Processive molecular motors take more-or-less uniformly sized steps, along spatially periodic tracks, mostly forwards but increasingly backwards under loads. Experimentally, the major steps can be resolved clearly within the noise but one knows biochemically that one or more mechanochemical substeps remain hidden in each enzymatic cycle. In order to properly interpret experimental data for back-to-forward step ratios, mean conditional step-to-step dwell times, etc., a first-passage analysis has been developed that takes account of hidden substeps in $N$-state sequential models. The explicit, general results differ significantly from previous treatments that identify the observed steps with complete mechanochemical cycles; e.g., the mean dwell times ${\tau }_{+}$ and ${\tau }_{-}$ prior to forward and back steps, respectively, are normally unequal although the dwell times ${\tau }_{++}$ and ${\tau }_{--}$ between successive forward and back steps are equal. Illustrative $(N=2)$-state examples display a wide range of behavior. The formulation extends to the case of two or more detectable transitions in a multistate cycle with hidden substeps.

Propagation failure of an action potential wave at a finite distance from its source (so-called type-II block) may cause spiral wave formation or wave breakup in the heart, phenomena that are believed to underlie lethal and nonlethal heart rhythm disorders. In this study, we develop a sufficient condition for this type of block in a homogeneous, spatially one-dimensional system. Using a topological argument, we find that type-II block of a wave will always occur when launched within a finite range of times if the velocity of the trailing edge of the preceding wave, as measured at the stimulus site, is smaller than the velocity of a wave launched with the minimum diastolic interval (DI) for which propagation is possible. This “blocking condition” is robust, remaining valid even when memory and waveback electrotonic effects are included. The condition suggests that type-II block is greatly facilitated when waves are initiated at irregular intervals in time such that (1) the velocities of consecutive waves are as different as possible and (2) the DIs preceding each wave fall on the steeply sloped portion of the action potential duration restitution curve as often as possible. The set of timing intervals between stimuli that are predicted by the blocking condition to produce block are found to be consistent with these guidelines, and also to agree well with a coupled-maps computer simulation model, for the case of waves launched by four rapidly and irregularly timed stimuli.

We study the transient regime of type-II biophysical neuron models and determine the scaling behavior of relaxation times $\tau$ near but below the repetitive firing critical current, $\tau \simeq C{(I_c-I)}^{-\Delta }$. For both the Hodgkin-Huxley and Morris-Lecar models we find that the critical exponent is independent of the numerical integration time step and that both systems belong to the same universality class, with $\Delta =1∕2$. For appropriately chosen parameters, the FitzHugh-Nagumo model presents the same generic transient behavior, but the critical region is significantly smaller. We propose an experiment that may reveal nontrivial critical exponents in the squid axon.

Different models of random walks on the dual graphs of compact urban structures are considered. Analysis of access times between streets helps to detect the city modularity. The statistical mechanics approach to the ensembles of lazy random walkers is developed. The complexity of city modularity can be measured by an informationlike parameter which plays the role of an individual fingerprint of Genius loci. Global structural properties of a city can be characterized by the thermodynamic parameters calculated in the random walk problem.

We study the stability and dynamics of non-Boussinesq convection in pure gases (${\mathrm{CO}}_2$ and ${\mathrm{SF}}_6$) with Prandtl numbers near $\mathrm{Pr}\simeq 1$ and in a ${\mathrm{H}}_2\text{−}\mathrm{Xe}$ mixture with $\mathrm{Pr}=0.17$. Focusing on the strongly nonlinear regime we employ Galerkin stability analyses and direct numerical simulations of the Navier-Stokes equations. For $\mathrm{Pr}\simeq 1$ and intermediate non-Boussinesq effects we find reentrance of stable hexagons as the Rayleigh number is increased. For stronger non-Boussinesq effects the usual, transverse side-band instability is superseded by a longitudinal side-band instability. Moreover, the hexagons do not exhibit any amplitude instability to rolls. Seemingly, this result contradicts the experimentally observed transition from hexagons to rolls. We resolve this discrepancy by including the effect of the lateral walls. Non-Boussinesq effects modify the spiral defect chaos observed for larger Rayleigh numbers. For convection in ${\mathrm{SF}}_6$ we find that non-Boussinesq effects strongly increase the number of small, compact convection cells and with it enhance the cellular character of the patterns. In ${\mathrm{H}}_2\text{−}\mathrm{Xe}$, closer to threshold, we find instead an enhanced tendency toward roll-like structures. In both cases the number of spirals and of targetlike components is reduced. We quantify these effects using recently developed diagnostics of the geometric properties of the patterns.

Backward Raman amplification (BRA) in plasmas holds the potential for longitudinal compression and focusing of powerful x-ray pulses. In principle, this method is capable of producing pulse intensities close to the vacuum breakdown threshold by manipulating the output of planned x-ray sources. The minimum wavelength limit of BRA applicability to compression of laser pulses in plasmas is found.

