We formulate a theory for the phase reduction of a beating flagellum. The theory enables us to describe the dynamics of a beating flagellum in a systematic manner using a single variable called the phase. The theory can also be considered as a phase reduction method for the limit-cycle solutions in infinite-dimensional dynamical systems, namely, the limit-cycle solutions to partial differential equations representing beating flagella. We derive the phase sensitivity function, which quantifies the phase response of a beating flagellum to weak perturbations applied at each point and at each time. Using the phase sensitivity function, we analyze the phase synchronization between a pair of beating flagella through hydrodynamic interactions at a low Reynolds number.

We present a degree-based theoretical framework to study the susceptible-infected-susceptible (SIS) dynamics on time-varying (rewired) configuration model networks. Using this framework on a given degree distribution, we provide a detailed analysis of the stationary state using the rewiring rate to explore the whole range of the time variation of the structure relative to that of the SIS process. This analysis is suitable for the characterization of the phase transition and leads to three main contributions: (1) We obtain a self-consistent expression for the absorbing-state threshold, able to capture both collective and hub activation. (2) We recover the predictions of a number of existing approaches as limiting cases of our analysis, providing thereby a unifying point of view for the SIS dynamics on random networks. (3) We obtain bounds for the critical exponents of a number of quantities in the stationary state. This allows us to reinterpret the concept of hub-dominated phase transition. Within our framework, it appears as a heterogeneous critical phenomenon: observables for different degree classes have a different scaling with the infection rate. This phenomenon is followed by the successive activation of the degree classes beyond the epidemic threshold.

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.

We study the effect of exponentially correlated noise on the $xy$ model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time $\tau$, indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.

A planar colloidal monolayer exhibits anomalous collective diffusion due to the hydrodynamic interactions. We investigate how this behavior is affected by the curvature of the monolayer when it resides on the interface of a spherical droplet. It is found that the characteristic times of the dynamics still exhibit the same anomalous scaling as in the planar case. The spatial distribution, however, shows a difference due to the relevance of the radius of the droplet. Since for the droplet this is both a global magnitude, i.e., pertaining to the spatial extent of the spherical surface, and a local one, i.e., the radius of curvature, the question remains open as to which of these two features actually dominates in the case of a generically curved interface.

We present a derivation of the triple-line kinetic boundary conditions for a solid film in contact with a solid substrate for both nonconserved (evaporation-condensation) and conserved (surface diffusion) dynamics. The result is obtained via a matched asymptotic expansion from a mesoscopic model with a thickness-dependent wetting potential (or disjoining pressure) and mobility. In the nonconserved case, we obtain a single boundary condition, which relates the triple-line velocity with the deviation of the contact angle from its equilibrium value. In the conserved case, two kinetic boundary conditions are needed. They relate the velocity and mass flux at the triple line to the contact angle deviation and discontinuity of the chemical potential. These linear relations are described by three kinetic coefficients. The conditions under which the kinetic coefficients remain finite are obtained. We find, for example, that some kinetic coefficients diverge within the conserved model in the presence of van der Waals interaction.

We introduce the frugal foraging model in which a forager performs a discrete-time random walk on a lattice in which each site initially contains $\mathcal{S}$ food units. The forager metabolizes one unit of food at each step and starves to death when it last ate $\mathcal{S}$ steps in the past. Whenever the forager eats, it consumes all food at its current site and this site remains empty forever (no food replenishment). The crucial property of the forager is that it is frugal and eats only when encountering food within at most $k$ steps of starvation. We compute the average lifetime analytically as a function of the frugality threshold and show that there exists an optimal strategy, namely, an optimal frugality threshold $k^{*}$ that maximizes the forager lifetime.

