The actin cytoskeleton of cells is in continuous motion due to both polymerization of new filaments and their contraction by myosin II molecular motors. Through adhesion to the substrate, such intracellular flow can be converted into cell migration. Recently, optogenetics has emerged as a new powerful experimental method to control both actin polymerization and myosin II contraction. While optogenetic control of polymerization can initiate cell migration by generating protrusion, it is less clear if and how optogenetic control of contraction can also affect cell migration. Here we analyze the latter situation using a minimal variant of active gel theory into which we include optogenetic activation as a spatiotemporally constrained perturbation. The model can describe the symmetrical flow of the actomyosin system observed in optogenetic experiments, but not the long-lasting polarization required for cell migration. Motile solutions become possible if cytoskeletal polymerization is included through the boundary conditions. Optogenetic activation of contraction can then initiate locomotion in a symmetrically spreading cell and strengthen motility in an asymmetrically polymerizing one. If designed appropriately, it can also arrest motility even for protrusive boundaries.

We perform an alternative approach to produce highly unipolar terahertz pulses. The idea is based on the nonuniform amplification of seed ultrashort carrier-envelope phase (CEP) pulses in nonequilibrium fast relaxing plasma of air or nitrogen. If the gain coefficient drops significantly within the duration of a one-cycle CEP pulse, it undergoes significant distortion where the leading edge of the pulse is amplified and the trailing tail of opposite polarity is absorbed. The obtained results involve a self-consistent solution of the second-order wave equation and kinetic Boltzmann equation for the electron velocity distribution function relaxation.

Ecological communities face a high risk of extinction to climate change which can destabilize ecological systems. In the face of accelerating environmental change, understanding the factors and the mechanisms that stabilize the ecological communities is a central focus in ecology. Although dispersal has been widely used as an important stabilizing process, it remains unclear how individual species dispersal affects the stability and persistence of an ecological community. In this study, using a spatially coupled predator-prey community, we address the effects of individual species dispersal and nutrient enrichment on metacommunity stability in constant and varying environments. We show two contrasting effects of dispersal on metacommunity persistence in temporally constant and varying environments. Specifically, predator dispersal in constant environments shows stronger stability through inhomogeneous (asynchronized) states, whereas prey dispersal shows an increasing extinction risk through a homogeneous (synchronized) state. On the contrary, the metacommunity dynamics in temporally varying environments reveal that predator dispersal causes a local extinction through tracking unstable states and also a delayed shift between dynamical states. Moreover, our results emphasize that metacommunity persistence depends on individual species dispersal and environmental variations. Thus, our findings of the individual species dispersal can help to develop conservation measures that are tailored to varying environmental conditions.

Symmetries naturally occur in real-world networks and can significantly influence the observed dynamics. For instance, many synchronization patterns result from the underlying network symmetries, and high symmetries are known to increase the stability of synchronization. Yet here we find that general macroscopic features of network solutions such as regularity can be induced by breaking their symmetry of interactions. We demonstrate this effect in an ecological multilayer network where the topological asymmetries occur naturally. These asymmetries rescue the system from chaotic oscillations by establishing stable periodic orbits and equilibria. We call this phenomenon asymmetry-induced order and uncover its mechanism by analyzing both analytically and numerically the absence of dynamics on the system's synchronization manifold. Moreover, the bifurcation scenario describing the route from chaos to order is also disclosed. We demonstrate that this result also holds for generic node dynamics by analyzing coupled paradigmatic Rössler and Lorenz systems.

In this paper we introduce a description of the equilibrium state of a bond percolation process on random graphs using the exact method of generating functions. This allows us to find the expected size of the giant connected component (GCC) of two sequential bond percolation processes in which the bond occupancy probability of the second process is modulated (increased or decreased) by a node being inside or outside of the GCC created by the first process. In the context of epidemic spreading this amounts to both an antagonistic partial immunity and a synergistic partial coinfection interaction between the two sequential diseases. We examine configuration model networks with tunable clustering. We find that the emergent evolutionary behavior of the second strain is highly dependent on the details of the coupling between the strains. Contact clustering generally reduces the outbreak size of the second strain relative to unclustered topologies; however, positive assortativity induced by clustered contacts inverts this conclusion for highly transmissible disease dynamics.

The concept of a multiplex network can be used to characterize the dispersal paths and states of different species in a patch habitat system. The multiplex network is one of three types of multilayer networks. In this study, the effect of a multiplex network on the long-term stable coexistence of species is investigated using the concept of metapopulation. Based on the mean field approximation, the stability analysis of a two-species system shows that, compared to the single layer network, the multiplex network is more conducive to the stable coexistence of species when one species has a stronger colonization ability. That is, in such a patch habitat system, if the dispersal paths of the stronger species are different than those of the weaker species, then the larger the heterogeneity of the dispersal network of the stronger species is, the more likely the long-term stable coexistence of species. This result provides a different perspective for understanding the biodiversity in heterogeneous habitats.

