The susceptible-infected-recovered (SIR) model with spatially inhomogeneous infection rate is studied with numerical simulations in one, two, and three dimensions, considering the case that the infection spreads inhomogeneously in densely populated regions or hot spots. We find that the total population of infection decays very slowly in the inhomogeneous systems in some cases, in contrast to the exponential decay of the infected population $I\left(t\right)$ in the SIR model of the ordinary differential equation. The slow decay of the infected population suggests that the infection is locally maintained for long and it is difficult for the disease to disappear completely.

The inverse problem of finding the optimal network structure for a specific type of dynamical process stands out as one of the most challenging problems in network science. Focusing on the susceptible-infected-susceptible type of dynamics on annealed networks whose structures are fully characterized by the degree distribution, we develop an analytic framework to solve the inverse problem. We find that, for relatively low or high infection rates, the optimal degree distribution is unique, which consists of no more than two distinct nodal degrees. For intermediate infection rates, the optimal degree distribution is multitudinous and can have a broader support. We also find that, in general, the heterogeneity of the optimal networks decreases with the infection rate. A surprising phenomenon is the existence of a specific value of the infection rate for which any degree distribution would be optimal in generating maximum spreading prevalence. The analytic framework and the findings provide insights into the interplay between network structure and dynamical processes with practical implications.

Monolayers of anisotropic cells exhibit long-ranged orientational order and topological defects. During the development of organisms, orientational order often influences morphogenetic events. However, the linkage between the mechanics of cell monolayers and topological defects remains largely unexplored. This holds specifically at the timescales relevant for tissue morphogenesis. Here, we build on the physics of liquid crystals to determine material parameters of cell monolayers. In particular, we use a hydrodynamical description of an active polar fluid to study the steady-state mechanical patterns at integer topological defects. Our description includes three distinct sources of activity: traction forces accounting for cell-substrate interactions as well as anisotropic and isotropic active nematic stresses accounting for cell-cell interactions. We apply our approach to C2C12 cell monolayers in small circular confinements, which form isolated aster or spiral topological defects. By analyzing the velocity and orientational order fields in spirals as well as the forces and cell number density fields in asters, we determine mechanical parameters of C2C12 cell monolayers. Our work shows how topological defects can be used to fully characterize the mechanical properties of biological active matter.

While causality processing is an essential cognitive capacity of the neural system, a systematic understanding of the neural coding of causality is still elusive. We propose a physically fundamental analysis of this issue and demonstrate that the neural dynamics encodes the original causality between external events near homomorphically. The causality coding is memory robust for the amount of historical information and features high precision but low recall. This coding process creates a sparser representation for the external causality. Finally, we propose a statistic characterization for the neural coding mapping from the original causality to the coded causality in neural dynamics.

Except for director orientation, the deformation modes of constrained liquid crystal elastomer thin plate display specimen geometry size dependence due to the boundary effect. In this paper, the effect of plate geometry size on the spontaneous deformation of a simply supported liquid crystal elastomer plate is studied. The relation between the deformation modes with director orientation and plate geometry size are investigated. Results show that the deformation modes are decided by the director orientation for a certain liquid crystal elastomer, but the geometry size affects the mode transformation with respect to the director. These results are supposed to be used in the design and application of liquid crystal elastomer-based smart actuators or sensors.

Two-dimensional free surface flows in Hele-Shaw configurations are a fertile ground for exploring nonlinear physics. Since Saffman and Taylor's work on linear instability of fluid-fluid interfaces, significant effort has been expended to determining the physics and forcing that set the linear growth rate. However, linear stability does not always imply nonlinear stability. We demonstrate how the combination of a radial and an azimuthal external magnetic field can manipulate the interfacial shape of a linearly unstable ferrofluid droplet in a Hele-Shaw configuration. We show that weakly nonlinear theory can be used to tune the initial unstable growth. Then, nonlinearity arrests the instability and leads to a permanent deformed droplet shape. Specifically, we show that the deformed droplet can be set into motion with a predictable rotation speed, demonstrating nonlinear traveling waves on the fluid-fluid interface. The most linearly unstable wave number and the combined strength of the applied external magnetic fields determine the traveling wave shape, which can be asymmetric.

