Recently, the breakup of spiral and concentric ringed spherulites has been observed experimentally in isothermal crystallization of poly(vinylidene fluoride) in its blends with ethylene vinyl acetate copolymer. To elucidate the phenomenon of spiral breakup in polymer spherulites, a theoretical simulation has been undertaken in the framework of the phase field model of solidification based on time-dependent Ginzburg-Landau equations (TDGL model C) pertaining to the conserved concentration and nonconserved phase field order parameters. The concentration order parameter was described in terms of the Landau-type potential, while the crystal order parameter was expressed in terms of an asymmetric double-well potential to account for the nonequilibrium nature (i.e., metastability) of polymer crystallization. After inserting these potentials into the TDGL model C, the resulting coupled time-evolution equations show the emergence of the target and spiral patterns that undergo fragmentation at a very shallow supercooling. It is concluded that the depth of supercooling is the major contributor to the formation of the spirals and subsequent breakup of the spiral arms.

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate $u_c$ is obtained separating two scenarios: above $u_c$ the population predominantly consists of a mixture of strategies whereas below $u_c$ the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

A kinetics model is proposed for the description of ion conductance of low- and high-conductance potassium ion channels. The model describes ion permeation through the selectivity filter, which is assumed to be the only conductance determining part of the open channel. The filter occupancy can vary from zero to three ions, affecting the ion entry and exit rates. Ion motion between the binding sites inside the filter is assumed fast compared to the latter rates allowing averaging the equilibrium entry and exit rate constants over the possible ion configurations in the filter with a particular occupancy. Averaged rate constants related to a pair of adjacent occupancy states characterize a particular ion permeation mechanism. An expression for the channel conductance as a function of the symmetrical external ion concentration is derived. It comprises a sum of concentration independent conductance amplitudes for different ion permeation mechanisms weighted by the equilibrium filter occupancy probabilities. It is shown that each amplitude (i.e., maximum contribution to the channel conductance from each conductance mechanism) is proportional to an averaged exit rate constant and to quantities characterizing the effect of the applied electric field on the rate constants and the equilibrium ion distribution in the filter. The conductance expression derived provides a good description of the experimentally observed conductance-concentration curves for low-conductance (e.g., Kir2.1) and high-conductance (e.g., KcsA) potassium channels. It enables one to obtain equilibrium ion binding constants at different filter occupancies and to calculate the average number of ions in the selectivity filter for a given external ion concentration. For KcsA this number (2.0 at $200\mathrm{mM}$) is in a good agreement with the available experimental value (2.1 at $200\mathrm{mM}$). For the high-conductance potassium channels the net negative electrical charge around the selectivity filter increases the ion binding constants, thereby causing the larger occupancy probabilities to occur at smaller external ion concentrations compared to the low-conductance channels. This substantially increases the contributions of the two- and three-ion permeation mechanisms, with the larger conductance amplitudes leading to increased channel conductance compared to the low-conductance channels.

The efficiency of traffic routing on complex networks can be reflected by two key measurements, i.e., the network capacity and the average travel time of data packets. In this paper we propose a mixing routing strategy by integrating local static and dynamic information for enhancing the efficiency of traffic on scale-free networks. The strategy is governed by a single parameter. Simulation results show that maximizing the network capacity and reducing the packet travel time can generate an optimal parameter value. Compared with the strategy of adopting exclusive local static information, the new strategy shows its advantages in improving the efficiency of the system. The detailed analysis of the mixing strategy is provided for explaining its effects on traffic routing. The work indicates that effectively utilizing the larger degree nodes plays a key role in scale-free traffic systems.

Starting from an initial wiring of connections, we show that the synchronizability of a network can be significantly improved by evolving the graph along a time dependent connectivity matrix. We consider the case of connectivity matrices that commute at all times, and compare several approaches to engineer the corresponding commutative graphs. In particular, we show that synchronization in a dynamical network can be achieved even in the case in which each individual commutative graphs does not give rise to synchronized behavior.

