Band structure and wave localization are investigated for sea surface water waves over large-scale sand wave topography. Sand wave height, sand wave width, water depth, and water width between adjacent sand waves have significant impact on band gaps. Random fluctuations of sand wave height, sand wave width, and water depth induce water wave localization. However, random water width produces a perfect transmission tunnel of water waves at a certain frequency so that localization does not occur no matter how large a disorder level is applied. Together with theoretical results, the field experimental observations in the Taiwan Bank suggest band gap and wave localization as the physical mechanism of sea surface water wave propagating over natural large-scale sand waves.

This study employs three-dimensional particle-tracking velocimetry (3D-PTV) for experimental investigation of the existence and properties of periodic lines in 3D lid-driven time-periodic flows inside a cylindrical cavity. These periodic lines, consisting of material points that periodically return to their initial position, play a central role in the transport properties of laminar flows, yet their existence has so far been demonstrated only in numerical simulations. The formation and characteristics of periodic lines are inextricably linked with spatiotemporal symmetries of the flow. 3D-PTV measurements determined that relevant symmetries, identified with previous symmetry analyses, are satisfied within experimental error bounds. These measurements subsequently isolated periodic lines in the designated symmetry planes, thus offering first experimental evidence of their physical existence and their fundamental reliance on symmetries. Experimental periodic lines are topologically equivalent to those in simulated flows with identical symmetries and exhibit the same response to changes in forcing conditions. The laboratory experiments by these observations bridge the gap from theoretical and numerical predictions on periodic lines to real 3D flows.

A theory of an acoustic vector soliton of self-induced transparency is constructed. By using the perturbative reduction method the magnetic Bloch equations and the equation of motion for the displacement field for the small area pulse are reduced to a system of two coupled nonlinear Schrödinger equations. The shape of an acoustic vector soliton with the sum and difference of the frequencies is presented. Explicit analytical expressions for the parameters of an acoustic vector soliton are obtained as well as simulations of an acoustic vector soliton presented with realistic parameters which can be reached in experiments. It is shown that the vector soliton in the special case can be reduced to the breather solution, and these nonlinear waves have different profiles.

We study the effect of noise recycling on nonequilibrium escape dynamics in a bistable system. For small noise, the non-Markovian problem is reduced to a two-state model with the master equation depending on not only the current state but also the earlier state, based on which we are able to derive the analytical formulas for the switching rate, the autocorrelation function, and the power spectrum density (PSD). Both the theoretical and the numerical results show that, with modulating the time delay in noise recycling, a monotonic PSD may switch to a nonmonotonic one; the amplitude of PSD at resonance frequency exhibits a pronounced maximum at a certain noise level, declaring the onset of stochastic resonance (SR) in the absence of a weak periodic signal. Further, we also demonstrate that the linear response to the external periodic force displays a maximum at a certain level of time delay, displaying the signature of SR.

The macroscopic theory of nematics is conveniently described in terms of the phenomenological Landau–de Gennes free energy. Here we show how such an effective free energy can be obtained explicitly from a microscopic model via the help of a systematic coarse-graining procedure. We test our approach for the two- and three-dimensional Lebwohl-Lasher model of nematics. The effective free energy that we obtain is consistent with the phenomenological Landau–de Gennes form for weak orientational ordering and the Maier-Saupe theory of the isotropic-nematic transition. For strong orientational ordering, however, the effective free energy increases rapidly and diverges logarithmically near the fully oriented state. The explicit form for the regularized Landau–de Gennes potential proposed here restricts the order parameter to physical admissible values and reproduces our numerical data accurately.

Epileptic electroencephalography recordings can be described in terms of four prototypic wave forms: fast sinusoidal oscillations, large slow waves, fast spiking, and spike waves. On the macroscopic level, these wave forms have been modeled by different mechanistic models which share canonical features. Here we derive a minimal model of excitatory and inhibitory processes with features common to all previous models. We can infer that at least three interacting processes are required to support the prototypic epileptic dynamics. Based on a separation of time scales we analyze the model in terms of interacting manifolds in phase space. This allows qualitative reverse engineering of all epileptic wave forms and transitions between them. We propose this method as a complement to traditional approaches to modeling epileptiform rhythms.

