Collagen consists of three peptides twisted together through a periodic array of hydrogen bonds. Here we use this as inspiration to find design rules for programmed specific interactions for self-assembling synthetic collagenlike triple helices, starting from disordered configurations. The assembly generically nucleates defects in the triple helix, the characteristics of which can be manipulated by spatially varying the enthalpy of helix formation. Defect formation slows assembly, evoking kinetic pathologies that have been observed to mutations in the primary collagen amino acid sequence. The controlled formation and interaction between defects gives a route for hierarchical self-assembly of bundles of twisted filaments.

We address the question of how interacting active systems in a nonequilibrium steady state respond to an external perturbation. We establish an extended fluctuation-dissipation theorem for active Brownian particles (ABP), which highlights the role played by the local violation of detailed balance due to activity. By making use of a Markovian approximation we derive closed Green-Kubo expressions for the diffusivity and mobility of ABP and quantify the deviations from the Stokes-Einstein relation. We compute the linear response function to an external force using unperturbed simulations of ABP and compare the results with the analytical predictions of the transport coefficients. Our results show the importance of the interplay between activity and interactions in the departure from equilibrium linear response.

The swimming of a rigid phoretic particle in an isotropic fluid is studied numerically as a function of the dimensionless solute emission rate (or Péclet number Pe). The particle sets into motion at a critical Pe. Whereas the particle trajectory is straight at a small enough Pe, it is found that it loses its stability at a critical Pe in favor of a meandering motion. When Pe is increased further, the particle meanders at a short scale but its trajectory wraps into a circle at a larger scale. Increasing even further, Pe causes the swimmer to escape momentarily the circular trajectory in favor of chaotic motion, which lasts for a certain time, before regaining a circular trajectory, and so on. The chaotic bursts become more and more frequent as Pe increases, until the trajectory becomes fully chaotic, via the intermittency scenario. The statistics of the trajectory is found to be of the run-and-tumble-like nature at a short enough time and of diffusive nature at a long time without any source of noise.

We employ a matrix-based solver for the linear rheology of fluid-immersed disordered spring networks to reveal four distinct dynamic response regimes. One regime—completely absent in the known vacuum response—exhibits coupled fluid flow and network deformation, with both components responding nonaffinely. This regime contains an additional plateau (peak) in the frequency-dependent storage (loss) modulus—features that vanish without full hydrodynamic interactions. The mechanical response of immersed networks such as biopolymers and hydrogels is thus richer than previously established and offers additional modalities for design and control through fluid interactions.

We present a complete analysis of the linearized dynamics of active solids with uniaxial orientational order, taking into account a hitherto overlooked consequence of rotation invariance. Our predictions include a purely active response of two-dimensional orientationally ordered solids to shear, the possibility of stable active solids with quasi-long-range order in two dimensions and long-range order in three dimensions, generic instability of the solid for one sign of active forcing, and the instability of the uniaxially ordered phase in momentum-conserved systems for large active forcing irrespective of its sign.

Unlike in thermodynamic equilibrium where coexisting phases always have the same temperature, here we show that systems comprising “active” self-propelled particles can self-organize into two coexisting phases at different kinetic temperatures, which are separated from each other by a sharp and persistent temperature gradient. Contrasting previous studies that have focused on overdamped descriptions of active particles, we show that a “hot-cold coexistence” occurs if and only if accounting for inertia, which is significant, e.g., in activated dusty plasmas, microflyers, whirling fruits, or beetles at interfaces. Our results exemplify a route to use active particles to create a self-sustained temperature gradient across coexisting phases. This phenomenon is fundamentally beyond equilibrium physics and is accompanied by a slow coarsening law with an exponent significantly smaller than the universal $1/3$ exponent seen in both equilibrium systems and overdamped active Brownian particles.

Understanding the spatial organization of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical—or epigenetic—marks that are deposited along the genome are thought to play an important, yet poorly understood, role in determining genome organization and cell identity. The physical principles underlying the interplay between epigenetic dynamics and genome folding remain elusive. Here we propose and study a theory that assumes a coupling between epigenetic mark and genome densities, and which can be applied at the scale of the whole nucleus. We show that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for nonequilibrium processes that can stabilize microphase separated epigenomic domains. We finally discuss the potential biophysical origin of these terms.

Biological function requires cell-cell adhesions to tune their cohesiveness; for instance, during the opening of new fluid-filled cavities under hydraulic pressure. To understand the physical mechanisms supporting this adaptability, we develop a stochastic model for the hydraulic fracture of adhesive interfaces bridged by molecular bonds. We find that surface tension strongly enhances the stability of these interfaces by controlling flaw sensitivity, lifetime, and optimal architecture in terms of bond clustering. We also show that bond mobility embrittles adhesions and changes the mechanism of decohesion. Our study provides a mechanistic background to understand the biological regulation of cell-cell cohesion and fracture.

