Thermal wall is a convenient idealization of a rapidly vibrating plate used for vibrofluidization of granular materials. The objective of this work is to incorporate the Knudsen temperature jump at thermal wall in the Navier-Stokes hydrodynamic modeling of dilute granular gases of monodisperse particles that collide nearly elastically. The Knudsen temperature jump manifests itself as an additional term, proportional to the temperature gradient, in the boundary condition for the temperature. Up to a numerical prefactor $O\left(1\right)$, this term is known from kinetic theory of elastic gases. We determine the previously unknown numerical prefactor by measuring, in a series of molecular dynamics (MD) simulations, steady-state temperature profiles of a gas of elastically colliding hard disks, confined between two thermal walls kept at different temperatures, and comparing the results with the predictions of a hydrodynamic calculation employing the modified boundary condition. The modified boundary condition is then applied, without any adjustable parameters, to a hydrodynamic calculation of the temperature profile of a gas of inelastic hard disks driven by a thermal wall. We find the hydrodynamic prediction to be in very good agreement with MD simulations of the same system. The results of this work pave the way to a more accurate hydrodynamic modeling of driven granular gases.

We systematically study the relationship between equilibrium and nonequilibrium phase diagrams of a system of short-ranged attractive colloids. Using Monte Carlo and Brownian dynamics simulations we find a window of enhanced crystallization that is limited at high interaction strength by a slowing down of the dynamics and at low interaction strength by the high nucleation barrier. We find that the crystallization is enhanced by the metastable gas-liquid binodal by means of a two-stage crystallization process. First, the formation of a dense liquid is observed and second the crystal nucleates within the dense fluid. In addition, we find at low colloid packing fractions a fluid of clusters, and at higher colloid packing fractions a percolating network due to an arrested gas-liquid phase separation that we identify with gelation. We find that this arrest is due to crystallization at low interaction energy and it is caused by a slowing down of the dynamics at high interaction strength. Likewise, we observe that the clusters which are formed at low colloid packing fractions are crystalline at low interaction energy, but glassy at high interaction energy. The clusters coalesce upon encounter.

We develop an extended version of the mode-coupling theory (MCT) for glass transition, which incorporates activated hopping processes via the dynamical theory originally formulated to describe diffusion-jump processes in crystals. The dynamical-theory approach adapted here to glass-forming liquids treats hopping as arising from vibrational fluctuations in the quasiarrested state where particles are trapped inside their cages, and the hopping rate is formulated in terms of the Debye-Waller factors characterizing the structure of the quasiarrested state. The resulting expression for the hopping rate takes an activated form, and the barrier height for the hopping is “self-generated” in the sense that it is present only in those states where the dynamics exhibits a well defined plateau. It is discussed how such a hopping rate can be incorporated into MCT so that the sharp nonergodic transition predicted by the idealized version of the theory is replaced by a rapid but smooth crossover. We then show that the developed theory accounts for the breakdown of the Stokes-Einstein relation observed in a variety of fragile glass formers. It is also demonstrated that characteristic features of dynamical heterogeneities revealed by recent computer simulations are reproduced by the theory. More specifically, a substantial increase of the non-Gaussian parameter, double-peak structure in the probability distribution of particle displacements, and the presence of a growing dynamic length scale are predicted by the extended MCT developed here, which the idealized version of the theory failed to reproduce. These results of the theory are demonstrated for a model of the Lennard-Jones system, and are compared with related computer-simulation results and experimental data.

Hippocampal-neocortical interactions are key to the rapid formation of novel associative memories in the hippocampus and consolidation to long term storage sites in the neocortex. We investigated the role of network correlates during information processing in hippocampal-cortical networks. We found that changes in the intrinsic network dynamics due to the formation of structural network heterogeneities alone act as a dynamical and regulatory mechanism for stimulus novelty and familiarity detection, thereby controlling memory management in the context of memory consolidation. This network dynamic, coupled with an anatomically established feedback between the hippocampus and the neocortex, recovered heretofore unexplained properties of neural activity patterns during memory management tasks which we observed during sleep in multiunit recordings from behaving animals. Our simple dynamical mechanism shows an experimentally matched progressive shift of memory activation from the hippocampus to the neocortex and thus provides the means to achieve an autonomous off-line progression of memory consolidation.