We present a generalization of a population density approach for modeling and analysis of stochastic gene expression. In the model, the gene of interest fluctuates stochastically between an inactive state, in which transcription cannot occur, and an active state, in which discrete transcription events occur; and the individual mRNA molecules are degraded stochastically in an independent manner. This sort of model in simplest form with exponential dwell times has been used to explain experimental estimates of the discrete distribution of random mRNA copy number. In our generalization, the random dwell times in the inactive and active states, $T_0$ and $T_1$, respectively, are independent random variables drawn from any specified distributions. Consequently, the probability per unit time of switching out of a state depends on the time since entering that state. Our method exploits a connection between the fully discrete random process and a related continuous process. We present numerical methods for computing steady-state mRNA distributions and an analytical derivation of the mRNA autocovariance function. We find that empirical estimates of the steady-state mRNA probability mass function from Monte Carlo simulations of laboratory data do not allow one to distinguish between underlying models with exponential and nonexponential dwell times in some relevant parameter regimes. However, in these parameter regimes and where the autocovariance function has negative lobes, the autocovariance function disambiguates the two types of models. Our results strongly suggest that temporal data beyond the autocovariance function is required in general to characterize gene switching.

Chromatin remodeling plays a crucial role in the activation or repression of transcription of eukaryotic genes. The chromatin remodeler ACF acts as a dimeric, processive motor to evenly space nucleosomes, favoring repression of gene transcription. Single-molecule experiments have established that ACF moves the nucleosome more efficiently towards the longer flanking DNA than towards the shorter flanking DNA, thereby centering an initially ill-positioned nucleosome on DNA substrates. In this paper we present a one-motor model with nucleosomal repositioning rates dependent on the DNA flanking length. The corresponding master equation is solved analytically with experimentally relevant parameter values. The velocity profile and the effective diffusion constant for nucleosome sliding, computed from the probability distributions, are in accordance with available experimental data. In order to address the observed kinetic pauses in experimental Förster Resonance Energy Transfer profiles, we extend the master equation to account for transitions between explicit motor states, i.e., adenosine triphosphate (ATP) loading and ATP hydrolysis in both ACF motors. The results of this extended two-motor model are compared to the previous effective one-motor model and allow insights into the role of the synchronization of the two motors acting on the nucleosome.

We consider self-similar solutions describing intermittent bursts in shell models of turbulence and study their relationship with blowup phenomena in continuous hydrodynamic models. First, we show that these solutions are very close to self-similar solution for the Fourier transformed inviscid Burgers equation corresponding to shock formation from smooth initial data. Then, the result is generalized to hyperbolic conservation laws in one space dimension describing compressible flows. It is shown that the renormalized wave profile tends to a universal function, which is independent both of initial conditions and of a specific form of the conservation law. This phenomenon can be viewed as a new manifestation of the renormalization group theory. Finally, we discuss possibilities for application of the developed theory for detecting and describing a blowup in incompressible flows.

Linear stability in Hagen-Poiseuille flow of a shear-thinning fluid is considered. The non-Newtonian viscosity is described by the Carreau rheological law. The effects of shear thinning on the stability are investigated using the energy method and the nonmodal stability theory. The energy analysis shows that the nonaxisymmetric disturbance with the azimuthal wave number $m=1$ has the lowest critical energy Reynolds number for both the Newtonian and shear-thinning cases. With the increase of shear thinning, the critical energy Reynolds number decreases for both the axisymmetric and nonaxisymmetric cases. For the nonmodal stability, we focus on two problems: response to external excitations and response to initial conditions. The former is studied by examining the $\epsilon$ pseudospectrum, and the latter by examining the energy growth function $G\left(t\right)$. For both Newtonian and shear-thinning fluids, it is found that there can be a rather large transient growth even though the linear operator of the Hagen-Poiseuille flow has no unstable eigenvalue. For the problem of response to external excitations, the optimal response is achieved by disturbance with $m=1$ for both the Newtonian and non-Newtonian cases. For the problem of response to initial conditions, the optimal disturbance is in the form of streamwise uniform streaks. Being different from the Newtonian case, the azimuthal wave number of the optimal disturbance may be greater than 1 for strongly shear-thinning cases.

We analyze the spread of a localized peak of energy into vacuum for nonlinear diffusive processes. In contrast with standard diffusion, the nonlinearity results in a compact wave with a sharp front separating the perturbed region from vacuum. In $d$ spatial dimensions, the front advances as $t^{1/(2+da)}$ according to hydrodynamics, with $a$ the nonlinearity exponent. We show that fluctuations in the front position grow as $\sim$$t^{\mu }\eta$, where $\mu <\frac{1}{2+da}$ is an exponent that we measure and $\eta$ is a random variable whose distribution we characterize. Fluctuating corrections to hydrodynamic profiles give rise to an excess penetration into vacuum, revealing scaling behaviors and robust features. We also examine the discharge of a nonlinear rarefaction wave into vacuum. Our results suggest the existence of universal scaling behaviors at the fluctuating level in nonlinear diffusion.

