In random sequential adsorption (RSA), objects are deposited randomly, irreversibly, and sequentially; attempts leading to an overlap with previously deposited objects are discarded. The process continues until the system reaches a jammed state when no further additions are possible. We analyze a class of lattice RSA models in which landing on an empty site in a segment is allowed when at least $b$ neighboring sites on the left and the right are unoccupied. For the minimal model ($b=1$), we compute the full counting statistics of the occupation number. We reduce the determination of the full counting statistics to a Riccati equation that appears analytically solvable only when $b=1$. We develop a perturbation procedure which, in principle, allows one to determine cumulants consecutively, and we compute the variance of the occupation number for all $b$.

Ecosystem stability is a central question both in theoretical and applied biology. Dynamical systems theory can be used to analyze how growth rates, carrying capacities, and patterns of species interactions affect the stability of an ecosystem. The response to increasing complexity has been extensively studied and the general conclusion is that there is a limit. While there is a complexity limit to stability at which global destabilisation occurs, the collapse rarely happens suddenly if a system is fully viable (no species is extinct). In fact, when complexity is successively increased, we find that the generic response is to go through multiple single-species extinctions before a global collapse. In this paper we demonstrate this finding via both numerical simulations and elaborations of theoretical predictions. We explore more biological interaction patterns, and, perhaps most importantly, we show that constrained interaction structures—a constant row sum in the interaction matrix—prevent extinctions from occurring. This makes an ecosystem more robust in terms of allowed complexity, but it also means singles-species extinctions do not precede or signal collapse—a drastically different behavior compared to the generic and commonly assumed case. We further argue that this constrained interaction structure—limiting the total interactions for each species—is biologically plausible.

We study the dynamics of a single semiflexible filament coupled to a Hookean spring at its boundary. The spring produces a fluctuating tensile force on the filament, the value of which depends on the filament's instantaneous end-to-end length. The spring thereby introduces a nonlinearity, which mixes the undulatory normal modes of the filament and changes their dynamics. We study these dynamics using the Martin–Siggia–Rose–Janssen–De Dominicis formalism, and compute the time-dependent correlation functions of transverse undulations and of the filament's end-to-end distance. The relaxational dynamics of the modes below a characteristic wavelength $\sqrt{\kappa /{\tau }_R}$, set by the filament's bending modulus $\kappa$ and spring-renormalized tension ${\tau }_R$, are changed by the boundary spring. This occurs near the crossover frequency between tension- and bending-dominated modes of the system. The boundary spring can be used to represent the linear elastic compliance of the rest of the filament network to which the filament is cross linked. As a result, we predict that this nonlinear effect will be observable in the dynamical correlations of constituent filaments of networks and in the networks' collective shear response. The system's dynamic shear modulus is predicted to exhibit the well-known crossover with increasing frequency from ${\omega }^{1/2}$ to ${\omega }^{3/4}$, but the inclusion of the network's compliance in the analysis of the individual filament dynamics shifts this transition to a higher frequency.