The number of photons produced by coherent x-ray scattering from a single biomolecule is very small because of its extremely small elastic-scattering cross section and low damage threshold. Even with a high x-ray flux of $3\times {10}^{12}$ photons per $100\text{−}\mathrm{nm}$-diameter spot and an ultrashort pulse of $10\mathrm{fs}$ driven by a future x-ray free electron laser (x-ray FEL), it has been predicted that only a few 100 photons will be produced from the scattering of a single lysozyme molecule. In observations of scattered x rays on a detector, the transfer of energy from wave to matter is accompanied by the quantization of the photon energy. Unfortunately, x rays have a high photon energy of $12\mathrm{keV}$ at wavelengths of $1\mathrm{\AA }$, which is required for atomic resolution imaging. Therefore, the number of photoionization events is small, which limits the resolution of imaging of a single biomolecule. In this paper, I propose a method: instead of directly observing the photons scattered from the sample, we amplify the scattered waves by superimposing an intense coherent reference pump wave on it and record the resulting interference pattern on a planar x-ray detector. Using a nanosized gold particle as a reference pump wave source, we can collect ${10}^4–{10}^5$ photons in single shot imaging where the signal from a single biomolecule is amplified and recorded as two-dimensional diffraction intensity data. An iterative phase retrieval technique can be used to recover the phase information and reconstruct the image of the single biomolecule and the gold particle at the same time. In order to precisely reconstruct a faint image of the single biomolecule in Angstrom resolution, whose intensity is much lower than that of the bright gold particle, I propose a technique that combines iterative phase retrieval on the reference pump wave and the digital Fourier transform holography on the sample. By using a large number of holography data, the three-dimensional electron density map can be assembled.

A defining feature of many large empirical networks is their intrinsic complexity. However, many networks also contain a large degree of structural repetition. An immediate question then arises: can we characterize essential network complexity while excluding structural redundancy? In this article we utilize inherent network symmetry to collapse all redundant information from a network, resulting in a coarse graining which we show to carry the essential structural information of the “parent” network. In the context of algebraic combinatorics, this coarse-graining is known as the “quotient.” We systematically explore the theoretical properties of network quotients and summarize key statistics of a variety of “real-world” quotients with respect to those of their parent networks. In particular, we find that quotients can be substantially smaller than their parent networks yet typically preserve various key functional properties such as complexity (heterogeneity and hub vertices) and communication (diameter and mean geodesic distance), suggesting that quotients constitute the essential structural skeletons of their parent networks. We summarize with a discussion of potential uses of quotients in analysis of biological regulatory networks and ways in which using quotients can reduce the computational complexity of network algorithms.

The problem of characterizing damage evolution in a generic material is addressed with the aim of tracing it back to existing growth models in other fields of research. Based on energetic considerations, a system evolution equation is derived for a generic damage indicator describing a material system subjected to an increasing external stress. The latter is found to fit into the framework of a recently developed phenomenological universality (PUN) approach and, more specifically, the so-called U2 class. Analytical results are confirmed by numerical simulations based on a fiber-bundle model and statistically assigned local strengths at the microscale. The fits with numerical data prove, with an excellent degree of reliability, that the typical evolution of the damage indicator belongs to the aforementioned PUN class. Applications of this result are briefly discussed and suggested.

With modification, a recently proposed laser array model is found to agree quantitatively with fiber laser experiments. Comparisons of transient behavior, stable dynamical states, and transitions are made using both previously published and new experiments. While the original model agrees well for fibers with relatively low losses, achieving quantitative agreement over a wide range of operating conditions requires more physically appropriate descriptions of gain dynamics. The refined model is derived, and its predictions are found to be in excellent agreement with experiments.

