We perform molecular dynamics simulations of the TIP5P water model and derive the physical parameters for a simple two-scale repulsive ramp potential model. We find that the regions of anomalous behavior in the phase diagrams of both systems can be mapped onto each other if (i) pressure $P$ and temperature $T$ are replaced by $T-T_C$ and $P-P_C$, respectively, where $(T_C,P_C)$ are the coordinates of the liquid-liquid critical point of the corresponding system; and (ii) a single ramp particle corresponds effectively to two TIP5P molecules. We present heuristic arguments supporting point (ii). We also argue that the waterlike anomalies in the ramp potential are due to the ability of the particles to reproduce, upon compression or heating, the migration of water molecules from the second shell to its first shell.

Using molecular dynamics simulation, we examine the dynamics of sheared polycrystal states in a binary mixture composed of small and large particles in two dimensions. We vary the composition $c$ of the large particles and the shear rate $\dot{\gamma }$ to realize changeovers among crystal, polycrystal, and glass. We find large stress fluctuations arising from sliding motions of the particles at the grain boundaries, which occur cooperatively to release the elastic energy stored. These stress fluctuations decrease as the system crosses over from polycrystal to glass. The dynamic processes are visualized with the aid of a sixfold angle ${\alpha }_j\left(t\right)$ representing the local crystal orientation and a disorder variable $D_j\left(t\right)$ representing a deviation from the hexagonal order for particle $j$.

We study a two-dimensional reaction-diffusion equation for calcium oscillation with a pacemaker region. When the pacemaker entrains the whole system, circular waves are observed as a target pattern. However, if the pace of the pacemaker is too fast, the pulse propagation to the outer region sometimes fails in a chaotic manner. We find that spiral waves are spontaneously created at the interface between the pacemaker region and the outer region.

We address the longstanding problem of recovering dynamical information from noisy acoustic emission signals arising from peeling of an adhesive tape subject to constant traction velocity. Using the phase space reconstruction procedure we demonstrate the deterministic chaotic dynamics by establishing the existence of correlation dimension as also a positive Lyapunov exponent in a midrange of traction velocities. The results are explained on the basis of the model that also emphasizes the deterministic origin of acoustic emission by clarifying its connection to stick-slip dynamics.

An experiment on LULI 2000 laser devoted to density determination of shocked plastic from a two-dimensional monochromatic x-ray radiography is presented. A spherical quartz crystal was set to select the $\mathrm{He}\text{−}\alpha$ line of vanadium at $2.382\mathrm{\AA }$ and perform the image of the main target. Rear side diagnostics were implemented to validate the new diagnostic. The density experimental results given by radiography are in good agreement with rear side diagnostics data and hydrodynamical simulations. The pressure regime into the plastic is $2–3\mathrm{Mbar}$, corresponding to a compression between 2.7–2.9.

We investigate analytically and numerically the modulational instability of a Bose-Einstein condensate with both two- and three-body interatomic interactions and trapped in an external parabolic potential. Analytical investigations performed lead us to establish an explicit time-dependent criterion for the modulational instability of the condensate. The effects of the potential as well as of the quintic nonlinear interaction are studied. Direct numerical simulations of the Gross-Pitaevskii equation with two- and three-body interactions describing the dynamics of the condensate agree with the analytical predictions.

The influence of a spatially localized heterogeneity defect, defined by failure of the diffusion effect, on spiral turbulence suppression in two-dimensional excitable media is studied numerically, based on the Bär model. It is shown that in certain parameter regions spiral turbulence without the defect can be suppressed by a boundary periodic forcing (called active control) if the forcing frequency is properly chosen. However, with a sufficiently large defect this active control method no longer works due to the wake turbulence following the defect. We suggest an auxiliary method of enclosing the defect with a thin layer of material of high excitability (called passive control) to screen the interaction between the defect and the turbulence and to restore the global control effect of the periodic forcing. The possible application of the method in cardiac defibrillation is discussed.