Using a united atom model, we performed molecular dynamics (MD) simulations on the 4-$n$-alkyl-$4^{\prime }$-cyanobiphenyl (nCB) liquid crystal homologous series for $n=5–9$ at a constant reduced temperature in the nematic phase. To evaluate the rotational diffusion coefficient (RDC), the second- and fourth-rank order parameters (OP’s) and correlation time were calculated from MD trajectories. We analyzed the rotational viscosity coefficient (RVC) by using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. The simulated RDC, RVC, and OP’s were found to be reasonable when compared with previous theoretical and experimental data. These quantities were also calculated for the rigid core and alkyl chain segments separately for each mesogen, to take a closer look at the molecule tail-chain flexibility. The properties calculated for a rigid core were compared with those for an alkyl chain, and satisfactory results were obtained. Odd-even effects for RDF, RVC, and molecular ordering parameters were calculated for five mesogens.

We propose a self-propelled particle model for the swarming of Daphnia that takes into account mutual repulsion and attraction to a center. Surprisingly, a vortex is formed only for an intermediate strength of propulsion. The phase diagram and the transitions between states with and without a vortex are analyzed, and the nature of the phase boundaries is discussed based on a linear stability analysis of the motion of individual swimmers. This allows us to identify various key parameters determining the characteristic features of the collective motion.

This paper develops a simplified model for sexual reproduction within the quasispecies formalism. The model assumes a diploid genome consisting of two chromosomes, where the fitness is determined by the number of chromosomes that are identical to a given master sequence. We also assume that there is a cost to sexual reproduction, given by a characteristic time ${\tau }_{\mathit{\text{seek}}}$ during which haploid cells seek out a mate with which to recombine. If the mating strategy is such that only viable haploids can mate, then when ${\tau }_{\mathit{\text{seek}}}=0$, it is possible to show that sexual reproduction will always out compete asexual reproduction. However, as ${\tau }_{\mathit{\text{seek}}}$ increases, sexual reproduction only becomes advantageous at progressively higher mutation rates. Once the time cost for sex reaches a critical threshold, the selective advantage for sexual reproduction disappears entirely. The results of this paper suggest that sexual reproduction is not advantageous in small populations per se, but rather in populations with low replication rates. In this regime, the cost for sex is sufficiently low that the selective advantage obtained through recombination leads to the dominance of the strategy. In fact, at a given replication rate and for a fixed environment volume, sexual reproduction is selected for in high populations because of the reduced time spent finding a reproductive partner.

In this work, we show a mathematical model for the angiogenesis by endothelial cells. We present the model at the level of partial differential equations, describing the spatiotemporal evolution of the cell population, the extracellular matrix macromolecules, the proteases, the tumor angiogenic factors, and the possible presence of inhibitors. We mainly focus, however, on a complementary, more physiologically realistic, hybrid approach in which the cells are treated as individual particles. We examine the model numerically in two-dimensional settings, discussing its comparison with experimental results.

A comparative study of the temperature dependence of the elastic constants of the nematic liquid crystals known as PAA ($p$-azoxyanisole), MBBA $4^{\prime }$-methoxybenzylidene-4-$n$-butylaniline, and 5CB (4-$n$-pentyl-$4^{\prime }$-cyanobiphenyl) will be made in this work. After a regularization of their values, and with use of a unique temperature scale, the experimental data of each of these parameters will be displayed along the lines of corresponding states that are not restricted to the neighborhoods of the nematic-isotropic phase transition point, as it would be the case in a usual corresponding states law, but encompass the entire nematic phase.

We study a class of heat engines including Feynman’s ratchet, which exhibits a directed motion of a particle in nonequilibrium steady states maintained by two heat baths. We measure heat transfer from each heat bath separately, and average them using a careful procedure that reveals the nature of the heat transfer associated with directed steps of the particle. Remarkably we find that steps are associated with nonvanishing heat transfer even in equilibrium, and there is a quantitative relation between this hidden heat transfer and the directed motion of the particle. This relation is clearly understood in terms of the principle of heat transfer enhancement, which is expected to apply to a large class of highly nonequilibrium systems.

Noise theory is used to study the temporal correlations of stationary random fluctuations that are homogeneous in space. Statistical properties of the fluctuations, such as the power spectrum and the correlation function, are computed. The results are compared with the observed plasma density fluctuations from tokamak experiments.

We consider the penetration length $l$ of random walkers diffusing in a medium of perfect or imperfect absorbers of number density $\rho$. We solve this problem on a lattice and in the continuum in all dimensions $D$, by means of a mean-field renormalization group. For a homogeneous system in $D>2$, we find that $l\sim \max (\xi ,{\rho }^{-1∕2})$, where $\xi$ is the absorber density correlation length. The cases of $D=1$ and $D=2$ are also treated. In the presence of long-range correlations, we estimate the temporal decay of the density of random walkers not yet absorbed. These results are illustrated by exactly solvable toy models, and extensive numerical simulations on directed percolation, where the absorbers are the active sites. Finally, we discuss the implications of our results for diffusion limited aggregation (DLA), and we propose a more effective method to measure $l$ in DLA clusters.

