We discuss the temporal efficiency of template-directed polymer synthesis, such as DNA replication and transcription, under a given template string. To weigh the synthesis speed and accuracy on the same scale, we propose a template-directed synthesis (TDS) rate, which contains an expression analogous to that for the Shannon entropy. Increasing the synthesis speed accelerates the TDS rate, but the TDS rate is lowered if the produced sequences are diversified. We apply the TDS rate to some production system models and investigate how the balance between the speed and the accuracy is affected by changes in the system conditions.

Recently much attention has been paid to the study of the robustness of interdependent and multiplex networks and, in particular, the networks of networks. The robustness of interdependent networks can be evaluated by the size of a mutually connected component when a fraction of nodes have been removed from these networks. Here we characterize the emergence of the mutually connected component in a network of networks in which every node of a network (layer) $\alpha$ is connected with $q_{\alpha }$ its randomly chosen replicas in some other networks and is interdependent of these nodes with probability $r$. We find that when the superdegrees $q_{\alpha }$ of different layers in a network of networks are distributed heterogeneously, multiple percolation phase transition can occur. We show that, depending on the value of $r$, these transition are continuous or discontinuous.

A person's decision to adopt an idea or product is often driven by the decisions of peers, mediated through a network of social ties. A common way of modeling adoption dynamics is to use threshold models, where a node may become an adopter given a high enough rate of contacts with adopted neighbors. We study the dynamics of threshold models that take both the network topology and the timings of contacts into account, using empirical contact sequences as substrates. The models are designed such that adoption is driven by the number of contacts with different adopted neighbors within a chosen time. We find that while some networks support cascades leading to network-level adoption, some do not: the propagation of adoption depends on several factors from the frequency of contacts to burstiness and timing correlations of contact sequences. More specifically, burstiness is seen to suppress cascade sizes when compared to randomized contact timings, while timing correlations between contacts on adjacent links facilitate cascades.

We study the phenomena of Anderson localization in the presence of nonlinear interaction on a lattice. A class of nonlinear Schrödinger models with arbitrary power nonlinearity is analyzed. We conceive the various regimes of behavior, depending on the topology of resonance overlap in phase space, ranging from a fully developed chaos involving Lévy flights to pseudochaotic dynamics at the onset of delocalization. It is demonstrated that the quadratic nonlinearity plays a dynamically very distinguished role in that it is the only type of power nonlinearity permitting an abrupt localization-delocalization transition with unlimited spreading already at the delocalization border. We describe this localization-delocalization transition as a percolation transition on the infinite Cayley tree (Bethe lattice). It is found in the vicinity of the criticality that the spreading of the wave field is subdiffusive in the limit $t\to +\infty$. The second moment of the associated probability distribution grows with time as a power law $\propto$ $t^{\alpha }$, with the exponent $\alpha =1/3$ exactly. Also we find for superquadratic nonlinearity that the analog pseudochaotic regime at the edge of chaos is self-controlling in that it has feedback on the topology of the structure on which the transport processes concentrate. Then the system automatically (without tuning of parameters) develops its percolation point. We classify this type of behavior in terms of self-organized criticality dynamics in Hilbert space. For subquadratic nonlinearities, the behavior is shown to be sensitive to the details of definition of the nonlinear term. A transport model is proposed based on modified nonlinearity, using the idea of “stripes” propagating the wave process to large distances. Theoretical investigations, presented here, are the basis for consistency analysis of the different localization-delocalization patterns in systems with many coupled degrees of freedom in association with the asymptotic properties of the transport.

