We studied transitions between spatiotemporal patterns that can be induced in a spatially extended nonlinear chemical system by a unidirectional flow in combination with constant inflow concentrations. Three different scenarios were investigated. (i) Under conditions where the system exhibited two stable fixed points, the propagation direction of trigger fronts could be reversed, so that domains of the less stable fixed point invaded the system. (ii) For bistability between a stable fixed point and a limit cycle we observed that above a critical flow velocity, the unstable focus at the center of the limit cycle could be stabilized. Increasing the flow speed further, a regime of damped flow-distributed oscillations was found and, depending on the boundary values at the inflow, finally the stable fixed point dominated. Similarly, also in the case of spatiotemporal chaos (iii), the unstable steady state could be stabilized and was replaced by the stable fixed point with increasing flow velocity. We finally outline a linear stability analysis that can explain part of our findings.

The variable-density spectral kinetic energy budget for the Richtmyer-Meshkov–induced turbulent mixing layer is presented using results from a ${512}^3$ implicit large eddy simulation. The budget is presented at several time instants and as a function of the inhomogeneous direction as the layer transitions from the initial impulse through to self-similarity. There are clear parallels in the development of the mixing layer with a previous analysis for the Rayleigh-Taylor instability. In the core of the layer, the quadratic terms are largely negative in the energy-containing scales. The transfer spectra are clearly asymmetric, where the majority of the activity occurrs on the spike side. The quadratic and pressure components are of opposite sign and almost cancel each other out in the spikes. The dilatational terms are negligible in comparison to the difference between the quadratic and pressure transfer. A notable result is that vortex rings are identified as the key source of alternating fields of negative and positive energy transfer within the mixing layer. This helps explain similar observations noted in direct numerical simulations of Rayleigh-Taylor instability. Finally, the spectral numerical dissipation for this scheme is computed for the self-similar layer. This demonstrated that the effects of numerical dissipation are small compared to the other terms at low wave numbers, whereas at higher wave numbers where modes become significantly underresolved the numerical dissipation is approximately twice the nonlinear transfer term and behaves in approximate analogy to an effective spectral eddy viscosity.

Transmission of a $p$-polarized electromagnetic wave through a two-layer plasma structure with spatially nonuniform distributions of electron density in the layers is studied. The case, when the electromagnetic wave is obliquely incident on the structure and is evanescent in both plasma layers, is considered. The conditions for total transparency of the two-layer structure are found for the thin slab case and when the plasma inhomogeneity is weak. It is shown that the transmission coefficient of the $p$-polarized wave can be about unity, even if the plasma inhomogeneity is large. The effects of plasma inhomogeneity on transparency of the structure are more important if the slabs are thick, comparing with the case of thin layers.

A shear flow of particles in a laser-driven two-dimensional (2D) dusty plasma is observed in a study of viscous heating and thermal conduction. Video imaging and particle tracking yields particle velocity data, which we convert into continuum data, presented as three spatial profiles: mean particle velocity (i.e., flow velocity), mean-square particle velocity, and mean-square fluctuations of particle velocity. These profiles and their derivatives allow a spatially resolved determination of each term in the energy and momentum continuity equations, which we use for two purposes. First, by balancing these terms so that their sum (i.e., residual) is minimized while varying viscosity $\eta$ and thermal conductivity $\kappa$ as free parameters, we simultaneously obtain values for $\eta$ and $\kappa$ in the same experiment. Second, by comparing the viscous heating and thermal conduction terms, we obtain a spatially resolved characterization of the viscous heating.

A novel generalized Lagrange multiplier method for functional optimization with inclusion of subsidiary conditions is presented and applied to the optimization of material distributions in thermoelectric converters. Multistaged devices are considered within the same formalism by inclusion of position-dependent electric current in the legs leading to a modified thermoelectric equation. Previous analytical solutions for maximized efficiencies for generators and coolers obtained by Sherman [J. Appl. Phys. 31, 1 (1960)], Snyder [Phys. Rev. B 86, 045202 (2012)], and Seifert et al. [Phys. Status Solidi A 207, 760 (2010)] by a method of local optimization of reduced efficiencies are recovered by independent proof. The outstanding maximization problems for generated electric power and cooling power can be solved swiftly numerically by solution of a differential equation-system obtained within the new formalism. As far as suitable materials are available, the inhomogeneous TE converters can have increased performance by use of purely temperature-dependent material properties in the thermoelectric legs or by use of purely spatial variation of material properties or by a combination of both. It turns out that the optimization domain is larger for the second kind of device which can, thus, outperform the first kind of device.