Butterflies fly with an abdomen oscillating relative to the thorax; the abdominal oscillation causes body parts to undulate translationally relative to the center of mass of a butterfly, which could generate a significant effect on flight. Based on experimental measurements, we created a numerical model to investigate this effect in a free-flying butterfly (Idea leuconoe). We fixed the motions of wing-flapping and thorax-pitching, and parametrized the abdominal oscillation by varied oscillating phase. To concentrate the analysis on translational dynamics, we used a motion of a thorax-abdomen node, a joint that the thorax and the abdomen rotate about, to express the translational motion of body parts relative to the center of mass. The results show that the abdominal oscillation enhances lift and thrust via the translational motion of the thorax-abdomen node relative to the center of mass. With the abdominal oscillating phase recorded from real butterflies, the abdominal oscillation causes the thorax-abdomen node to move downward relative to the center of mass in downstroke and move upward relative to the center of mass in upstroke. This constructive movement amplifies the wing-flapping speed relative to the center of mass, which enhances the angle of attack and the strength of leading- and trailing-edge vortices on the wings. The wings thereby generate increased values of instantaneous lift and thrust by 50.32% and 32.57% compared to the case of no abdominal oscillation. Natural butterflies are stated to utilize a particular phase offset of abdominal oscillation to fly. With comparing varied oscillating phases, only the abdominal oscillating phase recorded from natural butterflies produces the best constructive effect on the translational motion of thorax-abdomen node, which maximizes the lift and thrust generated on the wings. It clarifies that butterflies use this specific range of abdominal oscillating phase to regulate the translational motion between the thorax-abdomen node and the center of mass to enhance flight. Our work reveals the translational mechanism of the abdominal oscillation, which is as important as the thorax-pitching effect. The findings in this work provide insight into the flight of butterflies and the design of micro aerial vehicles.

We explore the link between the melting scenarios of two-dimensional systems of hard disks and squares through replica-exchange Monte Carlo simulations of hard superdisks. The well-known melting scenarios are observed in the disk and square limits, while we observe an unusual three-step scenario for dual shapes. We find that two mesophases mediate the melting: a hexatic phase and another fluid phase with a $D_2$ local symmetry, we call it rhombatic, where both bond and particle orientational orders are quasi-long-range. Our results show that not only can the melting process of liquid-crystal forming molecules be complicated, where elongated shapes stabilize several mesophases, but also that of anisotropic quasispherical molecules.

Using the phase field crystal model (PFC model), an analysis of slow and fast dynamics of solid-liquid interfaces in solidification and melting processes is presented. Dynamical regimes for cubic lattices invading metastable liquids (solidification) and liquids propagating into metastable crystals (melting) are described in terms of the evolving amplitudes of the density field. Dynamical equations are obtained for body-centered cubic (bcc) and face-centered cubic (fcc) crystal lattices in one- and two-mode approximations. A universal form of the amplitude equations is obtained for the three-dimensional dynamics for different crystal lattices and crystallographic directions. Dynamics of the amplitude's propagation for different lattices and PFC mode's approximations is qualitatively compared. The traveling-wave velocity is quantitatively compared with data of molecular dynamics simulation previously obtained by Mendelev et al. [Modell. Simul. Mater. Sci. Eng. 18, 074002 (2010)] for solidification and melting of the aluminum fcc lattice.

The viscosity tensor of the magnetized one-component plasma, consisting of five independent shear viscosity coefficients, a bulk viscosity coefficient, and a cross coefficient, is computed using equilibrium molecular dynamics simulations and the Green-Kubo relations. A broad range of Coulomb coupling and magnetization strength conditions are studied. Magnetization is found to strongly influence the shear viscosity coefficients when the gyrofrequency exceeds the Coulomb collision frequency. Three regimes are identified as the Coulomb coupling strength and magnetization strength are varied. The Green-Kubo relations are used to separate kinetic and potential energy contributions to each viscosity coefficient, showing how each contribution depends upon the magnetization strength. The shear viscosity coefficient associated with the component of the pressure tensor parallel to the magnetic field, and the two coefficients associated with the component perpendicular to the magnetic field, are all found to merge to a common value at strong Coulomb coupling.

The present paper considers the time evolution of a charged test particle of mass $m$ in a constant temperature heat bath of a second charged particle of mass $M$. The time dependence of the distribution function of the test particles is given by a Fokker-Planck equation with a diffusion coefficient for Coulomb collisions as well as a diffusion coefficient for wave-particle interactions. For the mass ratio $m/M\to 0$, the steady distribution is a Kappa distribution which has been employed in space physics to fit observed particle energy spectra. The time dependence of the distribution functions with some initial value is expressed in terms of the eigenvalues and eigenfunctions of the linear Fokker-Planck operator and also interpreted with the transformation to a Schrödinger equation. We also consider the explicit time dependence of the distribution function with a discretization of the Fokker-Planck equation. We study the stability of the Kappa distribution to Coulomb collisions.