We experimentally analyze the intermittent nature of granular silo flow when the discharge is controlled by an extracting belt at the bottom. We discover the existence of four different scenarios. For low extraction rates, the system is characterized by an on-off intermittency. When the extraction rate is increased the structure functions of the grains velocity increments, calculated for different lag times, reveal the emergence of multifractal intermittency. Finally, for very high extraction rates that approach the purely gravitational discharge, we observe that the dynamics become dependent on the outlet size. For large orifices the behavior is monofractal, whereas for small ones, the fluctuations of the velocity increments deviate from Gaussianity even for very large time lags.

We develop an iterated map model to describe the bifurcations and complex dynamics caused by the feedback between voltage and intracellular ${\mathrm{Ca}}^{2+}$ and ${\mathrm{Na}}^{+}$ concentrations in paced ventricular myocytes. Voltage and ${\mathrm{Ca}}^{2+}$ can form either a positive or a negative feedback loop, while voltage and ${\mathrm{Na}}^{+}$ form a negative feedback loop. Under certain diseased conditions, when the feedback between voltage and ${\mathrm{Ca}}^{2+}$ is positive, Hopf bifurcations occur, leading to periodic oscillatory behaviors. When this feedback is negative, period-doubling bifurcation routes to alternans and chaos occur.

Stress relaxation upon cessation of shear flow is known to be described by single-mode or multimode monotonic exponential decays. This is considered to be ubiquitous in nature. However, we found that, in some cases, the relaxation becomes anomalous in that an increase in the relaxing stress is observed. Those observations were made for physicochemically very different systems, having in common, however, the presence of self-associating units generating structures at large length scales. The nonmonotonic stress relaxation can be described phenomenologically by a generic model based on a redistribution of energy after the flow has stopped. When broken bonds are reestablished after flow cessation, the released energy is partly used to locally increase the elastic energy by the formation of deformed domains. If shear has induced order such that these elastic domains are partly aligned, the reestablishing of bonds gives rise to an increase of the overall stress.

We consider a model of an elastic manifold driven on a disordered energy landscape, with generalized long range elasticity. Varying the form of the elastic kernel by progressively allowing for the existence of zero modes, the model interpolates smoothly between mean-field depinning and finite dimensional yielding. We find that the critical exponents of the model change smoothly in this process. Also, we show that in all cases the Herschel-Buckley exponent of the flow curve depends on the analytical form of the microscopic pinning potential. Within the present elastoplastic description, all this suggests that yielding in finite dimensions is a mean-field transition.

To explore charge regulation (CR) in physicochemical and biophysical systems, we present a model of colloidal particles with sticky adsorption sites which account for the formation of covalent bonds between the hydronium ions and the surface functional groups. Using this model and Monte Carlo simulations, we find that the standard Ninham and Parsegian (NP) theory of CR leads to results which deviate significantly from computer simulations. The problem with the NP approach is traced back to the use of a bulk equilibrium constant to account for surface chemical reactions. To resolve this difficulty we present a new theory of CR. The fundamental ingredient of the new approach is the sticky length, which is nontrivially related to the bulk equilibrium constant. The theory is found to be in excellent agreement with computer simulations, without any adjustable parameters. As an application of the theory we calculate the effective charge of colloidal particles containing carboxyl groups, as a function of $p\mathrm{H}$ and salt concentration.

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain model to include statistically spaced, rigid kinks. On timescales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can vary by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer timescales, we show that continuous rerandomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that nucleosome spacing acts as the primary source of the structural heterogeneity that dominates local and global chromatin organization.

We demonstrate by molecular simulations that the Ostwald ripening of crystalline polymer nuclei within the fast-evaporation-induced 2D skin layer is retarded at suitable temperatures and evaporation rates. Such an anomalous ripening can be attributed to the interplay between the thermodynamically driven diffusion of noncrystalline fragments toward the growing nuclei and the diffusive current away from the free surface caused by the densification in the nonequilibrium skin layer. The growth orientation of the nuclei inside the skin plane can be adjusted during this anomalous ripening process, which is beneficial for fabricating 2D polymer crystals.

We present a generic framework for modeling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding environment. We find that the cross talk between the self-induced flows of active particles and dynamic reshaping of the shell can result in conformations that are tunable by varying the form and magnitude of active stresses. We further demonstrate and explain how self-induced topological defects in the active layer can direct the morphodynamics of the shell. These findings are relevant to understanding morphological changes during organ development and the design of bioinspired materials that are capable of self-organization.