Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical framework for such a system is, therefore, important. Vertex-model (VM) simulations have provided crucial insights into the dynamics of such systems, but their nonequilibrium nature makes theoretical development difficult. The cellular Potts model (CPM) of confluent monolayers provides an alternative model for such systems with a well-defined equilibrium limit. We combine numerical simulations of the CPM and an analytical study based on one of the most successful theories of equilibrium glass, the random first-order transition theory, and develop a comprehensive theoretical framework for a confluent glassy system. We find that the glassy dynamics within the CPM is qualitatively similar to that in the VM. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeter $P_0$ is varied. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in such systems. The fragility of the system decreases with increasing $P_0$ in the low-$P_0$ regime, whereas the dynamics is independent of $P_0$ in the other regime. The rigidity transition, found in the VM, is absent within the CPM; this difference seems to come from the nonequilibrium nature of the former. We show that the CPM captures the basic phenomenology of glassy dynamics in a confluent biological system via comparison of our numerical results with existing experiments on different systems.

Several scenarios for the formation of hydrodynamic flows in microsized hybrid aligned nematic (HAN) channels, based on the appropriate nonlinear extension of the classical Ericksen-Leslie theory, supplemented by thermomechanical correction of the shear stress and Rayleigh dissipation function, as well as taking into account the entropy balance equation, are analyzed. Detailed numerical simulations were performed to elucidate the role of the heat flux $\mathbf{\text{q}}$ caused by laser radiation focused on the lower boundary of the equally warmed up the HAN channel containing a monolayer of azobenzene with the possibility of a trans-cis and cis-trans conformational changes in formation of the vortex flow $\mathbf{\text{v}}$. It is shown that a thermally excited vortex flow is maintained with motion in a positive sense (clockwise) in the vicinity of the orientation defect at the lower boundary of the HAN channel caused by the trans-cis and cis-trans conformational changes. In the case of the same HAN channel, but without the azobenzene monolayer at the lower boundary, the heat flux $\mathbf{\text{q}}$ can also produce the vortical flow in the vicinity of the laser spot at the lower boundary, directed in a negative sense (counterclockwise). At that, the second vortex is characterized by a much slower speed than the vortical flow in the first case.

Controllable wrinkling of dielectric elastomer (DE) sheets is often applied to achieve some special applications such as diffraction gratings, optical sensors, soft actuators, and adjustable wetting surfaces. It is required to precisely predict and control the threshold voltage and wavelength of wrinkling. In view of the weakness of loss of tension criterion, a nonlinear plate theory considering the bending energy of DE sheet is utilized to investigate the wrinkling phenomenon in a prestretched DE sheet with striped electrodes. The results show that the threshold voltage of wrinkling is bigger than the corresponding voltage obtained from loss of tension, which results from the fact that the bending energy has a certain inhibiting effect on wrinkling of the DE sheet. Furthermore, the threshold voltage and wavelength of wrinkling can be effectively regulated by controlling prestretch. The striped electrodes can also effectively control the threshold voltage and wavelength. Especially, there exists an optimal width ratio of electrode corresponding to the lowest threshold voltage. The proposed method can be used to predict and control the behavior of wrinkling in the engineering applications of DE structures.

We investigate the evolution of the interface separating two Newtonian fluids of different viscosities in two-dimensional Stokes flow driven by suction or injection. A second-order, mode-coupling theory is used to explore key morphological aspects of the emerging interfacial patterns in the stage of the flow that bridges the purely linear and fully nonlinear regimes. In the linear regime, our analysis reveals that an injection-driven expanding interface is stable, while a contracting motion driven by suction is unstable. Moreover, we find that the linear growth rate associated with this suction-driven instability is independent of the viscosity contrast between the fluids. However, second-order results tell a different story, and show that the viscosity contrast is crucial in determining the morphology of the interface. Our theoretical description is applicable to the entire range of viscosity contrasts, and provides insights on the formation of near-cusp pattern-forming structures. Reproduction of fully nonlinear, $n$-fold symmetric near-cuspidal shapes previously obtained through conformal mapping techniques substantiates the validity of our mode-coupling approach.

