Relationship between dynamical heterogeneities and stretched exponential relaxation

Simdyankin, S. I.; Mousseau, Normand

doi:10.1103/physreve.68.041110

Cited by 21 publications

(16 citation statements)

References 46 publications

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“…In each case (and for those concentrations not explicitly shown here) the data were fit to a stretched exponential function: y ϭ y0 ϩ A⅐exp(Ϫxk) ␣ , where k is the rate constant and ␣ represents the deviations from monoexponentiality (i.e., ␣ ϭ 1 would indicate monoexponential kinetics). This function is particularly well suited for phenomenon where there is a distribution of rate constants (26); the parameter ␣ reflects the degree of heterogeneity.…”

Section: Resultsmentioning

confidence: 99%

“…The disorder in the aggregate organization is indicated by the band intensity and frequency of the 13 C amide IЈ band in the spectrum of the peptide specifically labeled at residue 117. A regular register, in which residue 117 is aligned at all positions, would result in a stronger coupling between the 13 C amide IЈ modes and a lower band frequency and slightly diminished band intensity in the spectrum (11,12,22,26). Over time, the aggregates adopt the ordered, equilibrium register, and the 13 C amide IЈ band shifts from 1,601 to 1,591 cm Ϫ1 .…”

Section: H1 Quickly Forms Disordered Heterogeneous Oligomers In Solumentioning

confidence: 99%

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Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates

Petty

Decatur²

2005

Proc. Natl. Acad. Sci. U.S.A.

124

147

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Many neurodegenerative diseases are characterized by the accumulation of amyloid fibers in the brain, which can occur when a protein misfolds into an extended ␤-sheet conformation. The nucleation of these ␤-sheet aggregates is of particular interest, not only because it is the rate-determining step toward fiber formation but also because early, soluble aggregate species may be the cytotoxic entities in many diseases. In the case of the prion peptide H1 (residues 109 -122 of the prion protein) stable amyloid fibers form only after the ␤-strands of the peptide have adopted their equilibrium antiparallel ␤-sheet configuration with residue 117 in register across all strands. In this article, we present the kinetic details of the realignment of these ␤-strands from their fastformed nonequilibrium structure, which has no regular register of the strands, into the more ordered ␤-sheets capable of aggregating into stable fibers. This process is likely the nucleating step toward the formation of stable fibers. Isotope-edited IR spectroscopy is used to monitor the alignment of the ␤-strands by the introduction of a 13 C-labeled carbonyl at residue 117. Nonexponential kinetics is observed, with a complex dependence on concentration. The results are consistent with a mechanism in which the ␤-sheet realigns by both the repeated detachment and annealing of strands in solution and reptation of polypeptide strands within an aggregate.IR spectroscopy ͉ peptide aggregation ͉ isotope-edited ͉ prion peptide ͉ amyloid fiber T he misfolding of proteins into a ␤-sheet configuration and the subsequent aggregation of these ␤-sheets is associated with many neurological disorders, including Alzheimer's, Huntington's, and Creutzfeldt-Jakob disease (1). These diseases are associated with the presence of large amyloid plaques, which contain fibrous aggregates of protein. Several detailed models for the mechanism of amyloid growth have been proposed, but all involve a conformational change in the protein that leads to the formation of soluble oligomers, which eventually nucleate the growth of larger fibers. With several diseases, including Alzheimer's and Parkinson's, the oligomeric intermediates may be the primary cytotoxic species (2-4).The soluble oligomeric intermediates are difficult to isolate and, because of their large size and dynamic nature, difficult to characterize with traditional biophysical techniques. For these reasons, many studies aimed at studying the aggregation process use small peptides, derived from full-length proteins of interest, which also show amyloidogenic behavior. Among the peptides studied extensively include the NFGAIL sequence from the islet amyloid polypeptide (5-7), fragments of the prion protein that include the AGAAAAGA amyloidogenic region (8-12), and many different fragments of the Alzheimer's A␤ peptide (13)(14)(15)(16)(17)(18). In simulations of these peptides, ensembles of ␤-sheet oligomers are initially formed, including species that have a non-native hydrogen-bonding registry or mix parallel and ant...