We explore the performance of the Gibbs-ensemble Monte Carlo simulation technique by calculating the miscibility gap of ${\mathrm{H}}_2\text{−}\mathrm{He}$ mixtures with analytical exponential-six potentials. We calculate several demixing curves for pressures up to 500 kbar and for temperatures up to $1800\mathrm{K}$ and predict a ${\mathrm{H}}_2\text{−}\mathrm{He}$ miscibility diagram for the solar He abundance for temperatures up to $1500\mathrm{K}$ and determine the demixing region. Our results are in good agreement with ab initio simulations in the nondissociated region of the phase diagram. However, the particle number necessary to converge the Gibbs-ensemble Monte Carlo method is yet too large to offer a feasible combination with ab initio electronic structure calculation techniques, which would be necessary at conditions where dissociation or ionization occurs.

The first Kelvin relation, which states the Peltier coefficient should be equal to the product of temperature and Seebeck coefficient, is a fundamental principle in thermoelectricity. It has been regarded as an important application and direct experimental verification of the Onsager reciprocal relation (ORR) that is a cornerstone of irreversible thermodynamics. However, some critical questions still remain: (a) why Kelvin's proof—which omits all irreversibility within a thermoelectric transport process—can reach the correct result, (b) how to properly select the generalized-force-flux pairs for deriving the first Kelvin relation from the ORR, and (c) whether the first Kelvin relation is restricted by the requirement of the linear transport regime. The aim of the present work is to answer these questions based on the fundamental thermodynamic principles. Since the thermoelectric effects are reversible, we can redefine the Seebeck and Peltier coefficients using the quantities in reversible processes with no time derivative involved; these are renamed “reversible Seebeck and Peltier coefficients.” The relation between them (called “the reversible reciprocal relation of thermoelectricity”) is derived from the Maxwell relations, which can be reduced to the conventional Kelvin relation, when the local equilibrium assumption (LEA) is adopted. In this sense, the validity of the first Kelvin relation is guaranteed by the reversible thermodynamic principles and the LEA, without the requirement of the linear transport process. Additionally, the generalized force-flux pairs to obtain the first Kelvin relation from the ORR can be proper both mathematically and thermodynamically, only when they correspond to the conjugate-variable pairs of which Maxwell relations can yield the reversible reciprocal relation. The present theoretical framework can be further extended to other coupled phenomena.

We study the low-temperature domain growth kinetics of the two-dimensional Ising model with long-range coupling $J\left(r\right)\sim r^{-(d+\sigma )}$, where $d=2$ is the dimensionality. According to the Bray-Rutenberg predictions, the exponent $\sigma$ controls the algebraic growth in time of the characteristic domain size $L\left(t\right), L\left(t\right)\sim t^{1/z}$, with growth exponent $z=1+\sigma$ for $\sigma <1$ and $z=2$ for $\sigma >1$. These results hold for quenches to a nonzero temperature $T>0$ below the critical temperature $T_c$. We show that, in the case of quenches to $T=0$, due to the long-range interactions, the interfaces experience a drift which makes the dynamics of the system peculiar. More precisely, we find that in this case the growth exponent takes the value $z=4/3$, independently of $\sigma$, showing that it is a universal quantity. We support our claim by means of extended Monte Carlo simulations and analytical arguments for single domains.

It is commonly accepted that in typical situations the rate of entropy production is non-negative. We show that this assertion is not entirely correct, not even in the linear regime, if a time-dependent, external perturbation is not compensated by a rapid enough decay of the response function. This is demonstrated for three variants of the Drude model to describe electrical conduction in noble metals, namely the classical free electron gas, the Drude-Sommerfeld model, and the extended Drude-Sommerfeld model. The analysis is concluded with a discussion of potential experimental verifications and ramifications of negative entropy production rates.

We study the spectral statistics of quantum systems with finite Hilbert spaces. We derive a theorem showing that eigenlevels in such systems cannot be globally uncorrelated, even in the case of fully integrable dynamics, as a consequence of the unfolding procedure. We provide an analytic expression for the power spectrum of the ${\delta }_n$ statistic for a model of intermediate statistics with level repulsion but independent spacings, and we show both numerically and analytically that the result is spoiled by the unfolding procedure. Then, we provide a simple model to account for this phenomenon, and test it by means of numerics on the disordered $XXZ$ chain, the paradigmatic model of many-body localization, and the rational Gaudin-Richardson model, a prototypical model for quantum integrability.