We investigate the heat transport between two nonthermal reservoirs based on a microscopic collision model. We consider a bipartite system consisting of two identical subsystems, and each subsystem interacts with its own local reservoir, which consists of a large collection of initially uncorrelated ancillas. Then a heat transport is formed between two reservoirs by a sequence of pairwise collisions (intersubsystem and subsystem-local reservoir). In this paper we consider two kinds of the reservoir's initial states: the thermal state and the state with coherence whose diagonal elements are the same as that of the thermal state and the off-diagonal elements are nonzero. In this way, we define the effective temperature of the reservoir with coherence according to its diagonal elements. We find that for two reservoirs having coherence the direction of the steady current of heat is different for different phase differences between the two initial states of two reservoirs, especially the heat can transfer from the “cold reservoir” to the “hot reservoir” in the steady regime for particular phase difference. In the limit of the effective temperature difference between the two reservoirs $\mathrm{\Delta }T\to 0$, for most of the phase differences, the steady heat current increases with the increase of effective temperature until it reaches the high effective temperature limit, while for the thermal state or particular phase difference the steady heat current decreases with the increase of temperature at high temperatures, and in this case the conductance can be obtained.

We study diffusion-controlled two-species annihilation with a finite number of particles. In this stochastic process, particles move diffusively, and when two particles of opposite type come into contact, the two annihilate. We focus on the behavior in three spatial dimensions and for initial conditions where particles are confined to a compact domain. Generally, one species outnumbers the other, and we find that the difference between the number of majority and minority species, which is a conserved quantity, controls the behavior. When the number difference exceeds a critical value, the minority becomes extinct and a finite number of majority particles survive, while below this critical difference, a finite number of particles of both species survive. The critical difference ${\mathrm{\Delta }}_c$ grows algebraically with the total initial number of particles $N$, and when $N\gg 1$, the critical difference scales as ${\mathrm{\Delta }}_c\sim N^{1/3}$. Furthermore, when the initial concentrations of the two species are equal, the average number of surviving majority and minority particles, $M_{+}$ and $M_{-}$, exhibit two distinct scaling behaviors, $M_{+}\sim N^{1/2}$ and $M_{-}\sim N^{1/6}$. In contrast, when the initial populations are equal, these two quantities are comparable $M_{+}\sim M_{-}\sim N^{1/3}$.

In real-world networked systems, the underlying structure is often affected by external and internal unforeseen factors, making its evolution typically inaccessible. An adaptive strategy was introduced for maintaining synchronization on unpredictably evolving networks [Sorrentino and Ott, Phys. Rev. Lett. 100, 114101 (2008)], which yet does not consider the noise disturbances widely existing in networks' environments. We provide here strategies to control dynamical synchronization on slowly and unpredictably evolving networks subjected to noise disturbances which are observed at the node and at the communication channel level. With our strategy, the nodes' coupling strength is adaptively adjusted with the aim of controlling synchronization, and according only to their received signal and noise disturbances. We first provide a theoretical analysis of the control scheme by introducing an error potential function to seek for the minimization of the synchronization error. Then, we show numerical experiments which verify our theoretical results. In particular, it is found that our adaptive strategy is effective even for the case in which the dynamics of the uncontrolled network would be explosive (i.e., the states of all the nodes would diverge to infinity).

Regulation of transcription is a vital process in cells, but mechanistic details of this regulation still remain elusive. The dominant approach to unravel the dynamics of transcriptional regulation is to first develop mathematical models of transcription and then experimentally test the predictions these models make for the distribution of mRNA and protein molecules at the individual cell level. However, these measurements are affected by a multitude of downstream processes which make it difficult to interpret the measurements. Recent experimental advancements allow for counting the nascent mRNA number of a gene as a function of time at the single-cell level. These measurements closely reflect the dynamics of transcription. In this paper, we consider a general mechanism of transcription with stochastic initiation and deterministic elongation and probe its impact on the temporal behavior of nascent RNA levels. Using techniques from queueing theory, we derive exact analytical expressions for the mean and variance of the nascent RNA distribution as functions of time. We apply these analytical results to obtain the mean and variance of nascent RNA distribution for specific models of transcription. These models of initiation exhibit qualitatively distinct transient behaviors for both the mean and variance which further allows us to discriminate between them. Stochastic simulations confirm these results. Overall the analytical results presented here provide the necessary tools to connect mechanisms of transcription initiation to single-cell measurements of nascent RNA.