The flows induced by acoustic streaming in a three-dimensional side-heated parallelepiped cavity of length $A_x$ representative of crystal growth configurations are numerically studied. Both the structure of the flows and their stability properties are determined. The flows have different symmetries, belonging to the group $D_4$ for pure streaming, $Z_2\times Z_2$ for pure buoyancy, and $Z_2$ for the mixed case, but these symmetries are generally broken at the first bifurcation points. Bifurcation diagrams are obtained which show that the flows become oscillatory periodic at a Hopf bifurcation, either directly on the primary steady solution branch, or on a secondary branch which bifurcates from the primary branch at a steady bifurcation point. The critical Grashof numbers for these bifurcation points are calculated as a function of the cavity length $A_x$, the Prandtl number $\text{Pr}$ and the acoustic streaming parameter $A$. The thresholds are generally found to increase when the acoustic streaming contribution is enhanced, which indicates a stabilizing effect induced by acoustic streaming and may explain the observed improvement of the crystal quality when ultrasound waves are applied during the growth process. Destabilization effects are, however, found in some parameter range.

According to Pruessner and Peters [G. Pruessner and O. Peters, Phys. Rev. E 73, 025106(R) (2006)], the finite-size scaling exponents of the order parameter in sandpile models depend on the tuning of driving and dissipation rates with system size. We point out that the same is not true for avalanches in the slow driving limit.

In R. Dickman, M. A. Muñoz, A. Vespignani, and S. Zapperi [Braz. J. Phys. 30, 27 (2000)], Dickman et al. suggested that self-organized criticality can be produced by coupling the activity of an absorbing state model to a dissipation mechanism and adding an external drive. We analyzed the proposed mechanism in G. Pruessner and O. Peters [Phys. Rev. E 73, 025106(R) (2006)] and found that if this mechanism is at work, the finite-size scaling found in self-organized criticality will depend on the details of the implementation of dissipation and driving. In the preceding paper [M. J. Alava, L. Laurson, A. Vespignani, and S. Zapperi, Phys. Rev. E 77, 048101 (2008)], Alava et al. show that one avalanche exponent in the absorbing state approach becomes independent of dissipation and driving. In our reply we clarify their findings and put them in the context of the original paper.

We numerically simulate a thermalization process in an energy landscape with hierarchically organized metastable states. The initial configuration is chosen to have a large energy excess relative to the thermal equilibrium value at the running temperature. We show that the initial energy surplus is dissipated in a series of intermittent bursts, or quakes, whose rate decreases as the inverse of the age of the system. In addition, one observes energy fluctuations with a zero-centered Gaussian distribution. These pertain to the pseudoequilibrium dynamics within a single metastable state and do not contribute to the energy dissipation. The derivative of the thermal energy with respect to the logarithm of time is asymptotically constant and comprises a temperature-independent part and a part with an Arrhenius temperature dependence. The findings closely mirror recent numerical simulation results obtained for microscopic glassy models. For these models, record-sized energy fluctuations have been claimed to trigger intermittent events during low-temperature thermalization. In the present model record-sized fluctuations are by construction needed to trigger changes from one metastable state to another. This property thus suffices to explain the statistical property of intermittent energy flow in complex metastable systems.

We study simple interacting particle systems on heterogeneous networks, including the voter model and the invasion process. These are both two-state models in which in an update event an individual changes state to agree with a neighbor. For the voter model, an individual “imports” its state from a randomly chosen neighbor. Here the average time $T_N$ to reach consensus for a network of $N$ nodes with an uncorrelated degree distribution scales as $N{\mu }_1^2∕{\mu }_2$, where ${\mu }_k$ is the $k\text{th}$ moment of the degree distribution. Quick consensus thus arises on networks with broad degree distributions. We also identify the conservation law that characterizes the route by which consensus is reached. Parallel results are derived for the invasion process, in which the state of an agent is “exported” to a random neighbor. We further generalize to biased dynamics in which one state is favored. The probability for a single fitter mutant located at a node of degree $k$ to overspread the population—the fixation probability—is proportional to $k$ for the voter model and to $1∕k$ for the invasion process.

We report a Brownian dynamics simulation study of the structure and dynamics of superparamagnetic colloids subject to external substrate potentials and confined in narrow channels. Our study is motivated by the importance of phenomena like commensurable-incommensurable phase transitions, anomalous diffusion, and stochastic activation processes that are closely related to the system under investigation. We focus mainly on the role of the substrate in the order-disorder mechanisms that lead to a rich variety of commensurate and incommensurate phases, as well as its effect on the single-file diffusion in interacting systems and the depinning transition in one dimension.

