We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and nonperfect repeats, i.e., repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long-range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long-range sequences.

Simulations of liquid-gas systems with interface terms evaluated by central difference discretizations are observed to fail to give accurate results for two reasons: the interface can get “stuck” on the lattice or a density overshoot develops around the interface. In the first case, the bulk densities can take a range of values, dependent on the initial conditions. In the second case, inaccurate bulk densities are found. We derived the minimum interface width required for the accurate simulation of liquid-gas systems with a diffuse interface. This criterion is demonstrated for lattice Boltzmann simulations of a van der Waals gas. Combining this criterion with predictions for the bulk stability defines the parameter range for stable and accurate simulation results even for high density ratios of over 1000.

This paper reviews some aspects of nonlinear model building from data with (gray box) and without (black box) prior knowledge. The model class is very important because it determines two aspects of the final model, namely (i) the type of nonlinearity that can be accurately approximated and (ii) the type of prior knowledge that can be taken into account. Such features are usually in conflict when it comes to choosing the model class. The problem of model structure selection is also reviewed. It is argued that such a problem is philosophically different depending on the model class and it is suggested that the choice of model class should be performed based on the type of a priori available. A procedure is proposed to build polynomial models from data on a Poincaré section and prior knowledge about the first period-doubling bifurcation, for which the normal form is also polynomial. The final models approximate dynamical data in a least-squares sense and, by design, present the first period-doubling bifurcation at a specified value of parameters. The procedure is illustrated by means of simulated examples.

We use a geometrical method to distinguish between ordered and chaotic motion in three-dimensional Hamiltonian systems. We show that this method gives results in agreement with the computation of Lyapunov characteristic exponents. We discuss some examples of unstable Hamiltonian systems in three dimensions, giving, as a particular illustration, detailed results for a potential obtained from a Hamiltonian obtained from a Yang-Mills system.

Experiments and numerical simulations are performed on the Rayleigh-Taylor instability with a complex acceleration history $g\left(t\right)$ consisting of consecutive periods of acceleration, deceleration, and acceleration. The dominant bubbles and spikes that grow in the initial unstable phase are found to be shredded by the trailing structures during the stable deceleration phase. This reduces their diameter at the front and increases the atomic mixing such that the growth during the final unstable acceleration is retarded. The simulations are able to describe the bubble evolution only if broadband initial perturbations are assumed. Such a complex $g\left(t\right)$ is useful for validating mix models.

The linear stability of viscoelastic (Oldroyd-B) film flow down an inclined plane lined with a deformable (neo-Hookean) solid layer is analyzed using low-wave-number asymptotic analysis and the Chebyshev-Tau spectral numerical method. The free surface of film flows of viscoelastic liquids, unlike that of their Newtonian counterparts, becomes unstable in flow down a rigid inclined surface even in the absence of fluid inertia, due to the elastic nature of the liquids. For film flow past a deformable solid, our low-wave-number asymptotic analysis reveals that the solid deformability has a stabilizing effect on the free-surface instability, and, remarkably, this prediction is insensitive to rheology of the liquid film, be it viscoelastic or Newtonian. Using the spectral numerical method, we demonstrate that the free-surface instability can be completely suppressed at all wave numbers when the solid becomes sufficiently deformable. For the case of pure polymeric liquids without any solvent, when the solid layer is made further deformable, both the free surface and the liquid-solid interface are destabilized at finite wave numbers. We also demonstrate a type of mode exchange phenomenon between the modes corresponding to the two interfaces. Importantly, our numerical results show that there is a sufficient range of shear modulus of the solid where both the modes are stable at all wave numbers. For polymer solutions described by the Oldroyd-B model, while the free-surface instability is suppressed by the deformable solid, a host of new unstable modes appear at finite Reynolds number and wave number because of the coupling between liquid flow and free shear waves in the solid. Our study thus demonstrates that the elastohydrodynamic coupling between liquid flow and solid deformation can be exploited either to suppress the free-surface instability (present otherwise in rigid inclines) in viscoelastic film flows, or to induce new instabilities that are absent in flow adjacent to rigid surfaces.

Kinetic theory is used to investigate cross-stream migration of a rigid polymer undergoing rectilinear flow in the vicinity of a wall. Hydrodynamic interactions between the polymers and the boundary result in a cross-stream migration. In simple shear flow, polymers migrate away from the wall, creating a depletion layer in the vicinity of the wall which thickens as the flow strength increases relative to the Brownian force. In pressure-driven flow, an off-center maximum in the center-of-mass distribution occurs due to a competition between hydrodynamic interactions with the wall and the anisotropic diffusivity induced by the inhomogeneous flow field.

