The adaptive resolution scheme (AdResS) for efficient hybrid particle-based atomistic/mesoscale molecular dynamics (MD) simulations recently introduced by us, [J. Chem. Phys. 123, 224106 (2005)] is extended to high density molecular liquids with spherical boundaries between the atomistic and mesoscale regions. The key feature of this approach is that it allows for a dynamical change of the number of molecular degrees of freedom during the course of a MD simulation by an on-the-fly switching between the atomistic and mesoscopic levels of detail. Pressure and density variations occurring at the atomistic/mesoscale boundary in the original version are considerably reduced employing the improved methodology presented here.

We measured the orientational order parameter of $F$-actin traversing the isotropic-nematic phase transition using a combination of techniques, including fluorescence imaging, local birefringence measurements, and small-angle x-ray scattering. The order parameter approaches a saturated value of 0.75 for actin concentrations above the region of the isotropic-nematic phase transition. This result implies a significant extent of misalignment and consequently entanglement among long actin filaments, even in the nematic phase. We determine the specific birefringence of completely aligned $F$-actin to be $\Delta n_0=2.3\times {10}^{-5}\mathrm{ml}∕\mathrm{mg}$. At concentrations slightly below the isotropic-nematic transition, nonzero values of the order parameter are detected for hours following an initial alignment, indicating extremely slow rotational kinetics of $F$-actin in the entangled networks.

In this work we propose an idealized model for competitive cluster growth in complex networks. Each cluster can be thought of as a fraction of a community that shares some common opinion. Our results show that the cluster size distribution depends on the particular choice for the topology of the network of contacts among the agents. As an application, we show that the cluster size distributions obtained when the growth process is performed on hierarchical networks, e.g., the Apollonian network, have a scaling form similar to what has been observed for the distribution of a number of votes in an electoral process. We suggest that this similarity may be due to the fact that social networks involved in the electoral process may also possess an underlining hierarchical structure.

Considering a discrete and finite statistical model of a general position we introduce an exact expression for the partition function in terms of a finite series. The leading term in the series is the Bethe-Peierls (belief propagation) (BP) contribution; the rest are expressed as loop contributions on the factor graph and calculated directly using the BP solution. The series unveils a small parameter that often makes the BP approximation so successful. Applications of the loop calculus in statistical physics and information science are discussed.

We have studied foaming dynamics in Hele-Shaw cells partially filled with a soap and water mixture. A series of upside-down flips produces an intermittent wetting of the cell and leads to foam formation. As a function of the number of flips, an increasing number of bubbles composes the foam, until saturation is observed. Statistical analysis shows that the bubble size follows a Gamma distribution. Contrary to common belief, this foaming dynamics by “shaking” creates homogeneous foam, even though the system may pass through transient heterogeneous configurations. A mechanistic interpretation is proposed and included into a theoretical model.

We present an extension of fiber bundle models considering that failed fibers still carry a fraction $0⩽\alpha ⩽1$ of their failure load. The value of $\alpha$ interpolates between the perfectly brittle failure $(\alpha =0)$ and perfectly plastic behavior $(\alpha =1)$ of fibers. We show that the finite load bearing capacity of broken fibers has a substantial effect on the failure process of the bundle. In the case of global load sharing it is found that for $\alpha \to 1$ the macroscopic response of the bundle becomes perfectly plastic with a yield stress equal to the average fiber strength. On the microlevel, the size distribution of avalanches has a crossover from a power law of exponent $\approx 2.5$ to a faster exponential decay. For localized load sharing, computer simulations revealed a sharp transition at a well-defined value ${\alpha }_c$ from a phase where macroscopic failure occurs due to localization as a consequence of local stress enhancements, to another one where the disordered fiber strength dominates the damage process. Analyzing the microstructure of damage, the transition proved to be analogous to percolation. At the critical point ${\alpha }_c$, the spanning cluster of damage is found to be compact with a fractal boundary. The distribution of bursts of fiber breakings shows a power-law behavior with a universal exponent $\approx 1.5$ equal to the mean-field exponent of fiber bundles of critical strength distributions. The model can be relevant to understand the shear failure of glued interfaces where failed regions can still transmit load by remaining in contact.

It has been shown that many complex networks shared distinctive features, which differ in many ways from the random and the regular networks. Although these features capture important characteristics of complex networks, their applicability depends on the type of networks. To unravel ubiquitous characteristics that complex networks may have in common, we adopt the clustering coefficient as the probability measure, and present a systematic analysis of various types of complex networks from the perspective of statistical self-similarity. We find that the probability distribution of the clustering coefficient is best characterized by the multifractal; moreover, the support of the measure had a fractal dimension. These two features enable us to describe complex networks in a unified way; at the same time, offer unforeseen possibilities to comprehend complex networks.