Recent works on network security have focused on whether a complex network can maintain its integrability under attack or random node failures. In applications of increasing importance such as sensor networks, a somewhat different problem, namely, the occurrence of isolated nodes (or blind spots), is of great interest. We show that, for networks with a stronger ability to form global spanning clusters, it is relatively more difficult to eliminate blind spots, and vice versa. We use the framework of percolation to investigate this phenomenon. Our analysis also yields a formula for the average number of blind spots, which provide an explanation for several numerical findings.

While current studies on complex networks focus on systems that change relatively slowly in time, the structure of the most visited regions of the web is altered at the time scale from hours to days. Here we investigate the dynamics of visitation of a major news portal, representing the prototype for such a rapidly evolving network. The nodes of the network can be classified into stable nodes, which form the time-independent skeleton of the portal, and news documents. The visitations of the two node classes are markedly different, the skeleton acquiring visits at a constant rate, while a news document’s visitation peaks after a few hours. We find that the visitation pattern of a news document decays as a power law, in contrast with the exponential prediction provided by simple models of site visitation. This is rooted in the inhomogeneous nature of the browsing pattern characterizing individual users: the time interval between consecutive visits by the same user to the site follows a power-law distribution, in contrast to the exponential expected for Poisson processes. We show that the exponent characterizing the individual user’s browsing patterns determines the power-law decay in a document’s visitation. Finally, our results document the fleeting quality of news and events: while fifteen minutes of fame is still an exaggeration in the online media, we find that access to most news items significantly decays after $36\text{hours}$ of posting.

The study of the long time behavior of systems with time-scale separation is considerably facilitated if the fast degrees of freedom can be eliminated without affecting the slow dynamics. We investigate a technique in which the fluctuations due to a fast chaotic subsystem are replaced by a suitable stochastic process so that a Fokker-Planck equation for the slow variables results. The accuracy and efficiency of this technique is verified by the detailed numerical investigation of several coupled systems. The asymptotic behavior as well as transients turn out to be well modeled by the reduced dynamics. We concentrate on low-dimensional problems and cover different types of coupling schemes as well as different chaotic subsystems. As a physical application we discuss the classical dynamics of a hydrogen atom in a strong magnetic field.

We study the phenomenon of unlimited energy growth for a classical particle moving in the annular billiard. The model is considered under two different geometrical situations: static and breathing boundaries. We show that when the dynamics is chaotic for the static case, the introduction of a time-dependent perturbation allows that the particle experiences the phenomenon of Fermi acceleration even when the oscillations are periodic.

Starting with an oscillatory net of neural elements, increasing variability induces a phase transition to excitability. This transition is explained by a systematic effect of the variability, which stabilizes the formerly unstable, spatially uniform, temporally constant solution of the net. Multiplicative noise may also influence the net in a systematic way and may thus induce a similar transition. Adding noise into the model, the interplay of noise and variability with respect to the reported transition is investigated. Finally, pattern formation in a diffusively coupled net is studied, because excitability implies the ability of pattern formation and information transmission.

The interaction of ultrashort laser pulses with matter is a topic of growing interest. In particular, recent developments on free-electron lasers have opened an unexplored field in which many interesting physical phenomena are to be expected. Since hydrodynamic descriptions of the interaction process need a microscopic “input,” a quantum statistical theory of energy absorption by matter is required. We present a kinetic theory of collisional absorption in dense plasmas and analyze the electron-ion collision frequency in warm dense aluminum in dependence on laser frequency and temperature.

We provide here a thorough analysis of the interplay between anharmonic lattice dynamics (with exponential repulsion between units) and electric conduction in a driven-dissipative electrically charged one-dimensional system. First, we delineate the ranges of parameter values where, respectively, subsonic and supersonic wave solitons are possible along the lattice. Then, we study the consequences of the soliton-mediated coupling of light negative to heavy positive charges (lattice units). In the presence of an external electric field we obtain the current-field characteristics for a wide range of values of all parameters defining the system. Finally, we discuss the conditions for an Ohmic–non-Ohmic transition of the electric current as the electric field strength is varied.