Residual stress field is a self-equilibrium state of stress in the bulk solid material with the inhomogeneous field of the inelastic deformations. The high level of tensile residual stress often leads to dynamic fracture resulting in the instantaneous and catastrophic destruction of the materials because the cracks are fed with the strain energy initially stored in the bulk materials due to the residual stress. The dissipation of the strain energy with crack growth results in the release and the redistribution of the residual stress. In this paper, we propose an effective mathematical model and a numerical analysis method for dynamic fracture in residual stress field. We formulate the dynamic behavior of solid continuum with residual stress field in the context of particle discretization scheme finite element method. This formulation enables the appropriate evaluation of (i) release and redistribution of residual stress due to dynamic propagation of the cracks and (ii) the effect of the elastic wave on crack propagation, which are the most substantial problems on dynamic fracture in residual stress field. We perform the experiments and the simulations of dynamic fracture process in chemically tempered glass sheets with residual stress field to validate the proposed numerical analysis method. The simulation results show remarkable agreement with the experiments of the catastrophic failure of the glass sheets with residual stress field in all aspects of crack behavior. These results indicate that the proposed model and method can rigorously evaluate the release and the autonomous redistribution of the residual stress in the dynamic fracture process.

Hydrodynamics is shown to induce non-Hermitian topological phenomena in ordinary, passive soft matter. This is demonstrated by subjecting a two-dimensional elastic lattice to a low-Reynolds viscous flow. The interplay of hydrodynamics and elasticity splits Dirac cones into bulk Fermi arcs, pairing exceptional points with opposite half-integer topological charges. The bulk Fermi arc is a generic hallmark of the system exhibited in all lattice and flow symmetries. An analytic model and simulations explain how the emergent singularities shape the spectral bands and give rise to a web of van Hove singularity lines in the density of states. The present findings suggest that non-Hermitian physics can be explored in a broad class of ordinary soft matter, living and artificial alike, opening avenues for topology-based technology in this regime.

We theoretically demonstrate the realization of a chiral edge mode in a system beyond natural science. Specifically, we elucidate that a kagome network of rock-paper-scissors (K-RPS) hosts a chiral edge mode of the population density which is protected by the nontrivial topology in the bulk. The emergence of the chiral edge mode is demonstrated by numerically solving the Lotka-Volterra (LV) equation. This numerical result can be intuitively understood in terms of the cyclic motion of a single rock-paper-scissors cycle, which is analogous to the cyclotron motion of fermions. Furthermore, we point out that a linearized LV equation is mathematically equivalent to the Schrödinger equation describing quantum systems. This equivalence allows us to clarify the topological origin of the chiral edge mode in the K-RPS; a nonzero Chern number of the payoff matrix induces the chiral edge mode of the population density, which exemplifies the bulk-edge correspondence in two-dimensional systems described by evolutionary game theory.

The chaotic dynamics of a low-order Galerkin truncation of the two-dimensional magnetohydrodynamic system, which reproduces the dynamics of fluctuations described by nearly incompressible magnetohydrodynamic in the plane perpendicular to a background magnetic field, is investigated by increasing the external forcing terms. Although this is the case closest to two-dimensional hydrodynamics, which shares some aspects with the classical Feigenbaum scenario of transition to chaos, the presence of magnetic fluctuations yields a very complex interesting route to chaos, characterized by the splitting into multiharmonic structures of the field amplitudes, and a mixing of phase-locking and free phase precession acting intermittently. When the background magnetic field lies in the plane, the system supports the presence of Alfvén waves thus lowering the nonlinear interactions. Interestingly enough, the dynamics critically depends on the angle between the direction of the magnetic field and the reference system of the wave vectors. Above a certain critical angle, independently from the external forcing, a breakdown of the phase locking appears, accompanied with a suppression of the chaotic dynamics, replaced by a simple periodic motion.