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Section: Resultsmentioning

confidence: 99%

Section: H1 Quickly Forms Disordered Heterogeneous Oligomers In Solumentioning

confidence: 99%

Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates

Petty

Decatur²

2005

Proc. Natl. Acad. Sci. U.S.A.

124

147

View full text Add to dashboard Cite

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“…Ref. [21] has analyzed stretched exponential relaxations in glassy systems, looking at it as a consequence of a renewal process for a single effective particle, where the distribution of renewal times is itself a stretched exponential, leading to stretched-exponential relaxation with the same exponent for the time correlations. It is not obvious whether the cooperative dynamics of the KA model could be mapped onto such a simple renewal process with a distribution of times equal to the distribution of persistence times P (τ ).…”

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confidence: 99%

Spatial correlations in the relaxation of the Kob-Andersen model

Marinari¹,

Pitard²

2005

Europhys. Lett.

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PACS. 64.70.Pf -Glass transitions. PACS. 05.50.+q -Lattice theory and statistics. PACS. 61.20.Lc -Time-dependent properties of liquid structure; relaxation.Abstract. -We describe spatio-temporal correlations and heterogeneities in a kinetically constrained glassy model, the Kob-Andersen model. The kinetic constraints of the model alone induce the existence of dynamic correlation lengths, that increase as the density ρ increases, in a way compatible with a double-exponential law. We characterize in detail the trapping time correlation length, the cooperativity length, and the distribution of persistent clusters of particles. This last quantity is related to the typical size of blocked clusters that slow down the dynamics for a given density.Glassy dynamics in kinetically constrained systems has been a subject of wide interest during the last years [1]. It indeed includes a large class of models of particles constrained by dynamical rules where the relaxation is slowed down when the density of particles increases or the temperature decreases, sharing similarities (though with a number of differences) with spin-glass models or glass models [2] when the temperature is decreased. In the former class, slowing down of the dynamics can be understood as a consequence of steric effects, that make certain moves of particles impossible because of an effective high local density, putting strong constraints on the number of allowed paths between configurations [3]; whereas for the latter class, frustration and/or disorder in the interactions produces a slow time relaxation. In real glasses both effects are likely to be present. While most studies on the glass state have focused for a long time on the latter class of models, more attention is paid to the fact that the former mechanism is also of importance, especially since the works of Harrowell [4] on spatio-temporal heterogeneities. These heterogeneities are also of great interest for experimentalists, since they have been identified in several glassy systems [5].In this paper we will focus on the numerical study of the Kob-Andersen (KA) model [6]. In this 3-dimensional model of lattice gas on a cubic lattice, a particle can hop to one of its empty nearest neighbor sites only if it has strictly less than m occupied nearest-neighbor sites, and if after the hop it will also have less than m occupied nearest-neighbor sites (which ensures detailed balance). In the original study of the KA model, the value of m is chosen c EDP Sciences

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“…Glass relaxation behaviors are generally found to follow a stretched exponential decay function f (t) [37]:…”

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confidence: 99%

Stretched Exponential Relaxation of Glasses at Low Temperature

Yu¹,

Wang²,

Zhang³

et al. 2015

Phys. Rev. Lett.

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The question of whether glass continues to relax at low temperature is of fundamental and practical interest. Here, we report a novel atomistic simulation method allowing us to directly access the longterm dynamics of glass relaxation at room temperature. We find that the potential energy relaxation follows a stretched exponential decay, with a stretching exponent β = 3/5, as predicted by Phillips' diffusion-trap model. Interestingly, volume relaxation is also found. However, it is not correlated to the energy relaxation, but is rather a manifestation of the mixed alkali effect.

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Relationship between dynamical heterogeneities and stretched exponential relaxation

Cited by 21 publications

References 46 publications

Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates

Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates

Spatial correlations in the relaxation of the Kob-Andersen model

Stretched Exponential Relaxation of Glasses at Low Temperature

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