Aging transition is an emergent behavior observed in networks consisting of active (self-oscillatory) and inactive (non-self-oscillatory) nodes, where the network transits from a global oscillatory state to an oscillation collapsed state when the fraction of inactive oscillators surpasses a critical value. However, the aging transition in quantum domain has not been studied yet. In this paper we investigate the quantum manifestation of aging transition in a network of active-inactive quantum oscillators. We show that, unlike classical case, the quantum aging is not characterized by a complete collapse of oscillation but by sufficient reduction in the mean boson number. We identify a critical “knee” value in the fraction of inactive oscillators around which quantum aging occurs in two different ways. Further, in stark contrast to the classical case, quantum aging transition depends upon the nonlinear damping parameter. We also explain the underlying processes leading to quantum aging that have no counterpart in the classical domain.

We study the dynamic structure factor of fluctuating elastic thin sheets subject to conservative (athermal) random forcing. In Steinbock et al. [Phys. Rev. Res. 4, 033096 (2022)] the static structure factor of such a sheet was studied. In this paper we recap the model developed there and investigate its dynamic properties. Using the self-consistent expansion, the time-dependent two-point function of the height profile is determined and found to decay exponentially in time. Despite strong nonlinear coupling, the decay rate of the dynamic structure factor is found to coincide with the effective coupling constant for the static properties, which suggests that the model under investigation exhibits certain quasilinear behavior. Confirmation of these results by numerical simulations is also presented.

Active fluctuations are detected in a growing number of systems due to self-propulsion mechanisms or collisions with an active environment. They drive the system far from equilibrium and can induce phenomena that are forbidden at equilibrium states by, e.g., fluctuation-dissipation relations and detailed balance symmetry. Understanding their role in living matter is emerging as a challenge for physics. Here we demonstrate a paradoxical effect in which a free-particle transport induced by active fluctuations can be boosted by many orders of magnitude when the particle is additionally subjected to a periodic potential. In contrast, within the realm of only thermal fluctuations, the velocity of a free particle exposed to a bias is reduced when the periodic potential is switched on. The presented mechanism is significant for understanding nonequilibrium environments such as living cells, where it can explain from a fundamental point of view why spatially periodic structures known as microtubules are necessary to generate impressively effective intracellular transport. Our findings can be readily corroborated experimentally, e.g., in a setup comprising a colloidal particle in an optically generated periodic potential.

In the present work we revisit the Salerno model as a prototypical system that interpolates between a well-known integrable system (the Ablowitz-Ladik lattice) and an experimentally tractable, nonintegrable one (the discrete nonlinear Schrödinger model). The question we ask is, for “generic” initial data, how close are the integrable to the nonintegrable models? Our more precise formulation of this question is, How well is the constancy of formerly conserved quantities preserved in the nonintegrable case? Upon examining this, we find that even slight deviations from integrability can be sensitively felt by measuring these formerly conserved quantities in the case of the Salerno model. However, given that the knowledge of these quantities requires a deep physical and mathematical analysis of the system, we seek a more “generic” diagnostic towards a manifestation of integrability breaking. We argue, based on our Salerno model computations, that the full spectrum of Lyapunov exponents could be a sensitive diagnostic to that effect.

We report on experimental studies of the distribution of the reflection coefficients, and the imaginary and real parts of Wigner's reaction ($K$) matrix employing open microwave networks with symplectic symmetry and varying size of absorption. The results are compared to analytical predictions derived for the single-channel scattering case within the framework of random-matrix theory (RMT). Furthermore, we performed Monte Carlo simulations based on the Heidelberg approach for the scattering ($S$) and $K$ matrix of open quantum-chaotic systems and the two-point correlation function of the $S$-matrix elements. The analytical results and the Monte Carlo simulations depend on the size of absorption. To verify them, we performed experiments with microwave networks for various absorption strengths. We show that deviations from RMT predictions observed in the spectral properties of the corresponding closed quantum graph and attributed to the presence of nonuniversal short periodic orbits does not have any visible effects on the distributions of the reflection coefficients and the $K$ and $S$ matrices associated with the corresponding open quantum graph.

Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on square lattices at which each node is embedded a loop which forms a Borromean link with pairs of its nearest neighbors. By mapping the Borromean link network onto a lattice representation, we investigate the percolation threshold of these networks (the fraction of occupied nodes required for a giant component), as well as the dissolution properties: the spectrum of topological links that would be released if the network were dissolved to varying degrees. We find that the percolation threshold of the Borromean square lattice occurs when approximately 60.75% of nodes are occupied, slightly higher than the 59.27% typical of a square lattice. Compared to the dissolution of Hopf-linked networks, a dissolved Borromean network will yield more isolated loops, and fewer isolated triplets per single loop. Our simulation results may be used to predict experiments from Borromean structures produced by synthetic chemistry.