We derive the virial theorem appropriate to the generalized Smoluchowski-Poisson (GSP) system describing self-gravitating Brownian particles in an overdamped limit. We extend previous works by considering the case of an unbounded domain and an arbitrary equation of state. We use the virial theorem to study the diffusion (evaporation) of an isothermal Brownian gas above the critical temperature $T_c$ in dimension $d=2$ and show how the effective diffusion coefficient and the Einstein relation are modified by self-gravity. We also study the collapse at $T=T_c$ and show that the central density increases logarithmically with time instead of exponentially in a bounded domain. Finally, for $d>2$, we show that the evaporation of the system is essentially a pure diffusion slightly slowed down by self-gravity. We also study the linear dynamical stability of stationary solutions of the GSP system representing isolated clusters of particles and investigate the influence of the equation of state and of the dimension of space on the dynamical stability of the system.

We propose a general kinetic and hydrodynamic description of self-gravitating Brownian particles in $d$ dimensions. We go beyond the usual approximations by considering inertial effects and finite-$N$ effects while previous works use a mean-field approximation valid in a proper thermodynamic limit $(N\to +\infty )$ and consider an overdamped regime $(\xi \to +\infty )$. We recover known models in some particular cases of our general description. We derive the expression of the virial theorem for self-gravitating Brownian particles and study the linear dynamical stability of isolated clusters of particles and uniform systems by using techniques introduced in astrophysics. We investigate the influence of the equation of state, of the dimension of space, and of the friction coefficient on the dynamical stability of the system. We obtain the exact expression of the critical temperature $T_c$ for a multicomponents self-gravitating Brownian gas in $d=2$. We also consider the limit of weak frictions, $\xi \to 0$, and derive the orbit-averaged Kramers equation.

The existence of a strong stochasticity threshold (SST) has been detected in many Hamiltonian lattice systems, including the Fermi-Pasta-Ulam (FPU) model, which is characterized by a crossover of the system dynamics from weak to strong chaos with increasing energy density $ϵ$. Correspondingly, the relaxation time to energy equipartition and the largest Lyapunov exponent exhibit different scaling behavior in the regimes below and beyond the threshold value. In this paper, we attempt to go one step further in this direction to explore further changes in the energy density dependence of other Lyapunov exponents and of hydrodynamic Lyapunov modes (HLMs). In particular, we find that for the FPU-$\beta$ and FPU-$\alpha \beta$ models the scalings of the energy density dependence of all Lyapunov exponents experience a similar change at the SST as that of the largest Lyapunov exponent. In addition, the threshold values of the crossover of all Lyapunov exponents are nearly identical. These facts lend support to the point of view that the crossover in the system dynamics at the SST manifests a global change in the geometric structure of phase space. They also partially answer the question of why the simple assumption that the ambient manifold representing the system dynamics is quasi-isotropic works quite well in the analytical calculation of the largest Lyapunov exponent. Furthermore, the FPU-$\beta$ model is used as an example to show that HLMs exist in Hamiltonian lattice models with continuous symmetries. Some measures are defined to indicate the significance of HLMs. Numerical simulations demonstrate that there is a smooth transition in the energy density dependence of these variables corresponding to the crossover in Lyapunov exponents at the SST. In particular, our numerical results indicate that strong chaos is essential for the appearance of HLMs and those modes become more significant with increasing degree of chaoticity.

In this paper, we examine in detail the principal branches of solutions that arise in vector discrete models with nonlinear intercomponent coupling and four wave mixing. The relevant four branches of solutions consist of two single mode branches (transverse electric and transverse magnetic) and two mixed mode branches, involving both components (linearly polarized and elliptically polarized). These solutions are obtained explicitly and their stability is analyzed completely in the anticontinuum limit (where the nodes of the lattice are uncoupled), illustrating the supercritical pitchfork nature of the bifurcations that give rise to the latter two, respectively, from the former two. Then the branches are continued for finite coupling constructing a full two-parameter numerical bifurcation diagram of their existence. Relevant stability ranges and instability regimes are highlighted and, whenever unstable, the solutions are dynamically evolved through direct computations to monitor the development of the corresponding instabilities. Direct connections to the earlier experimental work of Meier et al. [Phys. Rev. Lett., 91, 143907 (2003)] that motivated the present work are given.

Using a physiologically based model of brain activity, electroencephalogram (EEG) power spectra are calculated for signals derived from general linear combinations of voltages from multiple electrodes, with and without filtering by volume conduction. Two simple methods of combining scalp measurements to estimate unfiltered EEG power spectra are then proposed and their accuracy and robustness are explored, using the model predictions as an illustration. It is found that these methods, including a case that uses just three electrodes, enable improved estimation of the underlying spectrum relative to each of several widely used combinations alone.

The underlying mechanism of the low-frequency dielectric dispersion, called the $\alpha$ dispersion, of osmotically lysed erythrocytes (erythrocyte ghosts) has remained open since its finding [H. P. Schwan and E. L. Carstensen, Science 125, 985 (1957)]. The $\alpha$ dispersion is peculiar to erythrocyte ghosts and has never been observed for intact erythrocytes. Numerical calculation based on interfacial polarization revealed that the $\alpha$ dispersion is due to the presence of a hole of about $30\mathrm{nm}$ in radius in the plasma membrane.

