Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. ATP driven remodeling enzymes are known to be crucial for its establishment in vivo, but their nonequilibrium nature has hindered the development of a unified theoretical framework for nucleosome positioning. Using a perturbation theory, we show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the effective temperature and the radial distribution function, in biologically relevant regimes. The energy landscape view emerging from our study provides an intuitive understanding for the impact of remodeling enzymes in either reinforcing or overwriting intrinsic signals for nucleosome positioning, and may help improve the accuracy of computational models for its prediction in silico.

Using a geometric feedback model of the flagellar axoneme accounting for dynein motor kinetics, we study elastohydrodynamic phase synchronization in a pair of spontaneously beating filaments with waveforms ranging from sperm to cilia and Chlamydomonas. Our computations reveal that both in-phase and antiphase synchrony can emerge for asymmetric beats while symmetric waveforms go in phase, and elucidate the mechanism for phase slips due to biochemical noise. Model predictions agree with recent experiments and illuminate the crucial roles of hydrodynamics and mechanochemical feedback in synchronization.

We report a microscopic observation of the time-dependent dynamic tube dilation process on isofrictional bidisperse melts. By applying neutron spin echo (NSE) and dielectric techniques on blends of long polyisoprene (PI) chains with short PI additives with different topology, we access the dynamics of the tube dilation process on a molecular scale. The time-dependent tube dilation is directly revealed by NSE as an additional time dependence of the dynamic structure factor in the local reptation regime. We identify the characteristic time of tube dilation as the terminal time of the additive.

We report experimental observations of surface oscillations in an ultrasoft agarose gel drop. Ultrasonic levitation is used to excite shape oscillations in the gel drop and we report the natural frequency of the drop as it depends upon a nondimensional elastocapillary number, which we define as the ratio of the elastocapillary length to drop size. Our experiments span a wide range of experimental parameters and we recover the appropriate scaling laws in the elastic and capillary wave limits. The crossover between these two limits is observed and agrees well with a proposed frequency relationship.

Many systems, including biological tissues and foams, are made of highly packed units having high deformability but low compressibility. At two dimensions, these systems offer natural tesselations of a plane with fixed density, in which transitions from ordered to disordered patterns are often observed, in both directions. Using a modified cellular Potts model algorithm that allows rapid thermalization of extensive systems, we numerically explore the order-disorder transition of monodisperse, two-dimensional cellular systems driven by thermal agitation. We show that the transition follows most of the predictions of Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) theory developed for melting of 2D solids, extending the validity of this theory to systems with many-body interactions. In particular, we show the existence of an intermediate hexatic phase, which preserves the orientational order of the regular hexagonal tiling but loses its positional order. In addition to shedding light on the structural changes observed in experimental systems, our study shows that soft cellular systems offer macroscopic systems in which the KTHNY melting scenario can be explored, in the continuation of Bragg’s experiments on bubble rafts.

The cytoskeleton is a composite network of three types of protein filaments, among which intermediate filaments (IFs) are the most extensible ones. Two very important IFs are keratin and vimentin, which have similar molecular architectures but different mechanical behaviors. Here we compare the mechanical response of single keratin and vimentin filaments using optical tweezers. We show that the mechanics of vimentin strongly depends on the ionic strength of the buffer and that its force-strain curve suggests a high degree of cooperativity between subunits. Indeed, a computational model indicates that in contrast to keratin, vimentin is characterized by strong lateral subunit coupling of its charged monomers during unfolding of $\alpha$ helices. We conclude that cells can tune their mechanics by differential use of keratin versus vimentin.

The cell cortex, a thin film of active material assembled below the cell membrane, plays a key role in cellular symmetry-breaking processes such as cell polarity establishment and cell division. Here, we present a minimal model of the self-organization of the cell cortex that is based on a hydrodynamic theory of curved active surfaces. Active stresses on this surface are regulated by a diffusing molecular species. We show that coupling of the active surface to a passive bulk fluid enables spontaneous polarization and the formation of a contractile ring on the surface via mechanochemical instabilities. We discuss the role of external fields in guiding such pattern formation. Our work reveals that key features of cellular symmetry breaking and cell division can emerge in a minimal model via general dynamic instabilities.

