We carry out an analytic investigation of stochastic oscillations in a susceptible-infected-recovered model of disease spread on a network of $n$ cities. In the model a fraction $f_{jk}$ of individuals from city $k$ commute to city $j$, where they may infect, or be infected by, others. Starting from a continuous-time Markov description of the model the deterministic equations, which are valid in the limit when the population of each city is infinite, are recovered. The stochastic fluctuations about the fixed point of these equations are derived by use of the van Kampen system-size expansion. The fixed point structure of the deterministic equations is remarkably simple: A unique nontrivial fixed point always exists and has the feature that the fraction of susceptible, infected, and recovered individuals is the same for each city irrespective of its size. We find that the stochastic fluctuations have an analogously simple dynamics: All oscillations have a single frequency, equal to that found in the one-city case. We interpret this phenomenon in terms of the properties of the spectrum of the matrix of the linear approximation of the deterministic equations at the fixed point.

Cell communication is a key mechanism in tissue responses to radiation. Several molecules are implicated in radiation-induced signaling between cells, but their contributions to radiation risk are poorly understood. Meanwhile, Green's functions for diffusion-influenced reactions have appeared in the literature, which are applied to describe the diffusion of molecules near a plane membrane comprising bound receptors with the possibility of reversible binding of a ligand and activation of signal transduction proteins by the ligand-receptor complex. We have developed Brownian dynamics algorithms to simulate particle histories in this system which can accurately reproduce the theoretical distribution of distances of a ligand from the membrane, the number of reversibly bound particles, and the number of receptor complexes activating signaling proteins as a function of time, regardless of the number of time steps used for the simulation. These simulations will be of great importance to model interactions at low doses where stochastic effects induced by a small number of molecules or interactions come into play.

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by population dynamics in general. Especially for fast reproducing microbes which are subject to selection, both types of dynamics are often closely intertwined. We illustrate this by considering different growth scenarios. Depending on whether microbes die or stop to reproduce (dormancy), qualitatively different behaviors emerge. For cooperating bacteria, a permanent increase of costly cooperation can occur. Even if not permanent, cooperation can still increase transiently due to demographic fluctuations. We validate our analysis via stochastic simulations and analytic calculations. In particular, we derive a condition for an increase in the level of cooperation.

In this paper, we consider the problem of exploring structural regularities of networks by dividing the nodes of a network into groups such that the members of each group have similar patterns of connections to other groups. Specifically, we propose a general statistical model to describe network structure. In this model, a group is viewed as a hidden or unobserved quantity and it is learned by fitting the observed network data using the expectation-maximization algorithm. Compared with existing models, the most prominent strength of our model is the high flexibility. This strength enables it to possess the advantages of existing models and to overcome their shortcomings in a unified way. As a result, not only can broad types of structure be detected without prior knowledge of the type of intrinsic regularities existing in the target network, but also the type of identified structure can be directly learned from the network. Moreover, by differentiating outgoing edges from incoming edges, our model can detect several types of structural regularities beyond competing models. Tests on a number of real world and artificial networks demonstrate that our model outperforms the state-of-the-art model in shedding light on the structural regularities of networks, including the overlapping community structure, multipartite structure, and several other types of structure, which are beyond the capability of existing models.

The experimental and numerical results of the capillary-force-driven climb of wetting liquid in porous media, which is opposed by the gravity force, are analyzed with respect to the emergence of a multiphase flow front and flow stability of the climbing liquid. Two dynamic characteristics are used: (i) the multiphase flow front thickness as a function of time, and (ii) the capillary number as a function of Bond number, where both numbers are calculated from the harmonic average of pores radii. Throughout the climb, the influence of capillary, gravity, and viscous force variations on the flow behavior is investigated for different porous media. For a specific porous medium, a unique flow front power law function of time is observed for the capillary flow climbs with or without gravity force. Distinct dynamic flow front power law functions are found for different porous media. However, for capillary climb in different porous media, one is able to predict a unique behavior for the wetting height (the interface between wetted and dry regions of porous medium) using the capillary and Bond number. It is found that these two numbers correlate as a unique exponential function, even for porous media whose permeabilities vary for two orders of magnitude. For climbs without the gravity force (capillary spreads), the initial climb dynamics follows this exponential law, but for later flow times and when a significant flow front is developed, one observes a constant value of the capillary number. Using this approach to describe the capillary climb, only the capillary versus Bond number correlation is needed, which is completely measureable from the experiments.