Mechanical force has been widely used to study RNA folding and unfolding. Understanding how the force affects the opening and closing of a single base pair, which is a basic step for RNA folding and unfolding and a fundamental behavior in some important biological activities, is crucial to understanding the mechanism of RNA folding and unfolding under mechanical force. In this work, we investigated the opening and closing process of an RNA base pair under mechanical force with constant-force stretching molecular dynamics simulations. It was found that high mechanical force results in overstretching, and the open state is a high-energy state. The enthalpy and entropy change of the base-pair opening-closing transition were obtained and the results at low forces were in good agreement with the nearest-neighbor model. The temperature and force dependence of the opening and closing rates were also obtained. The position of the transition state for the base-pair opening-closing transition under mechanical force was determined. The free energy barrier of opening a base pair without force is the enthalpy increase, and the work done by the force from the closed state to the transition state decreases the barrier and increases the opening rate. The free energy barrier of closing the base pair without force results from the entropy loss, and the work done by the force from the open state to the transition state increases the barrier and decreases the closing rate. The transition rates are strongly dependent on the temperature and force, while the transition path times are weakly dependent on force and temperature.

The morphology and motion behavior of a cell are highly influenced by its external biological, chemical, and physical stimuli, and geometric confinement. In this paper, it is revealed that the mean curvature of the substrate significantly influences the adhesion of vesicles. By employing the variational method and investigating the Helfrich free energy, the configuration of axisymmetric vesicles adhered to curved spherical substrates is obtained theoretically. Moreover, numerical simulations based on the finite element method are also carried out to investigate the adhesion of vesicles on curved substrates with complex shapes. It is found that for a fixed area of a vesicle, its total free energy depends mainly on the mean curvature of the adhesion region but is insensitive to the specific shape of the substrate, and the total free energy monotonically decreases with the increase in the mean curvature. In addition, possible biological significances of the curvature-dependent adhesion, such as the shape of the cell and antibiofouling, are discussed. This study may deepen our understanding of the underlying mechanisms of adhesion in cellular activities.

Disordered mechanical systems can deform along a network of pathways that branch and recombine at special configurations called bifurcation points. Multiple pathways are accessible from these bifurcation points; consequently, computer-aided design algorithms have been sought to achieve a specific structure of pathways at bifurcations by rationally designing the geometry and material properties of these systems. Here, we explore an alternative physical training framework in which the topology of folding pathways in a disordered sheet is changed in a desired manner due to changes in crease stiffnesses induced by prior folding. We study the quality and robustness of such training for different “learning rules,” that is, different quantitative ways in which local strain changes the local folding stiffness. We experimentally demonstrate these ideas using sheets with epoxy-filled creases whose stiffnesses change due to folding before the epoxy sets. Our work shows how specific forms of plasticity in materials enable them to learn nonlinear behaviors through their prior deformation history in a robust manner.

In plasmas, electronic states can be well-localized bound states or itinerant free states, or something in between. In self-consistent treatments of plasma electronic structure such as the average-atom model, all states must be accurately resolved in order to achieve a converged numerical solution. This is a challenging numerical and algorithmic problem in large part due to the continuum of free states which is relatively expensive and difficult to resolve accurately. Siegert states are an appealing alternative. They form a complete eigenbasis with a purely discrete spectrum while still being equivalent to a representation in terms of the usual bound states and free states. However, many of their properties are unintuitive, and it is not obvious that they are suitable for self-consistent plasma electronic structure calculations. Here it is demonstrated that Siegert states can be used to accurately solve an average-atom model and offer advantages over the traditional finite-difference approach, including a concrete physical picture of pressure ionization and continuum resonances.

Intense surface eruptions are observed along the curved surface of a confined cylindrical film of hydrogel subject to laser-induced converging-diverging shock loading. Detailed numerical simulations are used to identify the dominant mechanisms causing mechanical instability. The mechanisms that produce surface instability are found to be fundamentally different from both acoustic parametric instability and shock-driven Richtmyer-Meshkov instability. The time scale of observed and simulated eruption formation is much larger than that of a single shock reflection, in stark contrast to previously studied shock-driven instabilities. Moreover, surface undulations are only found along external, as opposed to internal, soft solid boundaries. Specifically, classic bubble surface instability mechanisms do not occur in our experiments and here we comment only on the new surface undulations found along the outer boundary of solid hydrogel cylinders. Our findings indicate a new class of impulsively excited surface instability that is driven by cycles of internal shock reflections.