Recently, considerable progress has been made in understanding finite-size scaling in equilibrium systems. Here, we study finite-size scaling in nonequilibrium systems at the instance of directed percolation (DP), which has become the paradigm of nonequilibrium phase transitions into absorbing states, above, at, and below the upper critical dimension. We investigate the finite-size scaling behavior of DP analytically and numerically by considering its steady state generated by a homogeneous constant external source on a $d$-dimensional hypercube of finite edge length $L$ with periodic boundary conditions near the bulk critical point. In particular, we study the order parameter and its higher moments using renormalized field theory. We derive finite-size scaling forms of the moments in a one-loop calculation. Moreover, we introduce and calculate a ratio of the order parameter moments that plays a similar role in the analysis of finite size scaling in absorbing nonequilibrium processes as the famous Binder cumulant in equilibrium systems and that, in particular, provides a signature of the DP universality class. To complement our analytical work, we perform Monte Carlo simulations which confirm our analytical results.

This paper presents a recently developed theory of colloid dynamics as an alternative approach to the description of phenomena of dynamic arrest in monodisperse colloidal systems. Such theory, referred to as the self-consistent generalized Langevin equation (SCGLE) theory, was devised to describe the tracer and collective diffusion properties of colloidal dispersions in the short- and intermediate-time regimes. Its self-consistent character, however, introduces a nonlinear dynamic feedback, leading to the prediction of dynamic arrest in these systems, similar to that exhibited by the well-established mode coupling theory of the ideal glass transition. The full numerical solution of this self-consistent theory provides in principle a route to the location of the fluid-glass transition in the space of macroscopic parameters of the system, given the interparticle forces (i.e., a nonequilibrium analog of the statistical-thermodynamic prediction of an equilibrium phase diagram). In this paper we focus on the derivation from the same self-consistent theory of the more straightforward route to the location of the fluid-glass transition boundary, consisting of the equation for the nonergodic parameters, whose nonzero values are the signature of the glass state. This allows us to decide if a system, at given macroscopic conditions, is in an ergodic or in a dynamically arrested state, given the microscopic interactions, which enter only through the static structure factor. We present a selection of results that illustrate the concrete application of our theory to model colloidal systems. This involves the comparison of the predictions of our theory with available experimental data for the nonergodic parameters of model dispersions with hard-sphere and with screened Coulomb interactions.

We present an exact solution to the problem of the global shape description of a spherical vesicle distorted by a grafted latex bead. This solution is derived by treating the nonlinearity in bending elasticity through the (topological) Bogomol’nyi decomposition technique and elastic compatibility. We recover the “hat-model” approximation in the limit of a small latex bead and find that the region antipodal to the grafted latex bead flattens. We also derive the appropriate shape equation using the variational principle and relevant constraints.

We study how heterogeneous degree distributions and large-scale collective cooperation in social networks emerge in complex homogeneous systems by a simple local rule: learning from the best in both strategy selections and linking choices. The prisoner’s dilemma game is used as the local dynamics. We show that the social structure may evolve into single-scale, broad-scale, and scale-free (SF) degree distributions for different control parameters. In particular, in a relatively strong-selfish parameter region the SF property can be self-organized in social networks by dynamic evolutions and these SF structures help the whole node community to reach a high level of cooperation under the poor condition of a high selfish intention of individuals.

We study the dynamics of inertial particles in two-dimensional incompressible flows. The particle dynamics is modeled by four-dimensional dissipative bailout embedding maps of the base flow which is represented by $2-d$ area preserving maps. The phase diagram of the embedded map is rich and interesting both in the aerosol regime, where the density of the particle is larger than that of the base flow, as well as the bubble regime, where the particle density is less than that of the base flow. The embedding map shows three types of dynamic behavior, periodic orbits, chaotic structures, and mixed regions. Thus, the embedding map can target periodic orbits as well as chaotic structures in both the aerosol and bubble regimes at certain values of the dissipation parameter. The bifurcation diagram of the $4-d$ map is useful for the identification of regimes where such structures can be found. An attractor merging and widening crisis is seen for a special region for the aerosols. At the crisis, two period-10 attractors merge and widen simultaneously into a single chaotic attractor. Crisis induced intermittency is seen at some points in the phase diagram. The characteristic times before bursts at the crisis show power-law behavior as functions of the dissipation parameter. Although the bifurcation diagram for the bubbles looks similar to that of aerosols, no such crisis regime is seen for the bubbles. Our results can have implications for the dynamics of impurities in diverse application contexts.