An analysis method based on a multidomain pseudospectral method is proposed for calculating the band diagrams of two-dimensional photonic crystals and is shown to possess excellent numerical convergence behavior and accuracy. The proposed scheme utilizes the multidomain Chebyshev collocation method. By applying Chebyshev-Lagrange interpolating polynomials to the approximation of spatial derivatives at collocation points, the Helmholtz equation is converted into a matrix eigenvalue equation which is then solved for the eigenfrequencies by the shift inverse power method. Suitable multidomain division of the computational domain is performed to deal with general curved interfaces of the permittivity profile, and field continuity conditions are carefully imposed across the dielectric interfaces. The proposed method shows uniformly excellent convergence characteristics for both the transverse-electric and transverse-magnetic waves in the analysis of different structures. The analysis of a mini band gap is also shown to demonstrate the extremely high accuracy of the proposed method.

We analyze the synchronization dynamics of phase oscillators far from the synchronization manifold, including the onset of synchronization on scale-free networks with low and high clustering coefficients. We use normal coordinates and corresponding time-averaged velocities derived from the Laplacian matrix, which reflects the network’s topology. In terms of these coordinates, synchronization manifests itself as a contraction of the dynamics onto progressively lower-dimensional submanifolds of phase space spanned by Laplacian eigenvectors with lower eigenvalues. Differences between high and low clustering networks can be correlated with features of the Laplacian spectrum. For example, the inhibition of full synchoronization at high clustering is associated with a group of low-lying modes that fail to lock even at strong coupling, while the advanced partial synchronization at low coupling noted elsewhere is associated with high-eigenvalue modes.

The wait-and-switch stochastic model of relaxation is presented. Using the “random-variable” formalism of limit theorems of probability theory we explain the universality of the short- and long-time fractional-power laws in relaxation responses of complex systems. We show that the time evolution of the nonequilibrium state of a macroscopic system depends on two stochastic mechanisms: one, which determines the local statistical properties of the relaxing entities, and the other one, which determines the number (random or deterministic) of the microscopic and mesoscopic relaxation contributions. Within the proposed framework we derive the Havriliak-Negami and Kohlrausch-Williams-Watts functions. We also discuss the influence of the random-walk characteristics of migrating defects on the homogeneous and heterogeneous relaxation scenarios and show the origins of the stretched-exponential integral kernel in the integral representation of the ensemble-averaged relaxation function.

Two-dimensional colloidal suspensions exposed to periodic external fields exhibit a variety of molecular crystalline phases. There two or more colloids assemble at lattice sites of potential minima to build new structural entities, referred to as molecules. Using the strength of the potential and the filling fraction as control parameters, a phase transition to unconventional orientationally ordered states can be induced. We introduce an approach that focuses at the discrete set of orientational states relevant for the phase ordering. The orientationally ordered states are mapped to classical spin systems. We construct effective Hamiltonians for dimeric and trimeric molecules on triangular lattices suitable for a statistical mechanics discussion. A mean-field analysis produces a rich phase behavior which is substantiated by Monte Carlo simulations.

The classical Poisson-Boltzmann (PB) theory of electrolytes assumes a dilute solution of point charges with mean-field electrostatic forces. Even for very dilute solutions, however, it predicts absurdly large ion concentrations (exceeding close packing) for surface potentials of only a few tenths of a volt, which are often exceeded, e.g., in microfluidic pumps and electrochemical sensors. Since the 1950s, several modifications of the PB equation have been proposed to account for the finite size of ions in equilibrium, but in this two-part series, we consider steric effects on diffuse charge dynamics (in the absence of electro-osmotic flow). In this first part, we review the literature and analyze two simple models for the charging of a thin double layer, which must form a condensed layer of close-packed ions near the surface at high voltage. A surprising prediction is that the differential capacitance typically varies nonmonotonically with the applied voltage, and thus so does the response time of an electrolytic system. In PB theory, the differential capacitance blows up exponentially with voltage, but steric effects actually cause it to decrease while remaining positive above a threshold voltage where ions become crowded near the surface. Other nonlinear effects in PB theory are also strongly suppressed by steric effects: The net salt adsorption by the double layers in response to the applied voltage is greatly reduced, and so is the tangential “surface conduction” in the diffuse layer, to the point that it can often be neglected compared to bulk conduction (small Dukhin number).

