Block Analysis for the Calculation of Dynamic and Static Length Scales in Glass-Forming Liquids

We present {\it block analysis}, an efficient method to perform finite-size scaling for obtaining the length scale of dynamic heterogeneity and the point-to-set length scale for generic glass-forming liquids. This method involves considering blocks of varying sizes embedded in a system of a fixed (large) size. The length scale associated with dynamic heterogeneity is obtained from a finite-size scaling analysis of the dependence of the four-point dynamic susceptibility on the block size. The block size dependence of the variance of the $\alpha$-relaxation time yields the static point-to-set length scale. The values of the obtained length scales agree quantitatively with those obtained from other conventional methods. This method provides an efficient experimental tool for studying the growth of length scales in systems such as colloidal glasses for which performing finite-size scaling by carrying out experiments for varying system sizes may not be feasible.Comment: 5 pages, 3 figure

Glass Transition in Supercooled Liquids with Medium Range Crystalline Order

The origins of rapid dynamical slow down in glass forming liquids in the growth of static length scales, possibly associated with identifiable structural ordering, is a much debated issue. Growth of medium range crystalline order (MRCO) has been observed in various model systems to be associated with glassy behaviour. Such observations raise the question about the eventual state reached by a glass former, if allowed to relax for sufficiently long times. Is a slowly growing crystalline order responsible for slow dynamics? Are the molecular mechanisms for glass transition in liquids with and without MRCO the same? If yes, glass formers with MRCO provide a paradigm for understanding glassy behaviour generically. If not, systems with MRCO form a new class of glass forming materials whose molecular mechanism for slow dynamics may be easier to understand in terms of growing crystalline order, and should be approached in that manner, even while they will not provide generic insights. In this study we perform extensive molecular dynamics simulations of a number of glass forming liquids in two dimensions and show that the static and dynamic properties of glasses with MRCO are different from other glass forming liquids with no predominant local order. We also resolve an important issue regarding the so-called Point-to-set method for determining static length scales, and demonstrate it to be a robust, order agnostic, method for determining static correlation lengths in glass formers

Building a "trap model" of glassy dynamics from a local structural predictor of rearrangements

Here we introduce a variation of the trap model of glasses based on softness, a local structural variable identified by machine learning, in supercooled liquids. Softness is a particle-based quantity that reflects the local structural environment of a particle and characterizes the energy barrier for the particle to rearrange. As in the trap model, we treat each particle's softness, and hence energy barrier, as evolving independently. We show that such a model reproduces many qualitative features of softness, and therefore makes qualitatively reasonable predictions of behaviors such as the dependence of fragility on density in a model supercooled liquid. We also show failures of this simple model, indicating features of the dynamics of softness that may only be explained by correlations.Comment: 7 pages, 5 figures. Supplementary material: 3 pages, 4 figure

Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure

Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, the aspect ratio of amnioserosa cells increases markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments

How Does a Hydrophobic Macromolecule Respond to a Mixed Osmolyte Environment?

The role of the protecting osmolyte trimethyl <i>N</i>-oxide (TMAO) in counteracting the denaturing effect of urea on a protein is quite well established. However, the mechanistic role of osmolytes on the hydrophobic interaction underlying protein folding is a topic of contention and is emerging as a key area of biophysical interest. Although recent experiments and computer simulations have established that an individual aqueous solution of TMAO and urea respectively stabilizes and destabilizes the collapsed conformation of a hydrophobic polymer, it remains to be explored how a mixed aqueous solution of protecting and denaturing osmolytes influences the conformations of the polymer. In order to bridge the gap, we have simulated the conformational behavior of both a model hydrophobic polymer and a synthetic polymer polystyrene in an aqueous mixture of TMAO and urea. Intriguingly, our free energy based simulations on both of the systems show that, even though a pure aqueous solution of TMAO stabilizes the collapsed or globular conformation of the hydrophobic polymer, addition of TMAO to an aqueous solution of urea further destabilizes the collapsed conformation of the hydrophobic polymer. We also observe that the extent of destabilization in a mixed osmolyte solution is relatively higher than that in pure aqueous urea solution. The reinforcement of the denaturation effect of the hydrophobic macromolecule in a mixed osmolyte solution is in stark contrast to the well-known counteracting role of TMAO in proteins under denaturing condition of urea. In both model and realistic systems, our results show that, in a mixed aqueous solution, a greater number of cosolutes preferentially bind to the extended conformation of the polymer relative to that in the collapsed conformation, thereby complying with the Tanford–Wyman preferential solvation theory disfavoring the collapsed conformation. The results are robust across a range of osmolyte concentrations and multiple cosolute force fields. Our findings unequivocally imply that the action of mixed osmolyte solution on hydrophobic polymer is significantly distinct from that of proteins