DNA methylation is associated with a number of biological phenomena, and plays crucial roles in epigenetic regulation of eukaryotic gene expression. It is also suggested that DNA methylation alters the mechanical properties of DNA molecules, which is likely to affect epigenetic regulation. However, it has not been systematically investigated how methylation changes the structural and dynamic features of DNA. In this research, to elucidate the effects of methylation on DNA mechanics, a fully atomic molecular dynamics simulation of double-stranded DNA with several methylation patterns was performed. Through the analysis of the relative positioning of the nucleotides (base-step variables), characteristic changes in terms of local flexibility were observed, which further affected the overall DNA geometry and stiffness. These findings may serve as a basis for a discussion on methylation-dependent DNA dynamics in physiological conditions.

The mechanics of lower dimensional elastic structures depends strongly on the geometry of their stress-free state. Elastic deformations separate into in-plane stretching and lower energy out-of-plane bending deformations. For elastic structures with a curved stress-free state, these two elastic modes are coupled within linear elasticity. We investigate the effect of that curvature-induced coupling on wave propagation in lower dimensional elastic structures, focusing on the simplest example—a curved elastic rod in two dimensions. We focus only on the geometry-induced coupling between bending and longitudinal (in-plane) strain that is common to both rods in two dimensions and to elastic shells. We find that the dispersion relation of the waves becomes gapped in the presence of finite curvature; bending modes are absent below a frequency proportional to the curvature of the rod. By studying the scattering of undulatory waves off regions of uniform curvature, we find that undulatory waves with frequencies in the gap associated with the curved region tunnel through that curved region via conversion into compression waves. These results should be directly applicable to the spectrum and spatial distribution of phonon modes in a number of curved rod-like elastic solids, including carbon nanotubes and biopolymer filaments.

The laser interaction with an electron-positron-ion mixed plasma is studied from the perspective of the associated high-order harmonic generation. For an idealized mixed plasma which is assumed with a sharp plasma-vacuum interface and uniform density distribution, when it is irradiated by a weakly relativistic laser pulse, well-defined signals at harmonics of the plasma frequency in the harmonic spectrum are observed. These characteristic signals are attributed to the inverse two-plasmon decay of the counterpropagating monochromatic plasma waves which are excited by the energetic electrons and the positron beam accelerated by the laser. Particle-in-cell simulations show the signal at twice the plasma frequency can be observed for a pair density as low as $\sim {10}^{-5}$ of the plasma density. In the self-consistent scenario of pair production by an ultraintense laser striking a solid target, particle-in-cell simulations, which account for quantum electrodynamic effects (photon emission and pair production), show that dense (greater than the relativistically corrected critical density) and hot pair plasmas can be created. The harmonic spectrum shows weak low-order harmonics, indicating a high laser absorption due to quantum electrodynamic effects. The characteristic signals at harmonics of the plasma frequency are absent, because broadband plasma waves are excited due to the high plasma inhomogeneity introduced by the interaction. However, the high-frequency harmonics are enhanced due to the high-frequency modulations from the direct laser coupling with created pair plasmas.

A vibrational model of heat transfer in simple liquids with soft pairwise interatomic interactions is discussed. A general expression is derived, which involves an averaging over the liquid collective mode excitation spectrum. The model is applied to quantify heat transfer in a dense Lennard-Jones liquid and a strongly coupled one-component plasma. Remarkable agreement with the available numerical results is documented. A similar picture does not apply to the momentum transfer and shear viscosity of liquids.

The free-energy lattice Boltzmann (LB) model is one of the major multiphase models in the LB community. The present study is focused on a class of free-energy LB models in which the divergence of thermodynamic pressure tensor or its equivalent form expressed by the chemical potential is incorporated into the LB equation via a forcing term. Although this class of free-energy LB models may be thermodynamically consistent at the continuum level, it suffers from thermodynamic inconsistency at the discrete lattice level owing to numerical errors [Guo et al., Phys. Rev. E 83, 036707 (2010)]. The numerical error term mainly includes two parts: one comes from the discrete gradient operator and the other can be identified in a high-order Chapman-Enskog analysis. In this paper, we propose an improved scheme to eliminate the thermodynamic inconsistency of the aforementioned class of free-energy LB models. The improved scheme is constructed by modifying the equation of state of the standard LB equation, through which the discretization of $\mathbf{\nabla }\left(\rho c_s^2\right)$ is no longer involved in the force calculation and then the numerical errors can be significantly reduced. Numerical simulations are subsequently performed to validate the proposed scheme. The numerical results show that the improved scheme is capable of eliminating the thermodynamic inconsistency and can significantly reduce the spurious currents in comparison with the standard forcing-based free-energy LB model.