We have analyzed the dynamic phase transition of the kinetic Ising model in mean-field approximation by means of an analytical approach. Specifically, we study the evolution of the system under the simultaneous influence of time-dependent and time-independent magnetic fields. We demonstrate that within the approximate analytical treatment of our approach, the dynamic phase transition exhibits power-law dependencies for the order parameter that have the same critical exponents as the mean-field equilibrium case. Moreover we have obtained an equation of state, with which we can prove that the time-independent field component is effectively the conjugate field of the order parameter. Our analysis is limited to the parameter range, in which only second-order phase transitions occur, i.e., for small applied field amplitudes and temperatures close to the Curie point. In order to ensure the reliability of our analytical results we have corroborated them by comparison to numerical evaluations of the same model.

Folding transition states and their structures are crucial in understanding protein folding pathways and folding dynamics. As they cannot be detected directly by experiments due to their instability, many computational methods have been proposed to solve this problem. However, each of these methods can give only one part of the transition state ensemble for a peptide or protein. Here we present a folding-network approach to identify the transition states of peptides or proteins and test it on the β-hairpin peptide trpzip2, with the result that we identify all the folding transition states of tripzip2, which may only be determined separately by other methods. This suggests that the network approach can provide more complete information about the folding transition states, at least for peptides.

The shape transformations of red blood cells stuck in capillary narrowings with radii close to the critical radius where the maximum deformations occur are analyzed. The membrane skeleton deformations are studied within the effective network model and the continuum elastic model, whereas the area-difference elasticity model is applied to describe the phospholipid bilayer. A minimization of the total free energy is performed to determine the cell shapes in a stopped flow, which are calculated by a triangulated representation of the membrane surface. The shapes are asymmetric, characterized by a single invagination, which decreases with decreasing radii of the narrowing and vanishes at its critical radius. The largest stretching deformations of the skeleton are at the ends of the elongated shape, and remarkable shear deformations appear around the invagination. The membrane's mechanical energy increases with the decreasing radius of the narrowing, predominantly due to the deformation of membrane skeleton. The increase in the shear energy is significantly larger than any other energy contribution within both models. The pressure differences needed for the penetration into the narrowing are strongly coupled with the membrane's mechanical energy. Their values were found to be of the order of 10 Pa. Both models correspond well.

Neurons temporally integrate input signals, translating them into timed output spikes. Because neurons nonperiodically emit spikes, examining spike timing can reveal information about input signals, which are determined by activities in the populations of excitatory and inhibitory presynaptic neurons. Although a number of mathematical methods have been developed to estimate such input parameters as the mean and fluctuation of the input current, these techniques are based on the unrealistic assumption that presynaptic activity is constant over time. Here, we propose tracking temporal variations in input parameters with a two-step analysis method. First, nonstationary firing characteristics comprising the firing rate and non-Poisson irregularity are estimated from a spike train using a computationally feasible state-space algorithm. Then, information about the firing characteristics is converted into likely input parameters over time using a transformation formula, which was constructed by inverting the neuronal forward transformation of the input current to output spikes. By analyzing spike trains recorded in vivo, we found that neuronal input parameters are similar in the primary visual cortex V1 and middle temporal area, whereas parameters in the lateral geniculate nucleus of the thalamus were markedly different.

The kinetics of the flux of a charged macromolecular solution through an environment of changing geometry with wide and constricted regions is investigated analytically. A model device consisting of alternating deep and shallow slits known as an “entropic trap” is used to represent the environment. The flux is supported by the external electrostatic field. The “wormlike chain” model is used for the macromolecule (dsDNA in the present study). The chain entropy in both the deep and the shallow slits, the work by the electric field, and the energy of the elastic bending of the chain are taken into account accurately. Based on the calculated free energy, the kinetics and the scaling behavior of the chain escaping from the entropic trap are studied. We find that the escape process occurs in two kinetic stages with different time scales and discuss the possible influence of the surface roughness. The scope of the accuracy of the proposed model is discussed.