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forward stepping in a narrow window in configuration space is needed for generating high power at physiologically relevant loads. By deriving general thermodynamics laws for nonequilibrium motors, we find that the maximum torque (force) at stall is less than its theoretical limit for any realistic motor-track interactions due to speed fluctuations. Our study reveals a tradeoff for the motor-track interaction: while a strong interaction generates a high power output for forward steps, it also leads to a higher probability of wasteful spontaneous back steps. Our analysis and simulations show that this tradeoff sets a fundamental limit to the maximum motor efficiency in the presence of spontaneous back steps, i.e., loose-coupling. Balancing this tradeoff leads to an optimal design of the motor-track interaction for achieving a maximum efficiency close to 1 for realistic motors that are not perfectly coupled with the energy source. Comparison with existing data and suggestions for future experiments are discussed.

We investigate the structural, thermodynamic, and dynamic behavior of a two-dimensional (2D) core-corona system using Langevin dynamics simulations. The particles are modeled by employing a core-softened potential which exhibits waterlike anomalies in three dimensions. In previous studies in a quasi-2D system a new region in the pressure versus temperature phase diagram of structural anomalies was observed. Here we show that for the two-dimensional case two regions in the pressure versus temperature phase diagram with structural, density, and diffusion anomalies are observed. Our findings indicate that, while the anomalous region at lower densities is due the competition between the two length scales in the potential at higher densities, the anomalous region is related to the reentrance of the melting line.

In this paper, we have investigated the behavior of mesogens at smectic-C*–water interface confined in a liquid crystal (LC) cell with interfacial geometry. Polarized optical microscopy was used to probe the appearance of various smectic-C* domain patterns at water interface owing to the reorientation of mesogens. The undulated stripe domains observed at the air interface of smectic-C* meniscus vanished as the water entered into the smectic layers and focal conical domain patterns appeared at smectic-C*–water boundary. A spatially variable electro-optical switching of LC molecules was also observed outside the electrode area of the interfacial cell. The electrode region at the interface, as well as on the water side, was damaged upon application of an electric field of magnitude more than 150 kV/m. The change in dielectric parameters of mesogens was extensively studied at interface after evaporating the water. These studies give fundamental insights into smectic-C*–water interface and also will be helpful in fabricating better LC devices for electro-optical and sensing applications.

In a dry granular flow, size segregation had been shown to behave differently for a mixture containing a few large particles with a size ratio above 5 [N. Thomas, Phys. Rev. E 62, 961 (2000)]. For moderately large size ratios, large particles migrate to an intermediate depth in the bed: this is called “intermediate segregation.” For the largest size ratios, large particles migrate down to the bottom of the flow: this is called “reverse segregation,” in contrast with surface segregation. As the reversal and intermediate depth values depend on the fraction of particles, this numerical study mainly uses one single large tracer. Small fractions of large beads are also computed showing the link between single tracer behavior and collective segregation process. For each device (half-filled rotating tumbler and rough plane), two (2D) and three (3D) dimensional cases are distinguished. In the tumbler, the trajectories of a large tracer show that it reaches a constant depth during the flowing phase. For large size ratios, this depth is intermediate. A progressive sinking of the depth is obtained when the size ratio is increased. The largest size ratios correspond to tracers being at the bottom of the flowing layer. All 3D simulation results are in quantitative agreement with the experimental surface, intermediate, and reverse-segregation results. In the flow down a rough incline, a large tracer reaches an equilibrium depth during flow. For large size ratios, the depth is inside the bed, at an intermediate position, and for the largest size ratios, this depth is reverse, located near the bottom. Results are slightly different for a thin or a thick flow. For 3D thick flows, the reversal between surface and bottom positions occurs within a short range of size ratios: no tracer stabilizes near half-height and two reachable intermediate depth layers exist, below the surface and above the bottom reverse layer. For 3D thin flows, all intermediate depths are reachable by a tracer, depending on the size ratio. The numerical study of larger fractions of tracers (5% or 10%) shows the three segregation patterns (surface, intermediate, reverse) corresponding to the three types of equilibrium depth. The reversal is smoother than for a single tracer, and happens around the size ratio 4.5, in good agreement with experiments.