We present our exhaustive exploration of the densest ternary sphere packings (DTSPs) for 45 radius ratios and 237 kinds of compositions, which is a packing problem of three kinds of hard spheres with different radii, under periodic boundary conditions by a random structure searching method. To efficiently explore DTSPs we further develop the searching method based on the piling-up and iterative balance methods [Koshoji et al., Phys. Rev. E 103, 023307 (2021)]. The unbiased exploration identifies diverse 38 putative DTSPs appearing on phase diagrams in which 37 DTSPs of them are discovered in the study. The structural trend of DTSPs changes depending especially on the radius of small spheres. In case that the radius of small spheres is relatively small, structures of many DTSPs can be understood as derivatives of densest binary sphere packings (DBSPs), while characteristic structures specific to the ternary system emerge as the radius of small spheres becomes larger. In addition to DTSPs, we reveal a lot of semi-DTSPs (SDTSPs) which are obtained by excluding DBSPs in the calculation of phase diagram, and investigate the correspondence of DTSPs and SDTSPs with real crystals based on the space group, showing a considerable correspondence of SDTSPs having high symmetries with real crystals including ${\mathrm{Cu}}_2\mathrm{GaSr}$ and ${\mathrm{ThCr}}_2{\mathrm{Si}}_2$ structures. Our study suggests that the diverse structures of DBSPs, DTSPs, and SDTSPs can be effectively used as structural prototypes for searching complex crystal structures.

We discovered an out-of-equilibrium transition in the ideal gas between two walls, divided by an inner, adiabatic, movable wall. The system is driven out-of-equilibrium by supplying energy directly into the volume of the gas. At critical heat flux we have found a continuous transition to the state with a low-density, hot gas on one side of the movable wall and a dense, cold gas on the other side. Molecular dynamic simulations of the soft-sphere fluid confirm the existence of the transition in the interacting system. We introduce a stationary state Helmholtz-like function whose minimum determines the stable positions of the internal wall. This transition can be used as a paradigm of transitions in stationary states and the Helmholtz-like function as a paradigm of the thermodynamic description of these states.

We study the effects of roughness in the asymmetric periodic potential on the transport and diffusion of an inertial Brownian particle driven by a time-periodic force in a Gaussian environment. We find that moderate roughness leads to the loss of transient anomalous diffusion, and it helps to establish normal diffusion in the weak noise limit. We uncover a contrasting effect of roughness on the transport of particles in the weak and moderate to large noise limit. In the weak noise limit, small amplitude roughness results in the increase of directed transport, whereas in the moderate to large noise limit, roughness hinders transport. The deterministic dynamics of the system reveals that the purely periodic system under smooth potential transits into a chaotic system due to the moderate roughness in the potential. Therefore our calculations demonstrate the constructive role of roughness in the transport of particles in the inertial regime.

Stochastically perturbed Korteweg–de Vries (KdV) equations are widely used to describe the effect of random perturbations on coherent solitary waves. We present a collective coordinate approach to describe the effect on coherent solitary waves in stochastically perturbed KdV equations. The collective coordinate approach allows one to reduce the infinite-dimensional stochastic partial differential equation (SPDE) to a finite-dimensional stochastic differential equation for the amplitude, width and location of the solitary wave. The reduction provides a remarkably good quantitative description of the shape of the solitary waves and its location. Moreover, the collective coordinate framework can be used to estimate the timescale of validity of stochastically perturbed KdV equations for which they can be used to describe coherent solitary waves. We describe loss of coherence by blow-up as well as by radiation into linear waves. We corroborate our analytical results with numerical simulations of the full SPDE.

From social networks to biological networks, different types of interactions among the same set of nodes characterize distinct layers, which are termed multilayer networks. Within a multilayer network, some layers, confirmed through different experiments, could be structurally similar and interdependent. In this paper, we propose a maximum a posteriori-based method to study and reconstruct the structure of a target layer in a multilayer network. Nodes within the target layer are characterized by vectors, which are employed to compute edge weights. Further, to detect structurally similar layers, we propose a method for comparing networks based on the eigenvector centrality. Using similar layers, we obtain the parameters of the conjugate prior. With this maximum a posteriori algorithm, we can reconstruct the target layer and predict missing links. We test the method on two real multilayer networks, and the results show that the maximum a posteriori estimation is promising in reconstructing the target layer even when a large number of links is missing.

Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double-stranded DNA chains whose ends are subjected to a time-dependent periodic force with frequency $\omega$ and amplitude $G$ keeping the other end fixed. We find that the area of the hysteresis loop, $A_{\mathrm{loop}}$, scales as $1/\omega$ at higher frequencies, whereas it scales as ${(G-G_c)}^{\alpha }{\omega }^{\beta }$ with exponents $\alpha =1$ and $\beta =1.25$ in the low-frequency regime. These values are same as the exponents obtained in Monte Carlo simulation studies of a directed self-avoiding walk model of a homopolymer DNA [R. Kapri, Phys. Rev. E 90, 062719 (2014)], and the block copolymer DNA [R. K. Yadav and R. Kapri, Phys. Rev. E 103, 012413 (2021)] on a square lattice, and differs from the values reported earlier using Langevin dynamics simulation studies on a much shorter DNA hairpins.