The study and characterization of the diversity of spatiotemporal patterns generated when a rectangular layer of fluid is locally heated beneath its free surface is presented. We focus on the instability of a stationary cellular pattern of wave number $k_s$ which undergoes a globally subcritical transition to traveling waves by parity-breaking symmetry. The experimental results show how the emerging traveling mode $(2k_s∕3)$ switches on a resonant triad $(k_s,k_s∕2,2k_s∕3)$ within the cellular pattern yielding a “mixed” pattern. The nature of this transition is described quantitatively in terms of the evolution of the fundamental modes by complex demodulation techniques. The Bénard-Marangoni convection accounts for the different dynamics depending on the depth of the fluid layer and on the vertical temperature difference. The existence of a hysteresis cycle has been evaluated quantitatively. When the bifurcation to traveling waves is measured in the vicinity of the codimension-2 bifurcation point, we measure a decrease of the subcritical interval in which the traveling mode becomes unstable. From the traveling wave state the system undergoes a global secondary bifurcation to an alternating pattern which doubles the wavelength $(k_s∕2)$ of the primary cellular pattern; this result compares well with theoretical predictions [P. Coullet and G. Iooss, Phys. Rev. Lett. 64, 866 (1990)]. In this cascade of bifurcations towards a defect dynamics, bistability due to the subcritical behavior of our system is the reason for the coexistence of two different modulated patterns connected by a front. These fronts are stationary for a finite interval of the control parameters.

We study geometrical properties of the complete set of solutions of the random 3-satisfiability problem. We show that even for moderate system sizes the number of clusters corresponds surprisingly well with the theoretic asymptotic prediction. We locate the freezing transition in the space of solutions, which has been conjectured to be relevant in explaining the onset of computational hardness in random constraint satisfaction problems.

In this paper, the imaginary-time path-integral representation of the canonical partition function of a quantum system and nonequilibrium work fluctuation relations are combined to yield methods for computing free-energy differences in quantum systems using nonequilibrium processes. The path-integral representation is isomorphic to the configurational partition function of a classical field theory, to which a natural but fictitious Hamiltonian dynamics is associated. It is shown that if this system is prepared in an equilibrium state, after which a control parameter in the fictitious Hamiltonian is changed in a finite time, then formally the Jarzynski nonequilibrium work relation and the Crooks fluctuation relation hold, where work is defined as the change in the energy as given by the fictitious Hamiltonian. Since the energy diverges for the classical field theory in canonical equilibrium, two regularization methods are introduced which limit the number of degrees of freedom to be finite. The numerical applicability of the methods is demonstrated for a quartic double-well potential with varying asymmetry. A general parameter-free smoothing procedure for the work distribution functions is useful in this context.

Nonequilibrium path-integral methods for computing quantum free-energy differences are applied to a quantum particle trapped in a harmonic well of uniformly changing strength with the purpose of establishing the convergence properties of the work distribution and free energy as the number of degrees of freedom $M$ in the regularized path integrals goes to infinity. The work distribution is found to converge when $M$ tends to infinity regardless of the switching speed, leading to finite results for the free-energy difference when the Jarzynski nonequilibrium work relation or the Crooks fluctuation relation are used. The nature of the convergence depends on the regularization method. For the Fourier method, the convergence of the free-energy difference and work distribution go as $1∕M$, while both quantities converge as $1∕M^2$ when the bead regularization procedure is used. The implications of these results to more general systems are discussed.

Systems of reacting particles, which are well mixed or distributed homogeneously in space, are commonly modeled by deterministic rate equations. These equations, which are based on the mean-field approximation, are valid for macroscopic systems. However, they neglect fluctuations in the particle populations. As a result, under conditions of strong fluctuations, the reaction rates obtained from the rate equations are highly inaccurate. To account for the fluctuations, stochastic methods are required. However, these methods are computationally intensive and may become infeasible for complex reaction networks. Therefore, it is useful to identify the conditions under which the rate equations provide accurate results. Naively, one expects strong fluctuations when the average population sizes of some of the reactants are of order one or lower. Here we present a systematic approach, for testing the validity of the rate equations, in which we define characteristic scales in terms of the rate constants of the network. We show that the rate equations fail to accurately reproduce the reaction rates when the system size is reduced below these scales. Surprisingly, the rate equations are found to be applicable in a wider range than expected. Their validity depends not only on the population sizes of the reactive species but also on the kinetic properties of the reaction network.