The Monte Carlo (MC) estimates of thermal averages are usually functions of system control parameters $\lambda$, such as temperature, volume, and interaction couplings. Given the MC average at a set of prescribed control parameters ${\lambda }_0$, the problem of analytic continuation of the MC data to $\lambda$ values in the neighborhood of ${\lambda }_0$ is considered in both classic and quantum domains. The key result is the theorem that links the differential properties of thermal averages to the higher order cumulants. The theorem and analytic continuation formulas expressed via higher order cumulants are numerically tested on the classical Lennard-Jones cluster system of $N=13$, 55, and 147 neon particles.

We review two formulations of the fully nonlinear local induction equation approximating the self-induced motion of the vortex filament (in the local induction approximation), corresponding to the Cartesian and arc-length coordinate systems. The arc-length representation put forth by Umeki [Theor. Comput. Fluid Dyn. 24, 383 (2010)] results in a type of $1+1$ derivative nonlinear Schrödinger (NLS) equation describing the motion of such a vortex filament. We obtain exact stationary solutions to this derivative NLS equation; such exact solutions are a rarity. These solutions are periodic in space and we determine the nonlinear dependence of the period on the amplitude.

A model (further referred to as the V model) for the simulation of granular solids, such as rocks, ceramics, concrete, nanocomposites, and agglomerates, composed of bonded particles (rigid bodies), is proposed. It is assumed that the bonds, usually representing some additional gluelike material connecting particles, cause both forces and torques acting on the particles. Vectors rigidly connected with the particles are used to describe the deformation of a single bond. The expression for potential energy of the bond and corresponding expressions for forces and torques are derived. Formulas connecting parameters of the model with longitudinal, shear, bending, and torsional stiffnesses of the bond are obtained. It is shown that the model makes it possible to describe any values of the bond stiffnesses exactly; that is, the model is applicable for the bonds with arbitrary length/thickness ratio. Two different calibration procedures depending on bond length/thickness ratio are proposed. It is shown that parameters of the model can be chosen so that under small deformations the bond is equivalent to either a Bernoulli-Euler beam or a Timoshenko beam or short cylinder connecting particles. Simple analytical expressions, relating parameters of the V model with geometrical and mechanical characteristics of the bond, are derived. Two simple examples of computer simulation of thin granular structures using the V model are given.

We present a technique for the determination of viscoelastic properties of a medium by tracking the motion of an embedded probe particle by using molecular dynamics simulations. The approach involves the analysis of the simulated particle motion by continuum theory; it is shown to work in both passive and active modes. We demonstrate that, for passive rheology, an analysis based on the generalized Stokes-Einstein relationship is not adequate to obtain the values of the viscoelastic moduli over the frequency range studied. For both passive and active modes, it is necessary to account for the medium and particle inertia when analyzing the particle motion. For a polymer melt system consisting of short chains, the values calculated from the proposed approach are in good quantitative agreement with previous literature results that were obtained using completely different simulation approaches. The proposed particle rheology simulation technique is general and could provide insight into the characterization of the mechanical properties in biological systems, such as cellular environments and polymeric systems, such as thin films and nanocomposites that exhibit spatial variation in properties over the nanoscale.

Recent mathematical dynamical models of the conflict between two different actors, be they nations, groups, or individuals, have been developed that are capable of predicting various outcomes depending on the chosen feedback strategies, initial conditions, and the previous states of the actors. In addition to these factors, this paper examines the effect of time delayed feedback on the conflict dynamics. Our analysis shows that under certain initial and feedback conditions, a stable neutral equilibrium of conflict may destabilize for some critical values of time delay, and the two actors may evolve to new emotional states. We investigate the results by constructing critical delay surfaces for different sets of parameters and analyzing results from numerical simulations. These results provide new insights regarding conflict and conflict resolution and may help planners in adjusting and assessing their strategic decisions.