In a glass of stout beer, a very large number of small dispersed bubbles form a texture motion of a bubble swarm moving downwards. Such a cascading motion is caused by a gravity-driven hydrodynamic instability and depends on the interbubble distance. To estimate these two corresponding indicators, an experimentally measured velocity profile is required and, thus, is obtained a posteriori. However, it is unknown why the bubble cascade is observed only in stout beer with nitrogen, such as Guinness beer. To address this question via a priori estimation, here, we develop a mathematical continuum model of film flow in bubbly liquid, uncovering the essential dynamics among many physical processes occurring simultaneously in a glass. To validate the proposed model, we perform a numerical simulation of the distribution of massless Lagrangian particles in an inclined container. We investigate the effects of particle concentration, inclination angle, particle diameter, and container size on the cascading film flow. The results reveal that the motion and waviness of clear-fluid film can be successfully estimated a priori to experiments or simulations. Moreover, it is found that the continuum behavior of particles in the film flow is analogous to the continuum description of rarefied gas dynamics. These findings explain how the cascading bubbles in a pint glass of stout beer satisfy the continuum assumption and suggest a general condition for the onset of the cascade, for instance, a 200-l drum for carbonated water.

Hydrodynamic stagnation converts flow energy into internal energy. Here we develop a technique to directly analyze this hydrodynamic-dissipation process, which also yields a lengthscale associated with the conversion of flow energy to internal energy. We demonstrate the usefulness of this analysis for finding and comparing the hydrodynamic-stagnation dynamics of implosions theoretically, and in a test application to Z-pinch implosion data.

Generative neural samplers offer a complementary approach to Monte Carlo methods for problems in statistical physics and quantum field theory. This paper tests the ability of generative neural samplers to estimate observables for real-world low-dimensional spin systems. It maps out how autoregressive models can sample configurations of a quantum Heisenberg chain via a classical approximation based on the Suzuki-Trotter transformation. We present results for energy, specific heat, and susceptibility for the isotropic XXX and the anisotropic XY chain are in good agreement with Monte Carlo results within the same approximation scheme.

We present a multi-scale lattice Boltzmann scheme, which adaptively refines particles' velocity space. Different velocity sets of lower and higher order are consistently and efficiently coupled, allowing us to use the higher-order model only when and where needed. This includes regions of high Mach or high Knudsen numbers. The coupling procedure of discrete velocity sets consists of either a projection of the higher-order populations onto the lower-order lattice or lifting of the lower-order populations to the higher-order velocity space. Both lifting and projection are local operations, which enable a flexible adaptive velocity set. The proposed scheme is formulated for both a static and an optimal, co-moving reference frame, in the spirit of the recently introduced Particles on Demand method. The multi-scale scheme is validated with an advection of an athermal vortex and in a jet flow setup. The performance of the proposed scheme is further investigated in the shock structure problem and a high-Knudsen-number Couette flow, typical examples of highly non-equilibrium flows in which the order of the velocity set plays a decisive role. The results demonstrate that the proposed multi-scale scheme can operate accurately, with flexibility in terms of the underlying models and with reduced computational requirements.

The derivative nonlinear Schrödinger (DNLS) equation is the canonical model for the dynamics of nonlinear waves in plasma physics and optics. We study exact solutions describing rogue waves on the background of periodic standing waves in the DNLS equation. We show that the space-time localization of a rogue wave is only possible if the periodic standing wave is modulationally unstable. If the periodic standing wave is modulationally stable, the rogue wave solutions degenerate into algebraic solitons propagating along the background and interacting with the periodic standing waves. Maximal amplitudes of rogue waves are found analytically and confirmed numerically.

Bifurcations take place in molecular Hamiltonian nonlinear systems as the excitation energy increases, leading to the appearance of different classical resonances. In this paper, we study the quantum manifestations of these classical resonances in the isomerizing system $\mathrm{CN}\text{−}\mathrm{Li}\leftrightarrows \mathrm{Li}\text{−}\mathrm{CN}$. By using a correlation diagram of eigenenergies versus Planck constant, we show the existence of different series of avoided crossings, leading to the corresponding series of quantum resonances, which represent the quantum manifestations of the classical resonances. Moreover, the extrapolation of these series to $\hslash =0$ unveils the correspondence between the bifurcation energy of classical resonances and the energy of the series of quantum resonances in the semiclassical limit $\hslash \to 0$. Additionally, in order to obtain analytical expressions for our results, a semiclassical theory is developed.

Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of proteins. Having implications in both directions fosters the possibility of an “improve it or lose it” feedback loop, where higher expressed systems are more likely to improve and be expressed even higher, while those that are expressed less are eventually lost to drift. Using a minimal model to study this in the context of a changing environment, we demonstrate that one unexpected consequence of such a feedback loop is that a slow switch to a new environment can allow genotypes to reach higher fitness sooner than a direct exposure to it.

Suspensions of motile active particles with space-dependent activity form characteristic polarization and density patterns. Recent single-particle studies for planar activity landscapes identified several quantities associated with emergent density-polarization patterns that are solely determined by bulk variables. Naive thermodynamic intuition suggests that these results might hold for arbitrary activity landscapes mediating bulk regions, and thus could be used as benchmarks for simulations and theories. However, the considered system operates in a nonequilibrium steady state and we prove by construction that the quantities in question lose their simple form for curved activity landscapes. Specifically, we provide a detailed analytical study of polarization and density profiles induced by radially symmetric activity steps, and of the total polarization for the case of a general radially symmetric activity landscape. While the qualitative picture is similar to the planar case, all the investigated variables depend not only on bulk variables but also comprise geometry-induced contributions. We verified that all our analytical results agree with exact numerical calculations.

We present a discrete element method study of the uprising of an intruder immersed in a granular media under vibration, also known as the Brazil Nut Effect. Besides confirming granular ratcheting and convection as leading mechanisms to this odd behavior, we evince the role of the resonance on the rising of the intruder by using periodic boundary conditions (pbc) in the horizontal direction to avoid wall-induced convection. As a result, we obtain a resonance-qualitylike curve of the intruder ascent rate as a function of the external frequency, which is verified for different values of the inverse normalized gravity $\mathrm{\Gamma }$, as well as the system size. In addition, we introduce a large deviation function analysis which displays a remarkable difference for systems with walls or pbc.

We study ionization and transport processes in partially ionized multicomponent plasmas. The plasma composition is calculated via a system of coupled mass-action laws. The electronic transport properties are determined by the electron-ion and electron-neutral transport cross sections. The influence of electron-electron scattering is considered via a correction factor to the electron-ion contribution. Based on these data, the electrical and thermal conductivities as well as the Lorenz number are calculated. For the thermal conductivity, we consider also the contributions of the translational motion of neutral particles and of the dissociation, ionization, and recombination reactions. We apply our approach to a partially ionized plasma composed of hydrogen, helium, and a small fraction of metals (Li, Na, Ca, Fe, K, Rb, and Cs) as typical for atmospheres of hot Jupiters. We present results for the plasma composition and the transport properties as a function of density and temperature and then along typical $P\text{−}T$ profiles for the outer part of the hot Jupiter HD 209458b. The electrical conductivity profile allows revising the Ohmic heating power related to the fierce winds in the planet's atmosphere. We show that the higher temperatures suggested by recent interior models could boost the conductivity and thus the Ohmic heating power to values large enough to explain the observed inflation of HD 209458b.

This is a continuation of previous works [S. Takata and T. Noguchi, J. Stat. Phys. 172, 880 (2018); S. Takata, T. Matsumoto, A. Hirahara, and M. Hattori, Phys. Rev. E 98, 052123 (2018)]. The simple model proposed in the previous works is extended to be free from the isothermal assumption. The new model conserves the total mass, momentum, and energy in the periodic domain. A monotone functional is found, assuring the H theorem for the new model. Different approaches are taken to tell apart the stable, the metastable, and the unstable uniform equilibrium state. Numerical simulations are also conducted for spatially one-dimensional cases to demonstrate various features occurring in the time evolution process. A prediction method for the profile at the stationary state is discussed as well.

This paper shows that a large class of fading memory state-space systems driven by discrete-time observations of dynamical systems defined on compact manifolds always yields continuously differentiable synchronizations. This general result provides a powerful tool for the representation, reconstruction, and forecasting of chaotic attractors. It also improves previous statements in the literature for differentiable generalized synchronizations, whose existence was so far guaranteed for a restricted family of systems and was detected using Hölder exponent-based criteria.