We report detailed quantitative studies of elastic turbulence in a curvilinear channel flow in a dilute polymer solution of high molecular weight polyacrylamide in a high viscosity water-sugar solvent. Detailed studies of the average and rms velocity and velocity gradients profiles reveal the emergence of a boundary layer associated with the nonuniform distribution of the elastic stresses across the channel. The characteristic boundary width is independent of the Weissenberg number Wi and proportional to the channel width, which is consistent with the findings our early investigations of the boundary layer in elastic turbulence in different flow geometries. The nonuniform distribution of the elastic stresses across the channel and appearance of the characteristic spatial scales of the order of the boundary layer width of both velocity and velocity gradient in the correlation functions of the velocity and velocity gradient fields in a bulk flow may suggest that excessive elastic stresses, concentrated in the boundary layer, are ejected into the bulk flow similar to jets observed in passive scalar mixing in elastic turbulence observed recently. Finally, the experimental results show that one of the main predictions of the theory of elastic turbulence, namely, the saturation of the normalized rms velocity gradient in the bulk flow of elastic turbulence contradicts the experimental observations both qualitatively and quantitatively in spite of the fact that the theory explains well the observed sharp power-law decay of the velocity power spectrum. The experimental findings call for further development of theory of elastic turbulence in a bounded container, similar to what was done for a passive scalar problem.

We investigate convection patterns of binary mixtures with a positive separation ratio in porous media. As setup, we choose the Rayleigh-Bénard system of a fluid layer heated from below. Results are obtained by a multimode Galerkin method. Using this method, we compute square and crossroll patterns, and we analyze their structural, bifurcation, and stability properties. Evidence is provided that, for a strong enough Soret effect, both structures exist as stable forms of convection. Some of their properties are found to be similar to square and crossroll convection in the system without porous medium. However, there are also qualitative differences. For example, squares can be destabilized by oscillatory perturbations with square symmetry in porous media, and their velocity isolines are deformed in the so-called Soret regime.

We consider a long-wave oscillatory Marangoni convection in a layer of a binary liquid in the presence of the Soret effect. A weakly nonlinear analysis is carried out on a hexagonal lattice. It is shown that the derived set of cubic amplitude equations is degenerate. A three-parameter family of asynchronous hexagons (AH), representing a superposition of three standing waves with the amplitudes depending on their phase shifts, is found to be stable in the framework of this set of equations. To determine a dominant stable pattern within this family of patterns, we proceed to the inclusion of the fifth-order terms. It is shown that depending on the Soret number, either wavy rolls 2 (WR2), which represents a pattern descendant of wavy rolls (WR) family, are selected or no stable limit cycles exist. A heteroclinic cycle emerges in the latter case: the system is alternately attracted to and repelled from each of three unstable solutions.

We consider a liquid bearing gas bubbles in a porous medium. When gas bubbles are immovably trapped in a porous matrix by surface-tension forces, the dominant mechanism of transfer of gas mass becomes the diffusion of gas molecules through the liquid. Essentially, the gas solution is in local thermodynamic equilibrium with vapor phase all over the system, i.e., the solute concentration equals the solubility. When temperature and/or pressure gradients are applied, diffusion fluxes appear and these fluxes are faithfully determined by the temperature and pressure fields, not by the local solute concentration, which is enslaved by the former. We derive the equations governing such systems, accounting for thermodiffusion and gravitational segregation effects, which are shown not to be neglected for geological systems—marine sediments, terrestrial aquifers, etc. The results are applied for the treatment of non-high-pressure systems and real geological systems bearing methane or carbon dioxide, where we find a potential possibility of the formation of gaseous horizons deep below a porous medium surface. The reported effects are of particular importance for natural methane hydrate deposits and the problem of burial of industrial production of carbon dioxide in deep aquifers.

Using equilibrium and nonequilibrium molecular dynamic simulations, we found that engineering the strain on the graphene planes forming a channel can drastically change the interfacial friction of water transport through it. There is a sixfold change of interfacial friction stress when the strain changes from $-10\%$ to $10\%$. Stretching the graphene walls increases the interfacial shear stress, while compressing the graphene walls reduces it. Detailed analysis of the molecular structure reveals the essential roles of the interfacial potential energy barrier and the structural commensurateness between the solid walls and the first water layer. Our results suggest that the strain engineering is an effective way of controlling the water transport inside nanochannels. The resulting quantitative relations between shear stress and slip velocity and the understanding of the molecular mechanisms will be invaluable in designing graphene nanochannel devices.

The observation of Doppler splitting in K-shell x-ray lines emitted from optically thin dopants is used to infer implosion velocities of up to 70 cm/$\mu$s in wire-array and gas-puff $Z$ pinches at drive currents of 15–20 MA. These data can benchmark numerical implosion models, which produce reasonable agreement with the measured velocity in the emitting region. Doppler splitting is obscured in lines with strong opacity, but red-shifted absorption produced by the cooler halo of material backlit by the hot core assembling on axis can be used to diagnose velocity in the trailing mass.

Using the Darboux transformation technique and numerical simulations, we study the hierarchy of rational solutions of the nonlinear Schrödinger equation that can be considered as higher order rogue waves in this model. This analysis reveals the existence of rogue wave clusters with a high level of symmetry in the $(x,t)$ plane. These structures arise naturally when the shifts in the Darboux scheme are taken to be eigenvalue dependent. We have found single-shell structures where a central higher order rogue wave is surrounded by a ring of first order peaks on the $(x,t)$ plane.