In situations involving large potentials or surface charges, the Poisson-Boltzman (PB) equation has shortcomings because it neglects ion-ion interactions and steric effects. This has been widely recognized by the electrochemistry community, leading to the development of various alternative models resulting in different sets “modified PB equations,” which have had at least qualitative success in predicting equilibrium ion distributions. On the other hand, the literature is scarce in terms of descriptions of concentration dynamics in these regimes. Here, adapting strategies developed to modify the PB equation, we propose a simple modification of the widely used Poisson-Nernst-Planck (PNP) equations for ionic transport, which at least qualitatively accounts for steric effects. We analyze numerical solutions of these modified PNP equations on the model problem of the charging of a simple electrolyte cell, and compare the outcome to that of the standard PNP equations. Finally, we repeat the asymptotic analysis of Bazant, Thornton, and Ajdari [Phys. Rev. E 70, 021506 (2004)] for this new system of equations to further document the interest and limits of validity of the simpler equivalent electrical circuit models introduced in Part I [Kilic, Bazant, and Ajdari, Phys. Rev. E 75, 021502 (2007)] for such problems.

We study the capillary wave dynamics of a single viscoelastic supported film and of a double layer of immiscible viscoelastic supported films. Using both simple scaling arguments and a continuum hydrodynamic theory, we investigate the effects of viscoelasticity and interfacial slip on the relaxation dynamics of these capillary waves. Our results account for the recent observation of a wavelength-independent decay rate for capillary waves in a supported polystyrene/brominated polystyrene double layer [X. Hu et al., Phys. Rev. E 74, 010602(R) (2006)].

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few $k_{B}T$. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where the single strand of the denatured zone joins the still intact double strand, can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.

Using data retrieved from the INSPEC database we have quantitatively discussed a few syndromes of the publish-or-perish phenomenon, including the continuous growth of the rate of scientific productivity, and the continuously decreasing percentage of those scientists who stay in science for a long time. Making use of the maximum entropy principle and fluctuation-dissipation theorem, we have shown that the observed fat-tailed distributions of the total number of papers $x$ authored by scientists may result from the density-of-states function $g(x;\tau )$ underlying the scientific community. Although different generations of scientists are characterized by different productivity patterns, the function $g(x;\tau )$ is inherent to researchers of a given seniority $\tau$, whereas the publish-or-perish phenomenon is caused only by an external field $\theta$ influencing researchers.

We study the synchronization of dynamical systems induced by a common external noise which has an exponentially decaying time correlation. The synchronization threshold in the noise amplitude is discussed. We clarify how the synchronization threshold depends on the correlation decay rate of the noise for limit cycle and chaotic systems. The dependences are shown to be completely different: The threshold is independent of the correlation decay rate in limit cycle systems while it diverges in the limit of the large correlation decay rate and has the nonzero minimum value at a finite value of the correlation decay rate in chaotic systems. Effects of parameter mismatch between the driven systems on the synchronization quality are also discussed.

Synchronization of delayed coupled and stochastically perturbed systems with delayed nonlinear feedback is studied, using as an example circular chains of three and four delayed coupled Ikeda oscillators. It is proved that in the case of multiplicative noise the exact synchronization in the mean occurs for sufficiently large coupling, and an analytic estimate of the sufficient coupling is given. The sufficiency condition is compared with numerical computations, and typical effects of noise on the exact and some generalized types of synchronization are illustrated.

Gases perturbed by thermal gradients exert forces on surfaces exposed to the molecular bombardment. We calculate the force on thin plates with temperature differences between the opposite faces in dense gases. Using the Chapman-Enskog method we obtain an analytical formula that accounts for normal and shear stresses on the plate edge. We predict a force per unit length of the plate perimeter up to $6.6\times {10}^{-8}\mathrm{N}∕\mathrm{mm}$ per degree Kelvin of temperature difference in air. The present result is compared with experimental data from the literature finding an excellent agreement in those cases where experimental conditions and procedures permit comparison. The proposed analytical formula provides an effective tool for calculating forces in microstructures and nanostructures affected by temperature inequalities.

The results are given of an experimental investigation of heat transport processes in fluid dusty structures in rf-discharge plasmas under different conditions: for discharge in argon, and for discharge in air under an action of electron beam. The analysis of steady-state and unsteady-state heat transfer is used to obtain the coefficients of thermal conductivity and thermal diffusivity under the assumption that the observed heat transport is associated with a thermal conduction in the dusty component of plasmas. The temperature dependence of these coefficients is obtained, which agrees qualitatively with the results of numerical simulation for simple monatomic liquids.

We show that it is possible to construct stochastic source distributions that generate wave fields with any desired spatial coherence properties inside a prescribed finite region, regardless of the refractive-index distribution therein. In particular, we demonstrate that there is no universal sinc-function form for the field correlations produced by statistically homogeneous and isotropic source distributions within large lossless regions, contrary to what is suggested by previous work. The results also disprove the commonly held belief that in lossless source regions the coherence length of the light is bounded below by the blackbody coherence length—that is, by approximately half the wavelength of the field.