the finite sampling issue by introducing a tolerance parameter. The initially ordered spins become disordered by quenching the ferromagnetic coupling constant. For a sudden quench, the deviation from the Jarzynski equality evaluated from the ideal ensemble average could, in principle, depend on the reduced coupling constant ε0 of the initial state and the system size L. We find that, instead of depending on ε0 and L separately, this deviation exhibits a scaling behavior through a universal combination of ε0 and L for a given tolerance parameter, inherited from the critical scaling laws of second-order phase transitions. A similar scaling law can be obtained for the finite-speed quench as well within the Kibble-Zurek mechanism.

| S-EPMC4899778 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data