We develop a phenomenological coarse-graining procedure for activity in a large network of neurons, and apply this to recordings from a population of 1000+ cells in the hippocampus. Distributions of coarse-grained variables seem to approach a fixed non-Gaussian form, and we see evidence of scaling in both static and dynamic quantities. These results suggest that the collective behavior of the network is described by a nontrivial fixed point.

Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug design. Current techniques suffer from being model specific, requiring abundant computation resources and simulation at conditions far from the studied realization. Here, we present a universal scheme to calculate entropy using lossless-compression algorithms and validate it on simulated systems of increasing complexity. Our results show accurate entropy values compared to benchmark calculations while being computationally effective. In molecular-dynamics simulations of protein folding, we exhibit unmatched detection capability of the folded states by measuring previously undetectable entropy fluctuations along the simulation timeline. Such entropy evaluation opens a new window onto the dynamics of complex systems and allows efficient free-energy calculations.

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations; thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cell numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature.

Some of the key proteins essential for important cellular processes are capable of recruiting other proteins from the cytosol to phospholipid membranes. The physical basis for this cooperativity of binding is, surprisingly, still unclear. Here, we suggest a general feedback mechanism that explains cooperativity through mechanochemical coupling mediated by the mechanical properties of phospholipid membranes. Our theory predicts that protein recruitment, and therefore also protein pattern formation, involves membrane deformation and is strongly affected by membrane composition.

Unusual structures and dynamic properties found in polymer nanocomposites (PNCs) are often attributed to immobilized (adsorbed) polymers at nanoparticle-polymer interfaces, which are responsible for reducing the intrinsic incompatibility between nanoparticles and polymers in PNCs. Although tremendous effort has been made to characterize the presence of immobilized polymers, a systematic understanding of the structure and dynamics under different processing conditions is still lacking. Here, we report that the initial dispersing solvent, which is not present after producing PNCs, drives these nonequilibrium effects on polymer chain dynamics at interfaces. Employing extensive small-angle scattering, proton NMR spectroscopy, and rheometry experiments, we found that the thickness of the immobilized layer can be dependent on the initial solvent, changing the structure and the properties of the PNC significantly. In addition, we show that the outcome of the initial solvent effect becomes more effective at particle volume fractions where the immobile layers begin to interact.

Inserting a rigid object into a soft elastic tube produces conformal contact between the two, resulting in contact lines. The curvature of the tube walls near these contact lines is often large and is typically regularized by the finite bending rigidity of the tube. Here, it is demonstrated using experiments and a Föppl–von Kármán–like theory that a second, independent, mechanism of curvature regularization occurs when the tube is axially stretched. In contrast with the effects of finite bending rigidity, the radius of curvature obtained increases with the applied stretching force and decreases with sheet thickness. The dependence of the curvature on a suitably rescaled stretching force is found to be universal, independent of the shape of the intruder, and results from an interplay between the longitudinal stresses due to the applied stretch and hoop stresses characteristic of curved geometry. These results suggest that curvature measurements can be used to infer the mechanical properties of stretched tubular structures.

Transport properties of a hard-sphere colloidal fluid are investigated by Brownian dynamics simulations. We implement a novel algorithm for the time-dependent velocity-autocorrelation function (VACF) essentially eliminating the noise of the bare random motion. The measured VACF reveals persistent anti-correlations manifested by a negative algebraic power-law tail $t^{-5/2}$ at all densities. At small packing fractions the simulations fully agree with the analytic low-density prediction, yet the amplitude of the tail becomes dramatically suppressed as the packing fraction is increased. The mode-coupling theory of the glass transition provides a qualitative explanation for the strong variation in terms of the static compressibility as well as the slowing down of the structural relaxation.