We study the microscopic mechanical response of colloidal gels by manipulating single probe particles within the network. For this work, we use a refractive index and density-matched suspension of polymethylmethacrylate (PMMA) particles with nonadsorbing polymer: polystyrene. As the polymer concentration increases, a dynamically arrested, space-filling network is formed, exhibiting structural transitions from a clusterlike to a more homogeneous stringlike gel phase, consistent with observations by Dibble and co-workers [C. J. Dibble, M. Kogan, and M. J. Solomon, Phys. Rev. E 74, 041403 (2006)]. In a gel, probe particles are oscillated with an optical trap, creating the local strain field in the network. We find that the micromechanics correlate strongly with the gel structure. At high polymer concentration, the average deformation field decays as $1/r$ to a distance quite close to the probe particle, as expected for a purely elastic material. In contrast, at lower polymer concentrations, gels exhibit anomalous strain fields in the near field; the strain plateaus, indicating that many particles move together with the probe. By rescaling the probe size in the theoretical model, we obtain a micromechanical gel correlation length, which is consistent with the structural difference in terms of “clusterlike” and “stringlike.”

We study a simplified model for pulsed laser deposition [Hinnemann et al., Phys. Rev. Lett. 87, 135701 (2001)] by rate equations. We consider a set of equations where islands are assumed to be pointlike, as well as an improved one that takes the size of the islands into account. The first set of equations is solved exactly but its predictive power is restricted to a few pulses. The improved set of equations is integrated numerically, is in excellent agreement with simulations, and fully accounts for the crossover from continuous to pulsed deposition. Moreover, we analyze the scaling of the nucleation density and show numerical results indicating that a previously observed logarithmic scaling does not apply.

We investigated the spatial-dependent stochastic effects originating from the finite number of bicoid proteins in Drosophila melanogaster, which are crucial to cell development. We obtained an exact solution to the spatial-dependent stochastic chemical master equation and recovered the usual reaction-diffusion solution for the average of the bicoid concentration, valid in the bulk. We also used the steady state probability to get the spatial potential landscape. The stochastic effects are captured by the Poisson distribution; so, as the average of the bicoid concentration decreases from the anterior (A) to the posterior (P) of the embryo, the statistical fluctuations also decrease. An alternative way of interpreting this is that the shape of the spatial potential landscape shrinks from A to P. While the mathematical result is known, we offer a simple approach to understanding why it is what it is and give associated physical intuitions. The approach can be generalized and applied to any problem with a particle that diffuses, decays, and has a stochastic source.

We introduce a stochastic model of growing networks where both the number of new nodes which join the network and the number of connections vary stochastically. We provide an exact mapping between this model and the zero-range process, and calculate analytically the degree distribution for any given evolution rule. We argue that this mapping can be used to infer a possible evolution rule for any given network. This is being demonstrated for a protein-protein interaction network of Saccharomyces cerevisiae.

We introduce a continuum model describing data losses in a single node of a packet-switched network (like the Internet) which preserves the discrete nature of the data loss process. By construction, the model has critical behavior with a sharp transition from exponentially small to finite losses with increasing data arrival rate. We show that such a model exhibits strong fluctuations in the loss rate at the critical point and non-Markovian power-law correlations in time, in spite of the Markovian character of the data arrival process. The continuum model allows for rather general incoming data packet distributions and can be naturally generalized to consider the buffer server idleness statistics.

Numerical simulations of turbulent channel flows, with or without additives, are limited in the extent of the Reynolds number ($\text{Re}$) and Deborah number ($\text{De}$). The comparison of such simulations to theories of drag reduction, which are usually derived for asymptotically high $\text{Re}$ and $\text{De}$, calls for some care. In this paper we present a study of drag reduction by rodlike polymers in a turbulent channel flow using direct numerical simulation and illustrate how these numerical results should be related to the recently developed theory.

Bistable chemical fronts can be deformed by Marangoni-driven convective flows induced by gradients of surface tension across the front. We investigate here the nonlinear dynamics of such a system by simulations of two-dimensional Navier-Stokes equations coupled to a reaction-diffusion-convection equation for a surface-active chemical species present in the bulk of the solution and involved in a bistable kinetics. We show that Marangoni flows cannot only alter the shape and speed of the front but also change the relative stability of the two stable steady states, reversing in some cases the direction of propagation of the front with regard to the pure reaction-diffusion situation. A detailed parametric study discusses the properties of the asymptotic dynamics as a function of the Marangoni number $M$ and of a kinetic parameter $d$.