We study some dynamical properties of a charged particle that moves in a nonhomogeneous electric field and collides against an oscillating platform. Depending on the values of parameters, the system presents (i) predominantly regular dynamics or (ii) structures of chaotic behavior in phase space conditioned to the initial conditions. The localization of the fixed points and their stability are carefully discussed. Average properties of the chaotic sea are investigated under a scaling approach. We show that the system belongs to the same universality class as the Fermi-Ulam model.

Flow networks can describe many natural and artificial systems. We present a model for a flow system that allows for volume accumulation, includes conduits with a nonlinear relation between current and pressure difference, and can be applied to networks of arbitrary topology. The model displays complex dynamics, including self-sustained oscillations in the absence of any dynamics in the inputs and outputs. In this work we analytically show the origin of self-sustained oscillations for the one-dimensional case. We numerically study the behavior of systems of arbitrary topology under different conditions: we discuss their excitability, the effect of different boundary conditions, and wave propagation when the network has regions of conduits with linear conductance.

The steroid hormone glucocorticoid (GC) is a well-known immunosuppressant that controls T-cell-mediated adaptive immune response. In this work, we have developed a minimal kinetic network model of T-cell regulation connecting relevant experimental and clinical studies to quantitatively understand the long-term effects of GC on pro-inflammatory T-cell $\left(T_{\mathrm{pro}}\right)$ and anti-inflammatory T-cell $\left(T_{\mathrm{anti}}\right)$ dynamics. Due to the antagonistic relation between these two types of T cells, their long-term steady-state population ratio helps us to characterize three classified immune regulations: (i) weak $\left(\left[T_{\mathrm{pro}}\right]>\left[T_{\mathrm{anti}}\right]\right)$, (ii) strong $\left(\left[T_{\mathrm{pro}}\right]<\left[T_{\mathrm{anti}}\right]\right)$, and (iii) moderate $\left(\left[T_{\mathrm{pro}}\right]\sim \left[T_{\mathrm{anti}}\right]\right)$, holding the characteristic bistability. In addition to the differences in their long-term steady-state outcome, each immune regulation shows distinct dynamical phases. In the presteady state, a characteristic intermediate stationary phase is observed to develop only in the moderate regulation regime. In the medicinal field, the resting time in this stationary phase is distinguished as a clinical latent period. GC dose-dependent steady-state analysis shows an optimal level of GC to drive a phase transition from the weak or autoimmune prone to the moderate regulation regime. Subsequently, the presteady state clinical latent period tends to diverge near that optimal GC level where $\left[T_{\mathrm{pro}}\right]:\left[T_{\mathrm{anti}}\right]$ is highly balanced. The GC-optimized elongated stationary phase explains the rationale behind the requirement of long-term immune diagnostics, especially when long-term GC-based chemotherapeutics and other immunosuppressive drugs are administrated. Moreover, our study reveals GC sensitivity of clinical latent period, which might serve as an early warning signal in diagnosing different immune phases and determining immune phasewise steroid treatment.

We examine the collective states of run-and-tumble active matter disks driven over a periodic obstacle array. When the drive is applied along a symmetry direction of the array, we find a clog-free uniform liquid state for low activity, while at higher activity, the density becomes increasingly heterogeneous and an active clogged state emerges in which the mobility is strongly reduced. For driving along nonsymmetry or incommensurate directions, there are two different clogging behaviors consisting of a drive-dependent clogged state in the low activity thermal limit and a drive-independent clogged state at high activity. These regimes are separated by a uniform flowing liquid at intermediate activity. There is a critical activity level above which the thermal clogged state does not occur, as well as an optimal activity level that maximizes the disk mobility. Thermal clogged states are dependent on the driving direction while active clogged states are not. In the low activity regime, diluting the obstacles produces a monotonic increase in the mobility; however, for large activities, the mobility is more robust against obstacle dilution. We also examine the velocity-force curves for driving along nonsymmetry directions and find that they are linear when the activity is low or intermediate but become nonlinear at high activity and show behavior similar to that found for the plastic depinning of solids. At higher drives, the active clustering is lost. For low activity, we also find a reentrant fluid phase, where the system transitions from a high mobility fluid at low drives to a clogged state at higher drives and then back into another fluid phase at very high drives. We map the regions in which the thermally clogged, partially clogged, active uniform fluid, clustered fluid, active clogged, and directionally locked states occur as a function of disk density, drift force, and activity.