During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.

Fickian yet non-Gaussian diffusion (FnGD), a most intriguing open issue in soft matter, is generically associated with some dynamical and/or structural heterogeneity of the environment. Here we investigate the features of FnGD in glass-forming liquids, the epitome of dynamical heterogeneity, drawing on experiments on hard-sphere colloidal suspensions and simulations of a simple model of molecular liquid. We demonstrate that FnGD strengthens on approaching the glass transition, by identifying distinct timescales for Fickianity, ${\tau }_F$, and for restoring of Gaussianity, ${\tau }_G>{\tau }_F$, as well as their associated length scales, ${\xi }_F$ and ${\xi }_G$. We find ${\tau }_G\propto {\tau }_F^{\gamma }$ with $\gamma \simeq 1.8$ for both systems. In the deep FnGD regime, the displacement distributions display exponential tails. We show that, in simulations, the time-dependent decay lengths $l(t)$ at different temperatures all collapse onto a power-law master curve $[l(t)/({\xi }_G)]\propto (t/{\tau }_G{)}^{\alpha }$, with $\alpha =0.33$. A similar collapse, if less sharp, is also found in experiments, seemingly with the same exponent $\alpha$. We further discuss the connections of the timescales and length scales characterizing FnGD with structural relaxation and dynamic heterogeneity.

In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations in the ability of individual cells to sense and thereby respond to the chemical gradient. Specifically, cells at bulging parts of a front are exposed to a smaller gradient, which slows them down and promotes stability, but they also respond more strongly to the gradient, which speeds them up and promotes instability. We predict that this competition leads to chemotactic fingering when sensing is limited at too low chemical concentrations. Guided by this finding and by experimental data on E. coli chemotaxis, we suggest that the cells’ sensory machinery might have evolved to avoid these limitations and ensure stable front propagation. Finally, as sensing of any stimuli is necessarily limited in living and active matter in general, the principle of sensing-induced stability may operate in other types of directed migration such as durotaxis, electrotaxis, and phototaxis.

We report new dynamical modes in confined soft granular flows, such as stochastic jetting and dripping, with no counterpart in continuum viscous fluids. The new modes emerge as a result of the propagation of the chaotic behavior of individual grains—here, monodisperse emulsion droplets—to the level of the entire system as the emulsion is focused into a narrow orifice by an external viscous flow. We observe avalanching dynamics and the formation of remarkably stable jets—single-file granular chains—which occasionally break, resulting in a non-Gaussian distribution of cluster sizes. We find that the sequences of droplet rearrangements that lead to the formation of such chains resemble unfolding of cancer cell clusters in narrow capillaries, overall demonstrating that microfluidic emulsion systems could serve to model various aspects of soft granular flows, including also tissue dynamics at the mesoscale.

The isothermal crystallization near the glass transition temperature from the melt state of poly(trimethylene terephthalate) has been studied by wide-angle x-ray diffraction (WAXD), small-angle x-ray scattering (SAXS), and optical microscopy. The SAXS and WAXD results show the crystallization mechanism in which the crystalline nodules cover the entire sample with the formation of aggregation regions. The analysis of the SAXS results using Kolmogorov-Johnson-Mehl-Avrami theory indicates that the formation kinetics of the aggregation regions is of three-dimensional homogeneous nucleation type. The analysis of the SAXS profiles using Sekimoto’s theory provides the growth velocity and the nucleation rate of the aggregation region. The temperature dependence of the growth velocity of the aggregation region is a natural extrapolation of that of spherulite to the high supercooling region. The temperature dependence of the nucleation rate of the aggregation region is also represented by the parameters of the spherulitic growth rate. The result of the growth velocities of the aggregation region and the spherulite suggests the existence of precursors at the front of the crystal growth.

When stretched, both DNA and RNA duplexes change their twist angles through twist-stretch coupling. The coupling is negative for DNA but positive for RNA, which is not yet completely understood. Here, our magnetic tweezers experiments show that the coupling of RNA reverses from positive to negative by multivalent cations. Combining with the previously reported tension-induced negative-to-positive coupling reversal of DNA, we propose a unified mechanism of the couplings of both RNA and DNA based on molecular dynamics simulations. Two deformation pathways are competing when stretched: shrinking the radius causes positive couplings but widening the major groove causes negative couplings. For RNA whose major groove is clamped by multivalent cations and canonical DNA, their radii shrink when stretched, thus exhibiting positive couplings. For elongated DNA whose radius already shrinks to the minimum and canonical RNA, their major grooves are widened when stretched, thus exhibiting negative couplings.

Active matter broadly covers the dynamics of self-propelled particles. While the onset of collective behavior in homogenous active systems is relatively well understood, the effect of inhomogeneities such as obstacles and traps lacks overall clarity. Here, we study how interacting, self-propelled particles become trapped and released from a trap. We have found that captured particles aggregate into an orbiting condensate with a crystalline structure. As more particles are added, the trapped condensates escape as a whole. Our results shed light on the effects of confinement and quenched disorder in active matter.