We study the robustness of self-sustained oscillatory activity in a globally coupled ensemble of excitable and oscillatory units. The critical balance to achieve collective self-sustained oscillations is analytically established. We also report a universal scaling function for the ensemble’s mean frequency. Our results extend the framework of the “aging transition” [Phys. Rev. Lett. 93, 104101 (2004)] including a broad class of dynamical systems potentially relevant in biology.

In psychiatric and neurological diseases, sleep is often perturbed. Moreover, recent works on humans and animals tend to show that sleep plays a strong role in memory processes. Reciprocally, sleep dynamics following a learning task is modified [Hubert et al., Nature (London) 02663, 1 (2004), Peigneux et al., Neuron 44, 535 (2004)]. However, sleep analysis in humans and animals is often limited to the total sleep and wake duration quantification. These two parameters are not fully able to characterize the sleep dynamics. In mammals sleep presents a complex organization with an alternation of slow wave sleep (SWS) and paradoxical sleep (PS) episodes. Moreover, it has been shown recently that these sleep episodes are frequently interrupted by micro-arousal (without awakening). We present here a detailed analysis of the basal sleep properties emerging from the mechanisms underlying the vigilance states alternation in an animal model. These properties present a self-organized critical system signature and reveal the existence of two W, two SWS, and a PS structure exhibiting a criticality as met in sand piles. We propose a theoretical model of the sleep dynamics based on several interacting neuronal populations. This new model of sleep dynamics presents the same properties as experimentally observed, and explains the variability of the collected data. This experimental and theoretical study suggests that sleep dynamics shares several common features with critical systems.

The dynamical process of opinion formation within a model using a local majority opinion updating rule is studied numerically in networks with the small-world geometrical property. The network is one in which shortcuts are added to randomly chosen pairs of nodes in an underlying regular lattice. The presence of a small number of shortcuts is found to shorten the time to reach a consensus significantly. The effects of having shortcuts in a lattice of fixed spatial dimension are shown to be analogous to that of increasing the spatial dimension in regular lattices. The shortening of the consensus time is shown to be related to the shortening of the mean shortest path as shortcuts are added. Results can also be translated into that of the dynamics of a spin system in a small-world network.

The Swift-Hohenberg equation with quadratic and cubic nonlinearities exhibits a remarkable wealth of stable spatially localized states. The presence of these states is related to a phenomenon called homoclinic snaking. Numerical computations are used to illustrate the changes in the localized solution as it grows in spatial extent and to determine the stability properties of the resulting states. The evolution of the localized states once they lose stability is illustrated using direct simulations in time.

Recent experiments have demonstrated that ac electrokinetic micropumps permit integrable, local, and fast pumping (velocities $\sim \mathrm{mm}∕\mathrm{s}$) with low driving voltage of a few volts only. However, they also displayed many quantitative and qualitative discrepancies with existing theories. We therefore extend the latter theories to account for three experimentally relevant effects: (i) vertical confinement of the pumping channel, (ii) Faradaic currents from electrochemical reactions at the electrodes, and (iii) nonlinear surface capacitance of the Debye layer. We report here that these effects indeed affect the pump performance in a way that we can rationalize by physical arguments.

The eigenmode spectrum and transmission properties of a certain class of one-dimensional disordered photonic crystals have been studied statistically. It is shown that the relative fluctuation of the optical width of the period of the photonic crystal is a universal parameter allowing a quantitative description of the disordered photonic crystal for various models of disorder. It is shown that the tail of the density of states is characterized by a certain penetration depth and a quantitative relation between the penetration depth, the relative band gap width, and the disorder parameter is obtained. It is found that a threshold level of disorder exists, below which the density of states in the center of the photonic band gap vanishes, and the ensemble-averaged transmission coefficient does not change significantly with increasing disorder. Also, the standard deviation of the transmission coefficient is less than its mean value. Above threshold, the ensemble averaged transmission coefficient and density of states increase with the level of disorder rapidly, and the standard deviation of the transmission coefficient exceeds its mean value. A scaling formula is presented, which relates the logarithm of the transmission to the periodic refractive index modulation and the disorder.

In this paper, the lateral beam shift in a prism-waveguide coupling system at wavelengths ranging from visible to near infrared is theoretically examined. A simple theoretical formula is derived to analyze the behavior of the beam shift. We demonstrate that large positive and negative lateral optical beam shifts can be obtained when guided modes are excited. It is also found that the magnitude of the beam shift is closely related to the intrinsic and radiative damping. When the intrinsic damping is larger than the radiative damping, negative lateral beam shift occurs. Numerical calculations confirm the theoretical analysis and show that a beam shift of the order of millimeters is possible.