What is the optimal distribution of two types of crystalline phases on the surface of icosahedral shells, such as of many viral capsids? We here investigate the distribution of a thin layer of soft material on a crystalline convex icosahedral shell. We demonstrate how the shapes of spherical viruses can be understood from the perspective of elasticity theory of thin two-component shells. We develop a theory of shape transformations of an icosahedral shell upon addition of a softer, but still crystalline, material onto its surface. We show how the soft component “invades” the regions with the highest elastic energy and stress imposed by the 12 topological defects on the surface. We explore the phase diagram as a function of the surface fraction of the soft material, the shell size, and the incommensurability of the elastic moduli of the rigid and soft phases. We find that, as expected, progressive filling of the rigid shell by the soft phase starts from the most deformed regions of the icosahedron. With a progressively increasing soft-phase coverage, the spherical segments of domes are filled first (12 vertices of the shell), then the cylindrical segments connecting the domes (30 edges) are invaded, and, ultimately, the 20 flat faces of the icosahedral shell tend to be occupied by the soft material. We present a detailed theoretical investigation of the first two stages of this invasion process and develop a model of morphological changes of the cone structure that permits noncircular cross sections. In conclusion, we discuss the biological relevance of some structures predicted from our calculations, in particular for the shape of viral capsids.

We present the Fokker-Planck equation (FPE) for an inhomogeneous medium with a position-dependent mass particle by making use of the Langevin equation, in the context of a generalized deformed derivative for an arbitrary deformation space where the linear (nonlinear) character of the FPE is associated with the employed deformed linear (nonlinear) derivative. The FPE for an inhomogeneous medium with a position-dependent diffusion coefficient is equivalent to a deformed FPE within a deformed space, described by generalized derivatives, and constant diffusion coefficient. The deformed FPE is consistent with the diffusion equation for inhomogeneous media when the temperature and the mobility have the same position-dependent functional form as well as with the nonlinear Langevin approach. The deformed version of the $H$-theorem permits to express the Boltzmann-Gibbs entropic functional as a sum of two contributions, one from the particles and the other from the inhomogeneous medium. The formalism is illustrated with the infinite square well and the confining potential with linear drift coefficient. Connections between superstatistics and position-dependent Langevin equations are also discussed.

Heterogeneous diffusion processes (HDPs) with space-dependent diffusion coefficients $D\left(x\right)$ are found in a number of real-world systems, such as for diffusion of macromolecules or submicron tracers in biological cells. Here, we examine HDPs in quenched-disorder systems with Gaussian colored noise (GCN) characterized by a diffusion coefficient with a power-law dependence on the particle position and with a spatially random scaling exponent. Typically, $D\left(x\right)$ is considered to be centerd at the origin and the entire $x$ axis is characterized by a single scaling exponent $\alpha$. In this work we consider a spatially random scenario: in periodic intervals (“layers”) in space $D\left(x\right)$ is centerd to the midpoint of each interval. In each interval the scaling exponent $\alpha$ is randomly chosen from a Gaussian distribution. The effects of the variation of the scaling exponents, the periodicity of the domains (“layer thickness”) of the diffusion coefficient in this stratified system, and the correlation time of the GCN are analyzed numerically in detail. We discuss the regimes of superdiffusion, subdiffusion, and normal diffusion realisable in this system. We observe and quantify the domains where nonergodic and non-Gaussian behaviors emerge in this system. Our results provide new insights into the understanding of weak ergodicity breaking for HDPs driven by colored noise, with potential applications in quenched layered systems, typical model systems for diffusion in biological cells and tissues, as well as for diffusion in geophysical systems.