We report various regimes of capillary filling dynamics under electromagneto-hydrodynamic interactions, in the presence of electrical double layer effects. Our chosen configuration considers an axial electric field and transverse magnetic field acting on an electrolyte. We demonstrate that for positive interfacial potential, the movement of the capillary front resembles capillary rise in a vertical channel under the action of gravity. We also evaluate the time taken by the capillary front to reach the final equilibrium position for positive interfacial potential and show that the presence of a transverse magnetic field delays the time of travel of the liquid front, thereby sustaining the capillary motion for a longer time. Our scaling estimates reveal that the initial linear regime starts, as well as ends, much earlier in the presence of electrical and magnetic body forces, as compared to the corresponding transients observed under pure surface tension driven flow. We further obtain a long time solution for the capillary imbibition for positive interfacial potential, and derive a scaling estimate of the capillary stopping time as a function of the applied magnetic field and an intrinsic length scale delineating electromechanical influences of the electrical double layer. Our findings are likely to offer alternative strategies of controlling dynamical features of capillary imbibition, by modulating the interplay between electromagnetic interactions, electrical double layer phenomena, and hydrodynamics over interfacial scales.

We study the flow, through a model two-dimensional porous medium, of Newtonian fluids, power-law fluids, and viscoplastic fluids in the laminar regime and with moderate or dominant effects of the yielding term. A numerical technique able to take properly into account yielding effects in viscoplastic flows without any regularization is used to determine the detailed flow characteristics. We show that as soon as the distance between the disks forming the porous medium is sufficiently small, the velocity field and in particular the distribution function of the velocity of these different fluids in a wide range of flow regimes are similar. Moreover, the volume fraction of fluid at rest is negligible even at low flow rate. Thus the non-Newtonian character of a fluid flowing through such a complex geometry tends to be broken. We suggest that this is due to the fact that in a flow through a channel of rapidly varying cross section, the deformation, and thus the flow field, is imposed on the fluid, a situation that is encountered almost everywhere in a porous medium. These results make it possible to deduce a general expression for Darcy's law of these fluid types and estimate the parameters appearing in this expression.

Flow over the traveling wavy foil with a built-in rigid flapping plate at its trailing edge has been numerically studied using the multi-relaxation-time lattice Boltzmann method and immersed boundary method. The effect of the plate length on the propulsive performance such as the thrust force, energy consumption, and propeller efficiency has been investigated. Three modes (body force dominated, body and tail force competing and tail force dominated modes) have been identified that are associated with different hydrodynamics and flow structures. It is revealed that there exists a better performance plate length region and, within this region, a high propeller efficiency (close to its maximum value) is achieved due to a great increase in propulsive force at a cost of a slight increase in energy consumption. Furthermore, a weak stabilizing effect on locomotion movement is indicated by the slight decrease in the root-mean-square (rms) values of drag and lateral forces.

Incorporating the bolometric effect, the thermoelastic damping in a nanowaveguide resonator driven by an optical gradient force is investigated in this paper. Based on the Euler-Bernoulli beam theory, the governing equation of the optowaveguide resonator is derived by considering the complex distribution of injected optical power, which has significant influence on the thermoelastic damping. By solving the heat diffusion equation, the theoretical model of the thermoelastic damping is presented. In this model, the effects of injected optical power, representative temperatures, waveguide material, and geometries on the thermoelastic damping are studied and discussed respectively. The results show that the peak value of thermoelastic damping increases as the injected optical power is increasing within a low range. Hardly any changes exist for the intrinsic energy dissipation of different materials at higher injected optical power. When the environmental temperature falls in the range of 293–500 K, the thermoelastic damping increases slowly, and then drops down quickly as a function of the dimensionless frequency. However, the thermoelastic damping monotonically decreases when the representative temperature drops to lower than 293 K. In addition, the thermoelastic damping is found to be scale dependent, particularly with the effect of injected optical power.