The expanding medium is very common in many different fields, such as biology and cosmology. It brings a nonnegligible influence on particle's diffusion, which is quite different from the effect of an external force field. The dynamic mechanism of a particle's motion in an expanding medium has only been investigated in the framework of a continuous-time random walk. To focus on more diffusion processes and physical observables, we build the Langevin picture of anomalous diffusion in an expanding medium, and conduct detailed analyses in the framework of the Langevin equation. With the help of a subordinator, both subdiffusion process and superdiffusion process in the expanding medium are discussed. We find that the expanding medium with different changing rate (exponential form and power-law form) leads to quite different diffusion phenomena. The particle's intrinsic diffusion behavior also plays an important role. Our detailed theoretical analyses and simulations present a panoramic view of investigating anomalous diffusion in an expanding medium under the framework of the Langevin equation.

We analyze the scaled voter model, which is a generalization of the noisy voter model with time-dependent herding behavior. We consider the case when the intensity of herding behavior grows as a power-law function of time. In this case, the scaled voter model reduces to the usual noisy voter model, but it is driven by the scaled Brownian motion. We derive analytical expressions for the time evolution of the first and second moments of the scaled voter model. In addition, we have derived an analytical approximation of the first passage time distribution. By numerical simulation, we confirm our analytical results as well as showing that the model exhibits long-range memory indicators despite being a Markov model. The proposed model has steady-state distribution consistent with the bounded fractional Brownian motion, thus we expect it to be a good substitute model for the bounded fractional Brownian motion.

According to the evolutionary death-birth protocol, a player is chosen randomly to die and neighbors compete for the available position proportional to their fitness. Hence, the status of the focal player is completely ignored and has no impact on the strategy update. In this paper, we revisit and generalize this rule by introducing a weight factor to compare the payoff values of the focal and invading neighbors. By means of evolutionary graph theory, we analyze the model on joint transitive graphs to explore the possible consequences of the presence of a weight factor. We find that focal weight always hinders cooperation under weak selection strength. Surprisingly, the results show a nontrivial tipping point of the weight factor where the threshold of cooperation success shifts from positive to negative infinity. Once focal weight exceeds this tipping point, cooperation becomes unreachable. Our theoretical predictions are confirmed by Monte Carlo simulations on a square lattice of different sizes. We also verify the robustness of the conclusions to arbitrary two-player prisoner's dilemmas, to dispersal graphs with arbitrary edge weights, and to interaction and dispersal graphs overlapping arbitrarily.

Calcium oscillation is an important calcium homeostasis, imbalance of which is the key mechanism of initiation and progression of many major diseases. The formation and maintenance of calcium homeostasis are closely related to the spatial distribution of calcium channels on endoplasmic reticulum, whose complex structure was unveiled by recent observations with superresolution imaging techniques. In the current paper, a theoretical framework is established by abstracting the spatial distribution of the calcium channels as a nonlinear biological complex network with calcium channels as nodes and ${\mathrm{Ca}}^{2+}$ as edges. A dynamical model for a ryanodine receptor (RyR) is adopted to investigate the effect of spatial distribution on calcium oscillation. The mean-field model can be well reproduced from the complete graph and dense Erdös-Rényi network. The synchronization of RyRs is found important to generate a global calcium oscillation. Below a critical density of the Erdös-Rényi or BaraBási-Albert network, the amplitude and interspike interval decrease rapidly with the end of disappearance of oscillation due to the desynchronization. The clique graph with a cluster structure cannot produce a global oscillation due to the failure of synchronization between clusters. A more realistic geometric network is constructed in a two-dimensional plane based on the experimental information about the RyR arrangement of clusters and the frequency distribution of cluster sizes. Different from the clique graph, the global oscillation can be generated with reasonable parameters on the geometric network. The simulation also suggests that existence of small clusters and rogue RyRs plays an important role in the maintenance of global calcium oscillation through keeping synchronization between large clusters. Such results support the heterogeneous distribution of RyRs with different-size clusters, which is helpful to understand recent observations with superresolution nanoscale imaging techniques. The current theoretical framework can also be extent to investigate other phenomena in calcium signal transduction.