Granger causality (GC) is undoubtedly the most widely used method to infer cause-effect relations from observational time series. Several nonlinear alternatives to GC have been proposed based on kernel methods. We generalize kernel Granger causality by considering the variables' cross-relations explicitly in Hilbert spaces. The framework is shown to generalize the linear and kernel GC methods and comes with tighter bounds of performance based on Rademacher complexity. We successfully evaluate its performance in standard dynamical systems, as well as to identify the arrow of time in coupled Rössler systems, and it is exploited to disclose the El Niño–Southern Oscillation phenomenon footprints on soil moisture globally.

Recently, researchers have found time cells in the hippocampus that appear to contain information about the timing of past events. Some researchers have argued that time cells are taking a Laplace transform of their input in order to reconstruct the past stimulus. We argue that stimulus prediction, not stimulus reconstruction or redundancy reduction, is in better agreement with observed responses of time cells. In the process, we introduce new analyses of nonlinear, continuous-time reservoirs that model these time cells.

A pair of flat parallel surfaces, each freely diffusing along the direction of their separation, will eventually come into contact. If the shapes of these surfaces also fluctuate, then contact will occur when their centers-of-mass remain separated by a nonzero distance $\ell$. An example of such a situation is the motion of interfaces between two phases at conditions of thermodynamic coexistence, and in particular the annihilation of domain wall pairs under periodic boundary conditions. Here we present a general approach to calculate the probability distribution of the contact distance $\ell$ and determine how its most likely value ${\ell }^{*}$ depends on the surfaces' lateral size $L$. Using the Edward-Wilkinson equation as a model for interfaces, we demonstrate that ${\ell }^{*}$ scales weakly with system size, i.e., the dependence of ${\ell }^{*}$ on $L$ for both ($1+1$)- and ($2+1$)-dimensional interfaces is such that ${lim}_{L\to \infty }({\ell }^{*}/L)=0$. In particular, for ($2+1$)-dimensional interfaces ${\ell }^{*}$ is an algebraic function of $logL$, a result that is confirmed by computer simulations of slab-shaped domains formed under periodic boundary conditions. This weak scaling implies that such domains remain topologically intact until $\ell$ becomes very small compared to the lateral size of the interface, contradicting expectations from equilibrium thermodynamics.

In two-dimensional turbulent systems the redistribution of energy can be described by quadratic nonlinear three-wave interactions, which are limited by resonance conditions. The set of coupling modes can be understood as resonant manifold. It has been predicted by theory that, in the presence of a shear flow, the resonant manifold in wave-number space shrinks in time favoring large-scale structures. The phenomenon of manifold shrinking in the presence of shear flows is studied the first time experimentally in drift wave turbulence at the stellarator TJ-K by bicoherence analysis. By estimating effective mode numbers characterizing the width of the manifold, it is demonstrated that increasing shear leads to a shrinking of the resonance manifold.

The phase diagram of the prototypical two-dimensional Lennard-Jones (LJ) system, while extensively investigated, is still debated. In particular, there are controversial results in the literature with regard to the existence of the hexatic phase and the melting scenario. Here we study the phase behavior of two-dimensional range-limited LJ particles via large-scale numerical simulations. We demonstrate that at a high temperature, when the attraction in the potential plays a minor role, melting occurs via a continuous solid-hexatic transition followed by a first-order hexatic-fluid transition. The hexatic phase occurs in a density range that vanishes as the temperature decreases so that at low-temperature melting occurs via a first-order liquid-solid transition. The temperature where the hexatic phase disappears is well above the liquid-gas critical temperature. The evolution of the density of topological defects confirms this scenario.

This work sets the exact equations for the quasiclassical response function and susceptibility of a Brownian particle immersed in a bath of quantum harmonic oscillators driven by nonlinear harmonic potentials. A delta force perturbation gives rise to a response whose susceptibility is the combination of a linear term, owner of the harmonic oscillator, plus a nonlinear one involving an integral equation. It is provided a recursion method to find its solutions based on functional equations in the Banach space. The ODE for the response function is a highly nonlinear damped nonautonomous Duffing equation for which the aforementioned method is used to get its solution.