It is shown that a uniform electromagnetic plane wave can exert a negative force on a homogeneous medium with gain when there is no component of the electric field in that direction. A physical interpretation for this force is given, along with an estimate of the strength achievable in an experiment.

In a recent computational investigation, Yazdani et al. [Phys. Rev. E 83, 046305 (2011)] reported an exponential (logarithmic) dependence of the tank-treading frequency $F_{tt}$ with the viscosity ratio $\lambda$ at low (moderate) viscosity ratios for erythrocytes in shear flows. We argue that the authors misinterpreted the inverse linear dependence on $\lambda$ of the tank-treading frequency $F_{tt}$, as found by Wodson and Dimitrakopoulos [Biophys. J. 99, 2906 (2010)], owing to the fact that Yazdani et al. plotted their frequency-versus-$\lambda$ results in a log-log plot.

We study discontinuous percolation transitions (PTs) in the diffusion-limited cluster aggregation model of the sol-gel transition as an example of real physical systems, in which the number of aggregation events is regarded as the number of bonds occupied in the system. When particles are Brownian, in which cluster velocity depends on cluster size as $v_s\sim s^{\eta }$ with $\eta =-0.5$, a larger cluster has less probability to collide with other clusters because of its smaller mobility. Thus, the cluster is effectively more suppressed in growth of its size. Then the giant cluster size increases drastically by merging those suppressed clusters near the percolation threshold, exhibiting a discontinuous PT. We also study the tricritical behavior by controlling the parameter $\eta$, and the tricritical point is determined by introducing an asymmetric Smoluchowski equation.

Nucleosides are chemical compounds that have an extremely important biological role; they can be found in all types of living organisms. They are crucial components from which DNA and RNA acids are built. In addition, nucleosides are key regulators of many physiological processes. In this paper, the molecular dynamics in the liquid and glassy state of three selected nucleosides, β-adenosine, β-thymidine, and β-uridine, was investigated by means of dielectric spectroscopy. Our results revealed multiple relaxation processes associated with different types of molecular motions. Besides the primary α relaxation, two secondary modes in the glassy states of examined compounds were identified. Crystallization progress monitored by dielectric spectroscopy and x-ray diffraction technique at isostructural relaxation conditions revealed that the examined nucleosides possess completely different tendencies to recrystallize from the liquid as well as the glassy state. We have also made an attempt to predict the time scale of molecular motion below the glass transition temperatures of the respective nucleosides to discuss their potential stability at room temperature over prolonged storage time. Finally, combination of molecular mobility studies with evaluation of thermodynamic parameters from calorimetric measurements allowed us to discuss the fundamental roles of both kinetic and thermodynamic factors in governing the physical stability of the glassy state.

We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms may not be sufficiently effective. We study the flux of secondary electrons through the surface of nucleosomes and calculate the radial dose and the distribution of clustered damage around the ion's path. The calculated radial dose distribution is compared to simulations. The radial distribution of the complex damage is found to be different from that of the dose. A comparison with experiments may solve the question of what is more lethal for the cell, damage complexity or absorbed energy. We suggest a way to calculate the probability of cell death based on the complexity of the damage. This work is done within the framework of the phenomenon-based multiscale approach to radiation damage by ions.

The mesoscopic description of chemical kinetics, the chemical master equation, can be exactly solved in only a few simple cases. The analytical intractability stems from the discrete character of the equation, and hence considerable effort has been invested in the development of Fokker-Planck equations, second-order partial differential equation approximations to the master equation. We here consider two different types of higher-order partial differential approximations, one derived from the system-size expansion and the other from the Kramers-Moyal expansion, and derive the accuracy of their predictions for chemical reactive networks composed of arbitrary numbers of unimolecular and bimolecular reactions. In particular, we show that the partial differential equation approximation of order $Q$ from the Kramers-Moyal expansion leads to estimates of the mean number of molecules accurate to order ${\Omega }^{-(2Q-3)/2}$, of the variance of the fluctuations in the number of molecules accurate to order ${\Omega }^{-(2Q-5)/2}$, and of skewness accurate to order ${\Omega }^{-(Q-2)}$. We also show that for large $Q$, the accuracy in the estimates can be matched only by a partial differential equation approximation from the system-size expansion of approximate order $2Q$. Hence, we conclude that partial differential approximations based on the Kramers-Moyal expansion generally lead to considerably more accurate estimates in the mean, variance, and skewness than approximations of the same order derived from the system-size expansion.

Excitation waves on a subexcitable Belousov-Zhabotinsky (BZ) substrate can be manipulated by chemical variations in the substrate and by interactions with other waves. Symbolic assignment and interpretation of wave dynamics can be used to perform logical and arithmetic computations. We present chemical analogs of elementary logic and arithmetic circuits created entirely from interconnected arrangements of individual BZ encapsulated cell-like disk. Interdisk wave migration is confined in carefully positioned connecting pores. This connection limits wave expansion and unifies the input-output characteristic of the disks. Circuit designs derived from numeric simulations are optically encoded onto a homogeneous photosensitive BZ substrate.