The present Letter shows that the formation of ozone in ternary collisions $\mathrm{O}+{\mathrm{O}}_2+M$—the primary mechanism of ozone formation in the stratosphere—at temperatures below 200 K (for $M=\mathrm{Ar}$) proceeds through a formation of a temporary complex $M{\mathrm{O}}_2$, while at temperatures above $\sim 700\mathrm{K}$, the reaction proceeds mainly through a formation of long-lived vibrational resonances of ${\mathrm{O}}_3^{*}$. At intermediate temperatures 200–700 K, the process cannot be viewed as a two-step mechanism, often used to simplify and approximate collisions of three atoms or molecules. The developed theoretical approach is applied to the reaction $\mathrm{O}+{\mathrm{O}}_2+\mathrm{Ar}$ because of extensive experimental data available. The rate coefficients for the formation of ${\mathrm{O}}_3$ in ternary collisions $\mathrm{O}+{\mathrm{O}}_2+\mathrm{Ar}$ without using two-step approximations were computed for the first time as a function of collision energy. Thermally averaged coefficients were derived for temperatures 5–900 K. It is found that the majority of ${\mathrm{O}}_3$ molecules formed initially are weakly bound. Accounting for the process of vibrational quenching of the nascent population, a good agreement with available experimental data for temperatures 100–900 K is obtained.

Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. Using droplet interfaces to position compartment boundaries, we show that an assembly line can be self-organized by active droplets. As a consequence, assembly steps can be arranged spatially so that a specific order of assembly is achieved and incorrect assembly is strongly suppressed.

The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence. The computed force spectrum reveals bimodal $1/f$ noise, suggesting the use of a non-Markovian rate theory.

The conductivity of ionic solutions is arguably their most important trait, being widely used in electrochemical, biochemical, and environmental applications. The Debye-Hückel-Onsager theory successfully predicts the conductivity at very low ionic concentrations of up to a few millimolars, but there is no well-established theory applicable at higher concentrations. We study the conductivity of ionic solutions using a stochastic density functional theory, paired with a modified Coulomb interaction that accounts for the hard-core repulsion between the ions. The modified potential suppresses unphysical, short-range electrostatic interactions, which are present in the Debye-Hückel-Onsager theory. Our results for the conductivity show very good agreement with experimental data up to 3 molars, without any fit parameters. We provide a compact expression for the conductivity, accompanied by a simple analytical approximation.

External stress can accelerate molecular mobility of amorphous solids by several orders of magnitude. The changes in mobility are commonly interpreted through the Eyring model, which invokes an empirical activation volume. Here, we analyze constant-stress molecular dynamics simulations and propose a structure-dependent Eyring model, connecting activation volume to a machine-learned field, softness. We show that stress has a heterogeneous effect on the mobility that depends on local structure through softness. The barrier impeding relaxation reduces more for well-packed particles, which explains the narrower distribution of relaxation time observed under stress.

From the flashes of fireflies to Josephson junctions and power infrastructure, networks of coupled phase oscillators provide a powerful framework to describe synchronization phenomena in many natural and engineered systems. Most real-world networks are under the influence of noisy, random inputs, potentially inhibiting synchronization. While noise is unavoidable, here we show that there exist optimal noise patterns which minimize desynchronizing effects and even enhance order. Specifically, using analytical arguments we show that in the case of a two-oscillator model, there exists a sharp transition from a regime where the optimal synchrony-enhancing noise is perfectly anticorrelated, to one where the optimal noise is correlated. More generally, we then use numerical optimization methods to demonstrate that there exist anticorrelated noise patterns that optimally enhance synchronization in large complex oscillator networks. Our results may have implications in networks such as power grids and neuronal networks, which are subject to significant amounts of correlated input noise.

We investigate avalanches and clusters associated with plastic rearrangements and the nature of structural change in the prototypical strong glass, silica, computationally. We perform a detailed analysis of avalanches, and of spatially disconnected clusters that constitute them, for a wide range of system sizes. Although qualitative aspects of yielding in silica are similar to other glasses, the statistics of clusters exhibits significant differences, which we associate with differences in local structure. Across the yielding transition, anomalous structural change and densification, associated with a suppression of tetrahedral order, is observed to accompany strain localization.

Spider silk is a protein material that exhibits extraordinary and nontrivial properties such as the ability to soften, decrease in length (i.e., supercontract), and twist upon exposure to high humidity. These behaviors stem from a unique microstructure in combination with a transition from glassy to rubbery as a result of humidity-driven diffusion of water. In this Letter we propose four length scales that govern the mechanical response of the silk during this transition. In addition, we develop a model that describes the microstructural evolution of the spider silk thread and explains the response due to the diffusion of water molecules. The merit of the model is demonstrated through an excellent agreement to experimental findings. The insights from this Letter can be used as a microstructural design guide to enable the development of new materials with unique spiderlike properties.

The erythrocyte sedimentation rate is one of the oldest medical diagnostic methods whose physical mechanisms remain debatable today. Using both light microscopy and mesoscale cell-level simulations, we show that erythrocytes form a soft-particle gel. Furthermore, the high volume fraction of erythrocytes, their deformability, and weak attraction lead to unusual properties of this gel. A theoretical model for the gravitational collapse is developed, whose predictions are in agreement with detailed macroscopic measurements of the interface velocity.