Signal transduction networks can form highly interconnected systems within cells due to crosstalk between constituent pathways. To better understand the evolutionary design principles underlying such networks, we study the evolution of crosstalk for two parallel signaling pathways that arise via gene duplication. We use a sequence-based evolutionary algorithm and evolve the network based on two physically motivated fitness functions related to information transmission. We find that one fitness function leads to a high degree of crosstalk while the other leads to pathway specificity. Our results offer insights on the relationship between network architecture and information transmission for noisy biomolecular networks.

Recent studies on topological defects in conventional and active nematic liquid crystals have revealed their potential as sources of advanced functionality whereby the collective behavior of the constituent molecules or cells is controlled. On the other hand, the fact that they have high energies and are metastable makes their shape control a nontrivial issue. Here, we demonstrate stabilization of arbitrary-shaped closed disclination loops with 1/2 strength floating in the bulk by designing the twist angle distribution in a liquid crystal cell. Continuous variation of the twist angle from below to above $\left|\pi /2\right|$ allows us to unambiguously position reverse twist disclinations at will. We also analyze the elastic free energy and uncover the relationship between the twist angle pattern and shrink rate of the surface-stabilized disclination loop.

We develop a theory based on the method of collective variables to study the vapor-liquid equilibrium of asymmetric ionic fluids confined in a disordered porous matrix. The approach allows us to formulate the perturbation theory using an extension of the scaled particle theory for a description of a reference system presented as a two-component hard-sphere fluid confined in a hard-sphere matrix. Treating an ionic fluid as a size- and charge-asymmetric primitive model (PM) we derive an explicit expression for the relevant chemical potential of a confined ionic system which takes into account the third-order correlations between ions. Using this expression, the phase diagrams for a size-asymmetric PM are calculated for different matrix porosities as well as for different sizes of matrix and fluid particles. It is observed that general trends of the coexistence curves with the matrix porosity are similar to those of simple fluids under disordered confinement, i.e., the coexistence region gets narrower with a decrease of porosity and, simultaneously, the reduced critical temperature $T_c^{*}$ and the critical density ${\rho }_{i,c}^{*}$ become lower. At the same time, our results suggest that an increase in size asymmetry of oppositely charged ions considerably affects the vapor-liquid diagrams leading to a faster decrease of $T_c^{*}$ and ${\rho }_{i,c}^{*}$ and even to a disappearance of the phase transition, especially for the case of small matrix particles.

We present an approach to achieve adaptable band structures and nonreciprocal wave propagation by exploring and exploiting the concept of metastable modular metastructures. Through studying the dynamics of wave propagation in a chain composed of finite metastable modules, we provide experimental and analytical results on nonreciprocal wave propagation and unveil the underlying mechanisms that facilitate such unidirectional energy transmission. In addition, we demonstrate that via transitioning among the numerous metastable states, the proposed metastructure is endowed with a large number of bandgap reconfiguration possibilities. As a result, we illustrate that unprecedented adaptable nonreciprocal wave propagation can be realized using the metastable modular metastructure. Overall, this research elucidates the rich dynamics attainable through the combinations of periodicity, nonlinearity, spatial asymmetry, and metastability and creates a class of adaptive structural and material systems capable of realizing tunable bandgaps and nonreciprocal wave transmissions.