The dynamics of dark spatial soliton beams and their interaction under the presence of a continuous wave (CW), which dynamically induces a photonic lattice, are investigated. It is shown that appropriate selection of the characteristic parameters of the CW result in controllable steering of a single soliton as well as controllable interaction between two solitons. Depending on the CW parameters, the soliton angle of propagation can be changed drastically, while two-soliton interaction can be either enhanced or reduced, suggesting a reconfigurable soliton control mechanism. Our analytical approach, based on the variational perturbation method, provides a dynamical system for the dark soliton evolution parameters. Analytical results are shown in good agreement with direct numerical simulations.

It is shown that all the known experimental (quasi)stationary dielectric response functions of glassy media can be derived from a standard generalized Langevin description of overdamped torsional dipole oscillators in trapping potentials with random orientations under some minimal assumptions. The non-Markovian theory obeys the fluctuation-dissipation theorem and the Onsager regression theorem. Moreover, it displays no aging on the time scale of the dielectric response, all in assumption of local thermal (quasi)equilibrium. Aging might come from jumping among metastable traps. It occurs on a quite different time scale which is not related to the principal dielectric response. We put the old phenomenological theory of Cole and Cole, Davidson and Cole, and others on a firm basis within a stochastic, thermodynamically consistent approach.

We consider a classical interacting dimer model which interpolates between the square lattice case and the triangular lattice case by tuning a chemical potential in the diagonal bonds. The interaction energy simply corresponds to the number of plaquettes with parallel dimers. Using transfer matrix calculations, we find in the anisotropic triangular case a succession of different physical phases as the interaction strength is increased: a short-range disordered liquid dimer phase at low interactions, then a critical phase similar to the one found for the square lattice, and finally a transition to an ordered columnar phase for large interactions. Our results indicate that criticality and nonbipartiteness are compatible in a dimer model. For the isotropic triangular case, we have indications that the system undergoes a first-order phase transition to an ordered phase, without appearance of an intermediate critical phase.

Discrete particle simulations are used to model segregation in granular mixtures of three different particle species in a horizontal rotating drum. Axial band formation is observed, with medium-size particles tending to be located between alternating bands of big and small particles. Partial radial segregation also appears; it precedes the axial segregation and is characterized by an inner core region richer in small particles. Axial bands are seen to merge during the long simulation runs, leading to a coarsening of the band pattern; the relocation of particles involved in one such merging event is examined. Overall, the behavior is similar to experiment and represents a generalization of what occurs in the simpler two-component mixture.

Parallel experiments in long, axially rotated cylinders are used to study the influence of interstitial fluid viscosity on particle segregation in bidisperse granular slurries. A uniformly mixed initial state segregates into surface bands, which alternate between regions of large particles and regions composed of a mixture of small and large particles. As the tumbler rotates, the relative area of the mixed particle bands increases and saturates, while the number of bands reaches a peak and then decreases logarithmically in time for all viscosities studied. With increasing interstitial fluid viscosity, the asymptotic mixed band area increases proportionally, the time for bands to appear at the surface decreases, and the peak number of bands goes through a maximum at a viscosity of $\sim 3\text{cP}$. Extrapolation to the low-viscosity limit matches the data for dry granular systems; at the high-end viscosity there is a value beyond which no axial banding occurs. A heuristic mechanism based on the coexistence of pure and mixed particle phases and their dependence on viscosity is presented to rationalize key aspects of the results.

Charged, nonwetting colloids with a contact angle $\theta =180°$ are attracted to an oil-water interface due to image charge forces. Near the interface, the attractive image charge forces are balanced by repulsive van der Waals forces, and thus the colloids are trapped at a finite distance from the interface. Electrostatic and van der Waals pressure lead to a deformation of the interface in the equilibrium state. For parameters relevant to experiment, however, the effects of the deformed interface are negligible and thus the mutual interactions of such interfacially trapped colloids should be well characterized by electrostatic dipole repulsions.

A model for the aggregation of molecules with two internal states is studied by kinetic Monte Carlo simulations. Molecules are represented by simple beads, discarding all stereochemical specificity. Monomers are placed in a three-dimensional lattice and diffusion processes are simulated, as well as internal state conversions of the molecules. The two internal states feature a stable (S) not assembly competent configuration, and an unstable assembly competent (A) configuration. Monomers in A state are given a higher energy if isolated, but they can reach the lowest energy level through short-range interactions between each other, so that their aggregation is promoted. Kinetics of cluster formation are examined, as well as the basic mechanisms ruling growth in our system. The simulations show that the aggregation process is preceded by a lag phase, which is followed by a fast growth phase. The duration of the lag phase is determined by the strength of the A-A interaction, whereas the time slope of the growth phase is mainly influenced by the conversion rate between internal states. The whole work has been inspired by the biological problem of amyloid aggregation, whose aggregation curves often present a sigmoidal behavior which is reproduced by the present model.