A multiple-relaxation-time discrete Boltzmann model (DBM) is proposed for multicomponent mixtures, where compressible, hydrodynamic, and thermodynamic nonequilibrium effects are taken into account. It allows the specific heat ratio and the Prandtl number to be adjustable, and is suitable for both low and high speed fluid flows. From the physical side, besides being consistent with the multicomponent Navier-Stokes equations, Fick's law, and Stefan-Maxwell diffusion equation in the hydrodynamic limit, the DBM provides more kinetic information about the nonequilibrium effects. The physical capability of DBM to describe the nonequilibrium flows, beyond the Navier-Stokes representation, enables the study of the entropy production mechanism in complex flows, especially in multicomponent mixtures. Moreover, the current kinetic model is employed to investigate nonequilibrium behaviors of the compressible Kelvin-Helmholtz instability (KHI). The entropy of mixing, the mixing area, the mixing width, the kinetic and internal energies, and the maximum and minimum temperatures are investigated during the dynamic KHI process. It is found that the mixing degree and fluid flow are similar in the KHI process for cases with various thermal conductivity and initial temperature configurations, while the maximum and minimum temperatures show different trends in cases with or without initial temperature gradients. Physically, both heat conduction and temperature exert slight influences on the formation and evolution of the KHI morphological structure.

The binary Monte Carlo (MC) collision algorithm is a standard and robust method to include binary Coulomb collision effects in particle-in-cell (PIC) simulations of plasmas. Here we show that the coupling between PIC and MC algorithms can give rise to (nonphysical) numerical heating of the system that significantly exceeds that observed when these algorithms operate independently. We argue that this deleterious effect results from an inconsistency between the particle motion associated with MC collisions and the work performed by the collective electromagnetic field on the PIC grid. This inconsistency manifests as the (artificial) stochastic production of electromagnetic energy, which ultimately heats the plasma particles. The MC-induced numerical heating can significantly impact the evolution of the simulated system for long simulation times ($\gtrsim {10}^3$ collision periods, for typical numerical parameters). We describe the source of the MC-induced numerical heating analytically and discuss strategies to minimize it.

There is a deep connection between the ground states of transverse-field spin systems and the late-time distributions of evolving viral populations—within simple models, both are obtained from the principal eigenvector of the same matrix. However, that vector is the wave-function amplitude in the quantum spin model, whereas it is the probability itself in the population model. We show that this seemingly minor difference has significant consequences: Phase transitions that are discontinuous in the spin system become continuous when viewed through the population perspective, and transitions that are continuous become governed by new critical exponents. We introduce a more general class of models that encompasses both cases and that can be solved exactly in a mean-field limit. Numerical results are also presented for a number of one-dimensional chains with power-law interactions. We see that well-worn spin models of quantum statistical mechanics can contain unexpected new physics and insights when treated as population-dynamical models and beyond, motivating further studies.

Coined discrete-time quantum walks are studied using simple deterministic dynamical systems as coins whose classical limit can range from being integrable to chaotic. It is shown that a Loschmidt echo-like fidelity plays a central role, and when the coin is chaotic this is approximately the characteristic function of a classical random walker. Thus the classical binomial distribution arises as a limit of the quantum walk and the walker exhibits diffusive growth before eventually becoming ballistic. The coin-walker entanglement growth is shown to be logarithmic in time as in the case of many-body localization and coupled kicked rotors, and saturates to a value that depends on the relative coin and walker space dimensions. In a coin-dominated scenario, the chaos can thermalize the quantum walk to typical random states such that the entanglement saturates at the Haar averaged Page value, unlike in a walker-dominated case when atypical states seem to be produced.