Cross-frequency coupling (CFC) refers to the nonlinear interaction between oscillations in different frequency bands, and it is a rather ubiquitous phenomenon that has been observed in a variety of physical and biophysical systems. In particular, the coupling between the phase of slow oscillations and the amplitude of fast oscillations, referred as phase-amplitude coupling (PAC), has been intensively explored in the brain activity recorded from animals and humans. However, the interpretation of these CFC patterns remains challenging since harmonic spectral correlations characterizing nonsinusoidal oscillatory dynamics can act as a confounding factor. Specialized signal processing techniques are proposed to address the complex interplay between spectral harmonicity and different types of CFC, not restricted only to PAC. For this, we provide an in-depth characterization of the time locked index (TLI) as a tool aimed to efficiently quantify the harmonic content of noisy time series. It is shown that the proposed TLI measure is more robust and outperforms traditional phase coherence metrics (e.g., phase locking value, pairwise phase consistency) in several aspects. We found that a nonlinear oscillator under the effect of additive noise can produce spurious CFC with low spectral harmonic content. On the other hand, two coupled oscillatory dynamics with independent fundamental frequencies can produce true CFC with high spectral harmonic content via a rectification mechanism or other post-interaction nonlinear processing mechanisms. These results reveal a complex interplay between CFC and harmonicity emerging in the dynamics of biologically plausible neural network models and more generic nonlinear and parametric oscillators. We show that, contrary to what is usually assumed in the literature, the high harmonic content observed in nonsinusoidal oscillatory dynamics is neither a sufficient nor necessary condition to interpret the associated CFC patterns as epiphenomenal. There is mounting evidence suggesting that the combination of multimodal recordings, specialized signal processing techniques, and theoretical modeling is becoming a required step to completely understand CFC patterns observed in oscillatory rich dynamics of physical and biophysical systems.

Upon the Joyeux-Buyukdagli model of DNA, the helicoidal interactions are introduced, and their effects on the dynamical behaviors of the molecule investigated. A theoretical framework for the analysis is presented in an external force field, taking into account Stokes and hydrodynamics viscous forces. In the semi-discrete approximation, the dynamics of the molecule is found governed by the cubic complex Ginzburg-Landau (CGL) equation. By choosing an appropriate decoupling ansatz, the cubic CGL equation is transformed into a nonlinear differential equation whose analytical solitary wave-like solutions can be explored by means of the direct method, which is more tractable in case where the form of soliton solutions is known. Based on this, a dissipative bright-like soliton solution is obtained. Numerical experiments have been done, and relevant results were brought out, such as the quantitative and qualitative influences of the helical interactions on the parameters of the traveling bubble. The important role-played by these interactions in the DNA biological processes is brought out, showing that depending on the wave number, their effects can increase, decrease, or keep constant the bubble angular frequency, velocity, amplitude, and width, as well as the energy involved by enzymes in the initiation of DNA biological processes. This can prevent some coding or reading errors and resulting genetic damages. Analytical predictions and numerical experiments were in good agreement.

Voluntary human movements are stereotyped. When modeled in the framework of classical mechanics they are expected to minimize cost functions that may include energy, a natural candidate from a physiological point of view also. In time-changing environments, however, energy is no longer conserved—regardless of frictional energy dissipation—and it is therefore not the preferred candidate for any cost function able to describe the subsequent changes in motor strategies. Adiabatic invariants are known to be relevant observables in such systems, although they still need to be investigated in human motor control. We fill this gap and show that the theory of adiabatic invariants provides an accurate description of how human participants modify a voluntary, rhythmic, one-dimensional motion of the forearm in response to variable gravity (from 1 to $3g$). Our findings suggest that adiabatic invariants may reveal generic hidden constraints ruling human motion in time-changing gravity.