We experimentally measure the decay of a quasi-two-dimensional granular gas under gravity. A granular gas is created by vibrofluidization, after which the energy input is halted, and the time-dependent statistical properties of the decaying gas are measured with video particle tracking. There are two distinct cooling stages separated by a high temperature settling shock. In the final stage, the temperature of a fluid packet decreases as a power law $T\propto {(t_c-t)}^{\alpha }$ just before the system collapses to a static state. The measured value of $\alpha$ ranges from 3.3 to 6.1 depending on the height, significantly higher than the exponent of 2 found in theoretical work on this problem [D. Volfson, B. Meerson, and L. S. Tsimring, Phys Rev. E 73, 61305 (2006)]. We also address the question of whether the collapse occurs simultaneously at different heights in the system.

The normal modes and the melting character of a bilayer system consisting of binary charged particles with different charge and/or different mass, interacting through a Coulomb potential and confined in a parabolic trap are investigated. The normal mode spectrum is discussed as a function of the charge ratio (CR) and mass ratio (MR) of the two kinds of charged particles as well as the interlayer separation. We show that the dependence of the normal modes on the excited states can be tuned by varying the CR, the MR, and the interlayer distance. Once the interlayer distance is larger than a critical value, the first excited state corresponds only to the intershell rotation mode. In addition, the intershell rotation melting temperature is discussed as a function of the CR and MR as well as the interlayer separation.

In two recent papers [D. Jamet and C. Misbah, Phys. Rev. E 76, 051907 (2007); 78, 031902 (2008)], we considered a thermodynamically consistent model for vesicles and membranes, where we dealt, in the first paper, with the membrane local incompressibility condition, while in the second one with the bending energy and the derivation of a constitutive law of the composite fluid: ambient $\text{fluid}+\text{membrane}$. This is the last paper of this series and focuses on the elimination of surface tension (inherent in phase-field models), retaining the thermodynamically consistent model. We write down the complete set of equations and the full constitutive law for membranes embedded in a Newtonian fluid.

The simulation of problems in electrocardiography using the bidomain model for cardiac tissue often creates issues with satisfaction of the boundary conditions required to obtain a solution. Recent studies have proposed approximate methods for solving such problems by satisfying the boundary conditions only approximately. This paper presents an analysis of their approximations using a similar method, but one which ensures that the boundary conditions are satisfied during the whole solution process. Also considered are additional functional forms, used in the approximate solutions, which are more appropriate to specific boundary conditions. The analysis shows that the approximations introduced by Patel and Roth [Phys. Rev. E 72, 051931 (2005)] generally give accurate results. However, there are certain situations where functional forms based on the geometry of the problem under consideration can give improved approximations. It is also demonstrated that the recent methods are equivalent to different approaches to solving the same problems introduced $20\text{years}$ earlier.

We explore the problem of the ergodicity of magnetohydrodynamics and Hall magnetohydrodynamics in three-dimensional, ideal Galerkin systems that are truncated to a finite number of Fourier modes. We show how single Fourier modes follow the Gibbs ensemble prediction, and how the ergodicity of the phase space is restored for long-time Galerkin solutions. Running time averages and two-time correlation functions show, at long times, a convergence towards zero of time averaged single Fourier modes. This suggests a delayed approach to, rather than a breaking of, ergodicity. Finally, we present some preliminary ideas concerning the origin of the associated time scales.

We study the steady-state characterization of an advecting-diffusing three-dimensional flow defined in the annular region between coaxial cylinders of finite length that can rotate independently. A phase transition occurs when the cylinder velocities vary, which controls the spectral properties of the dominant eigenvalue and eigenfunction of the advection-diffusion equation for high Péclet numbers. The localization abscissa of the dominant eigenfunction can be used as the order parameter of the transition, and is a continuous function of the wall velocity. Conversely, the exponent characterizing the scaling of the real part of the dominant eigenvalue displays a discontinuous behavior at the critical point. Theoretical arguments support the localization properties observed numerically and provide a simple explanation of this phenomenon.

Deterministic lateral displacement (DLD) devices separate micrometer-scale particles in solution based on their size using a laminar microfluidic flow in an array of obstacles. We investigate array geometries with rational row-shift fractions in DLD devices by use of a simple model including both advection and diffusion. Our model predicts multidirectional sorting modes that could be experimentally tested in high-throughput DLD devices containing obstacles that are much smaller than the separation between obstacles.