We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is introduced by the polydispersity index (PDI) $\epsilon$, which is the width of the uniform distribution of the particle's radius. The self-propulsion speed of the particles controls the activity $v$. We observe enhanced dynamics for large size diversity among the particles. We calculate the effective diffusion coefficient $D_{\mathrm{eff}}$ in the steady state. The system exhibits four distinct phases, jammed phase with small $D_{\mathrm{eff}}$ for small activity and liquid phase with enhanced $D_{\mathrm{eff}}$ for large activity. The number fluctuation is larger and smaller than the equilibrium limit in the liquid and jammed phases, respectively. Further, the jammed phase is of two types: solid jammed and liquid jammed for small and large PDI. Whereas the liquid phase is called motility induced phase separation (MIPS) liquid for small PDI and for large PDI, we find enhanced diffusivity and call it the pure liquid phase. The system is studied for three packing densities $\varphi$, and the response of the system for polydispersity is the same for all $\varphi$'s. Our study can help understand the behavior of cells of various sizes in a tissue, artificial self-driven granular particles, or living organisms of different sizes in a dense environment.

We study the radiation from charged particles crossing a cholesteric plate in the shortwave approximation when the wavelength of photons is much smaller than the pitch of the cholesteric helix, whereas the escaping angle of the photon and the anisotropy of the permittivity tensor can be arbitrary. The radiation of photons is treated in the framework of quantum electrodynamics with classical currents. The radiation of the plane-wave photons and the photons with definite projection of the angular momentum (the twisted photons) produced by charged particles crossing the cholesteric plate and moving rectilinearly and uniformly is considered. The explicit expressions for the average number of radiated photons and their spectra with respect to the energy and the projection of the angular momentum are obtained in this case. It turns out that in the paraxial approximation the projection of the orbital angular momentum, $l$, of radiated twisted photons is related to the harmonic number $n\in \mathbb{Z}$ as $l=2n+1$, i.e., the given system is a pure source of twisted photons as expected. It is shown that in the paraxial shortwave regime the main part of radiated photons is linearly polarized with $l=\pm 1$ at the harmonics $n=\{-1,0\}$. The applicability conditions of the approach developed are discussed. As the examples, we consider the production of 6.3 eV twisted photons from uranium nuclei and the production of x-ray twisted photons from 120 MeV electrons.

The behavior of granular media under quasistatic loading has recently been shown to attain a stable evolution state corresponding to a manifold in the space of micromechanical variables. This state is characterized by sudden transitions between metastable jammed states, involving the partial micromechanical rearrangement of the granular medium. Using numerical simulations of two-dimensional granular media under quasistatic biaxial compression, we show that the dynamics in the stable evolution state is characterized by scale-free avalanches well before the macromechanical stationary flow regime traditionally linked to a self-organized critical state. This, together with the nonuniqueness and the nonmonotony of macroscopic deformation curves, suggests that the statistical avalanche properties and the susceptibilities of the system cannot be reduced to a function of the macromechanical state. The associated scaling exponents are nonuniversal and depend on the interactions between particles. For stiffer particles (or samples at low confining pressure) we find distributions of avalanche properties compatible with the predictions of mean-field theory. The scaling exponents decrease below the mean-field values for softer interactions between particles. These lower exponents are consistent with observations for amorphous solids at their critical point. We specifically discuss the relationship between microscopic and macroscopic variables, including the relation between the external stress drop and the internal potential energy released during kinetic avalanches.

Plasmonic bubbles are of great relevance in numerous applications, including catalytic reactions, micro/nanomanipulation of molecules or particles dispersed in liquids, and cancer therapeutics. So far, studies have been focused on bubble nucleation in pure liquids. Here we investigate plasmonic bubble nucleation in ternary liquids consisting of ethanol, water, and trans-anethole oil, which can show the so-called ouzo effect. We find that oil (trans-anethole) droplet plumes are produced around the growing plasmonic bubbles. The nucleation of the microdroplets and their organization in droplet plumes is due to the symmetry breaking of the ethanol concentration field during the selective evaporation of ethanol from the surrounding ternary liquids into the growing plasmonic bubbles. Numerical simulations show the existence of a critical Marangoni number Ma (the ratio between solutal advection rate and the diffusion rate), above which the symmetry breaking of the ethanol concentration field occurs, leading to the emission of the droplet plumes. The numerical results agree with the experimental observation that more plumes are emitted with increasing ethanol-water relative weight ratios and hence Ma. Our findings on the droplet plume formation reveal the rich phenomena of plasmonic bubble nucleation in multicomponent liquids and help to pave the way to achieve enhanced mixing in multicomponent liquids in chemical, pharmaceutical, and cosmetic industries.