We study the development of nonlinear traveling waves on the interface separating two viscous fluids flowing in parallel in a vertical Hele-Shaw cell. One of the fluids is a ferrofluid and a uniform magnetic field is applied in the plane of the cell, making an angle with the initially undisturbed interface. We employ a mode-coupling theory that predicts the possibility of controlling the speed of the waves by purely magnetic means. The influence of the tilted magnetic field on the waves shape profile and the establishment of stationary traveling wave structures are investigated.

In an electron-proton plasma, electrostatic solitary waves and hole structures can easily be generated by streaming instability due to the asymmetric inertia between ions and electrons. It has been argued theoretically whether electrostatic solitons and/or hole structures can form in a pair plasma. This paper presents results on the formation of pair electrostatic hole structure in an electron-positron plasma based on one-dimensional electrostatic particle-in-cell simulations. In particular, we show the feature of interlacing electron and positron holes in phase space generated by current-free electron and positron beams streaming in a stationary electron-positron background plasma. The coexistent electron and positron holes are associated with periodic interlacing of positive and negative potentials, respectively. Detailed comparisons between simulation results and linear theory of streaming instability in pair plasmas are made and the thermodynamic state is inferred.

Heterogeneous flows are observed to result from variations in the geometry and topology of pore structures within stochastically generated three dimensional porous media. A stochastic procedure generates media comprising complex networks of connected pores. Inside each pore space, the Navier-Stokes equations are numerically integrated until steady state velocity and pressure fields are attained. The intricate pore structures exert spatially variable resistance on the fluid, and resulting velocity fields have a wide range of magnitudes and directions. Spatially nonuniform fluid fluxes are observed, resulting in principal pathways of flow through the media. In some realizations, up to $25\%$ of the flux occurs in $5\%$ of the pore space depending on porosity. The degree of heterogeneity in the flow is quantified over a range of porosities by tracking particle trajectories and calculating their attributes including tortuosity, length, and first passage time. A representative elementary volume is first computed so the dependence of particle based attributes on the size of the domain through which they are followed is minimal. High correlations between the dimensionless quantities of porosity and tortuosity are calculated and a logarithmic relationship is proposed. As the porosity of a medium increases the flow field becomes more uniform.

The short-time behavior of the ($1+1$)-dimensional Kardar-Parisi-Zhang (KPZ) growth equation with a flat initial condition is obtained from the exact expressions for the moments of the partition function of a directed polymer with one end point free and the other fixed. From these expressions, the short-time expansions of the lowest cumulants of the KPZ height field are exactly derived. The results for these two classes of cumulants are checked in high-precision lattice numerical simulations. The short-time limit considered here is relevant for the study of the interface growth in the large-diffusivity or weak-noise limit and describes the universal crossover between the Edwards-Wilkinson and the KPZ universality classes for an initially flat interface.

We report the results of studies of the collective and pair diffusion coefficients of particles in two quasi-one-dimensional geometries: straight 2-mm-long channels and rings with radii between 3 and 35 μm. We find a contribution to the packing fraction dependence of the collective diffusion coefficient that confirms the behavior predicted by Frydel and Diamant [D. Frydel and H. Diamant, Phys. Rev. Lett. 104, 248302 (2010)], indicative of long-range hydrodynamic coupling resulting from collective motion of particles in periodic quasi-one-dimensional geometries. Specifically, we find a proportionality constant of 0.19 ± 0.01 μm${}^2$/s between the residual collective diffusion coefficient (defined as the collective diffusion coefficient less the mean self-diffusion coefficient of colloids) and the packing fraction for the ring geometries, independent of ring curvature, and a proportionality constant of 0.14 ± 0.01 μm${}^2$/s for 2-mm straight channels. Both of these values, for circular geometries in particular, are significantly larger than predicted when only ensemble averaging over particle positions is accounted for, which strongly suggests the presence of additional hydrodynamic coupling. These findings are signficant because they imply that the global geometry of the confined suspension influences collective colloidal diffusion even when single file motion of colloids is maintained.