Membrane proteins typically deform the surrounding lipid bilayer membrane, which can play an important role in the function, regulation, and organization of membrane proteins. Membrane elasticity theory provides a beautiful description of protein-induced lipid bilayer deformations, in which all physical parameters can be directly determined from experiments. While analytic solutions of protein-induced elastic bilayer deformations are most easily developed for proteins with approximately circular cross sections, structural biology has shown that membrane proteins come in a variety of distinct shapes, with often considerable deviations from a circular cross section. We develop here a boundary value method (BVM) that permits the construction of analytic solutions of protein-induced elastic bilayer deformations for protein shapes with arbitrarily large deviations from a circular cross section, for constant as well as variable boundary conditions along the bilayer-protein interface. We apply this BVM to protein-induced lipid bilayer thickness deformations. Our BVM reproduces available analytic solutions for proteins with circular cross section and yields, for proteins with noncircular cross section, excellent agreement with numerical, finite element solutions. On this basis, we formulate a simple analytic approximation of the bilayer thickness deformation energy associated with general protein shapes and show that, for modest deviations from rotational symmetry, this analytic approximation is in good agreement with BVM solutions. Using the BVM, we survey the dependence of protein-induced elastic bilayer thickness deformations on protein shape, and thus explore how the coupling of protein shape and bilayer thickness deformations affects protein oligomerization and transitions in protein conformational state.

Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete wormlike chain polymer as a function of the applied force has been calculated both numerically and analytically, the latter as an effective approximation. The numerical evaluation uses the transfer matrix formalism to obtain an exact calculation of the partition function, while the analytic derivations generalize the simple phenomenological formulas largely used up to now. The obtained formulas are simple enough to be implemented in the fit analysis of experimental data of semiflexible extensible polymers, with the result that the elastic parameters obtained are compatible with previous measurements, and more, their accuracy strongly improves in a large range of chain extensibility.

We study translocation of a flexible polymer chain through a membrane pore under the influence of active forces and steric exclusion using Langevin dynamics simulations within a minimal two-dimensional model. The active forces on the polymer are imparted by nonchiral and chiral active particles that are introduced on one side or both sides of a rigid membrane positioned across the midline of a confining box. We show that the polymer can translocate through the pore to either side of the dividing membrane in the absence of external forcing. Translocation of the polymer to a given side of the membrane is driven (hindered) by an effective pulling (pushing) exerted by the active particles that are present on that side. The effective pulling results from accumulation of active particles around the polymer. This crowding effect signifies persistent motion of active particles causing prolonged detention times for them close to the confining walls and the polymer. The effective pushing that hinders the translocation, on the other hand, results from steric collisions that occur between the polymer and active particles. As a result of the competition between these effective forces, we find a transition between two rectified cis-to-trans and trans-to-cis translocation regimes. This transition is identified by a sharp peak in the average translocation time. The effects of active particles on the transition is studied by analyzing how the translocation peak is regulated by the activity (self-propulsion) strength of these particles, their area fraction, and chirality strength.

This study aims to examine experimental conditions in which active particles are forced by their surroundings to move forward and backward in a continuous oscillatory manner. The experimental design is based on using a vibrating self-propelled toyrobot called hexbug, which is placed inside a narrow channel closed on one end by a rigid moving wall. Using the end-wall velocity as a controlling factor, the main forward mode of the hexbug movement can be turned to mostly rearward mode. We investigate the bouncing hexbug motion on both experimental and theoretical grounds. The Brownian model of active particles with inertia is employed in the theoretical framework. The model itself uses a pulsed Langevin equation in order to simulate abrupt changes in velocity that mimic hexbug propulsion in the moments when its legs make contact with the base plate. Significant directional asymmetry is caused by the legs bending backward. We demonstrate that the simulation successfully reproduces the experimental characteristics of hexbug motion after regressing the spatial and temporal statistical characteristics, especially when directional asymmetry is under consideration.

In equilibrium hard-rod fluids, and in effective hard-rod descriptions of anisotropic soft-particle systems, the transition from the isotropic (I) phase to the nematic phase (N) is observed above the rod aspect ratio $L/D=3.70$ as predicted by Onsager. We examine the fate of this criterion in a molecular dynamics study of a system of soft repulsive spherocylinders rendered active by coupling half the particles to a heat bath at a higher temperature than that imposed on the other half. We show that the system phase-separates and self-organizes into various liquid-crystalline phases that are not observed in equilibrium for the respective aspect ratios. In particular, we find a nematic phase for $L/D=3$ and a smectic phase for $L/D=2$ above a critical activity.