We performed extensive Monte Carlo simulations of the irreversible adsorption of polydispersed disks inside the cells of a patterned substrate. The model captures relevant features of the irreversible adsorption of spherical colloidal particles on patterned substrates. The pattern consists of (equal) square cells, where adsorption can take place, centered at the vertices of a square lattice. Two independent, dimensionless parameters are required to control the geometry of the pattern, namely, the cell size and cell-cell distance, measured in terms of the average particle diameter. However, to describe the phase diagram, two additional dimensionless parameters, i.e., the minimum and maximum particle radii, are also required. We find that the transition between any two adjacent regions of the phase diagram solely depends on the largest and smallest particle sizes, but not on the shape of the distribution function of the radii. We consider size dispersions up to $20\%$ of the average radius using a physically motivated, truncated, Gaussian-size distribution, and focus on the regime where adsorbing particles do not interact with those previously adsorbed on neighboring cells to characterize the jammed state structure. The study generalizes previous exact relations on monodisperse particles to account for size dispersion. Due to the presence of the pattern, the coverage shows a nonmonotonic dependence on the cell size. The pattern also affects the radius of adsorbed particles, where one observes preferential adsorption of smaller radii, particularly at high polydispersity.

We study the geometrical frustration of an extended Hubbard model on a diamond chain, where vertical lines correspond to the hopping and repulsive Coulomb interaction terms between sites while the remaining lines represent only the Coulomb repulsion term. The phase diagrams at zero temperature show quite curious phases: five types of frustrated states and four types of nonfrustrated states, ordered antiferromagnetically. Although a decoration transformation was derived for spin-coupling systems, this approach can be applied to electron-coupling systems. Thus the extended Hubbard model can be mapped onto another effective extended Hubbard model in the atomic limit with additional three- and four-body couplings. This effective model is solved exactly using the transfer-matrix method. In addition, using the exact solution of this model, we discuss several thermodynamic properties away from the half-filled band, such as chemical potential behavior, electronic density, and entropy, for which we study geometrical frustration. Consequently, we investigate the specific heat as well.

We study a Brownian particle on a moving periodic potential. We focus on the statistical properties of the work done by the potential and the heat dissipated by the particle. When the period and the depth of the potential are both large, by using a boundary layer analysis, we calculate a cumulant generating function and a biased distribution function. The result allows us to understand a Zon-Cohen singularity for an extended fluctuation theorem from a viewpoint of rare trajectories characterized by a negative inverse temperature of the biased distribution function.

A modified phase-field crystal model in which the free energy may be minimized by an order parameter profile having isolated bumps is investigated. The phase diagram is calculated in one and two dimensions and we locate the regions where modulated and uniform phases are formed and also regions where localized states are formed. We investigate the effectiveness of the phase-field crystal model for describing fluids and crystals with defects. We further consider a two-component model and elucidate how the structure transforms from hexagonal crystalline ordering to square ordering as the concentration changes. Our conclusion contains a discussion of possible interpretations of the order parameter field.

Single-particle tracking is increasingly used to extract quantitative parameters on single molecules and their environment, while advances in spatial and temporal resolution of tracking techniques inspire new questions and avenues of investigation. Correspondingly, sophisticated analytical methods are constantly developed to obtain more refined information from measured trajectories. Here we point out some fundamental limitations of these approaches due to the finite length of trajectories, the presence of localization error, and motion blur, focusing on the simplest motion regime of free diffusion in an isotropic medium (Brownian motion). We show that two recently proposed algorithms approach the theoretical limit of diffusion coefficient uncertainty. We discuss the practical performance of the algorithms as well as some important implications of these results for single-particle tracking.

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along its central axis. The relative stability of these two phases depends on the interpolymer interactions. The existence the two phases suggests a mechanism in which marginal changes in these interactions, possibly induced by nuclear transport receptors, cause the pore to transform between open and closed configurations, which will influence transport through the pore.

Pedestrian dynamics exhibits various collective phenomena. Here, we study bidirectional pedestrian flow in a floor field cellular automaton model. Under certain conditions, lane formation is observed. Although it has often been studied qualitatively, e.g., as a test for the realism of a model, there are almost no quantitative results, either empirically or theoretically. As basis for a quantitative analysis, we introduce an order parameter which is adopted from the analysis of colloidal suspensions. This allows us to determine a phase diagram for the system where four different states (free flow, disorder, lanes, gridlock) can be distinguished. Although the number of lanes formed is fluctuating, lanes are characterized by a typical density. It is found that the basic floor field model overestimates the tendency towards a gridlock compared to experimental bounds. Therefore, an anticipation mechanism is introduced which reduces the jamming probability.

We study heat conduction behavior of one-dimensional lattices with asymmetric, momentum conserving interparticle interactions. We find that with a certain degree of interaction asymmetry, the heat conductivity measured in nonequilibrium stationary states converges in the thermodynamical limit. Our analysis suggests that the mass gradient resulting from asymmetric interactions may provide a phonon scattering mechanism in addition to that caused by nonlinear interactions.