The nonequilibrium absorbing phase transition of the discrete conserved Manna model was studied via Monte Carlo simulations on a one-dimensional chain, using the natural initial states with a sequential update. The critical density of the particles was found to be smaller than the recently reported value, and the order-parameter exponent was considerably different from the directed percolation (DP) value. The influence of quenched disorder was also studied on a diluted strip of $L_x\times L_y$ lattice sites with $L_x\gg L_y$, and the results were compared with those of the contact process (CP). It was found that the Manna model and the CP exhibited distinctly different behaviors; the CP exhibited nonuniversal power-law decreases of active-site densities in the Griffith phase, whereas the Manna model showed a standard critical behavior. These results consistently suggest that the Manna model belongs to a universality class that is different from the DP class.

Liquid helium does not obey the Gibbs fluctuation-compressibility relation, which was noted more than six decades ago. However, still missing is a clear explanation of the reason for the deviation or the correct fluctuation-compressibility relation for the quantum liquid. Here we present the fluctuation-compressibility relation valid for any grand canonical system. Our result shows that the deviation from the Gibbs formula arises from a nonextensive part of thermodynamic potentials. The particle-exchange symmetry of many-body wave function of a strongly degenerate quantum gas is related to the thermodynamic extensivity of the system; a Bose gas does not always obey the Gibbs formula, while a Fermi gas does. Our fluctuation-compressibility relation works for classical systems as well as quantum systems. This work demonstrates that the application range of the Gibbs-Boltzmann statistical thermodynamics can be extended to encompass nonextensive open systems without introducing any postulate other than the principle of equal a priori probability.

We study the effects of smooth inhomogeneities at first-order transitions. We show that a temperature gradient at a thermally driven first-order transition gives rise to nontrivial universal scaling behaviors with respect to the length scale $l_t$ of the variation of the local temperature $T_x$. We propose a scaling ansatz to describe the crossover region at the surface where $T_x=T_c$, where the typical discontinuities of a first-order transition are smoothed out. The predictions of this scaling theory are checked, and get strongly supported, by numerical results for the two-dimensional (2D) Potts models, for a sufficiently large number of states to have first-order transitions. Comparing with analogous results at the 2D Ising transition, we note that the scaling behaviors induced by a smooth inhomogeneity appear quite similar in first-order and continuous transitions.

The critical behavior of absorbing phase transitions for two typical models in the Manna universality class, the conserved Manna model and the conserved lattice gas model, both on a square lattice, was investigated using the natural initial states. Various critical exponents were estimated using the static and dynamic simulations. The exponents characterizing dynamics of active particles differ considerably from the known exponents obtained using the random initial states, whereas those associated with the steady-state quantities remain the same. The critical exponents for both models were consistent with errors of less than 1% and satisfied the known scaling relations; thus, the known violation of scaling relations for models with a conserved field was resolved using the natural initial states. The results differed by 7%$\sim$12% from the directed percolation values.

We study the maximum efficiency of a heat engine based on a small system. It is revealed that due to the finiteness of the system, irreversibility may arise when the working substance contacts with a heat reservoir. As a result, there is a working-substance-dependent correction to the Carnot efficiency. We derive a general and simple expression for the maximum efficiency of a Carnot cycle heat engine in terms of the relative entropy. This maximum efficiency approaches the Carnot efficiency asymptotically when the size of the working substance increases to the thermodynamic limit. Our study extends Carnot's result of the maximum efficiency to an arbitrary working substance and elucidates the subtlety of thermodynamic laws in small systems.

The short-time diffusivity of dicolloid particles as a function of particle volume fraction $\varphi$ from $0.01\le \varphi \le 0.6$ is measured using diffusing wave spectroscopy. The diffusivities of symmetric and asymmetric dicolloids are compared with similarly sized spheres. The short-time diffusivity is independent of salt concentration and decreases with increasing volume fraction for both spheres and asymmetric dicolloids. Symmetric dicolloids have a higher diffusivity than spheres at similar volume fractions. This difference is accounted for by rescaling the dicolloid volume fraction based on the ratio of the random close-packing volume fractions of spheres and dicolloids. Finally, a useful method is provided for calculating the diffusivity of symmetric dicolloid particles of arbitrary aspect ratio based on the calculated hydrodynamic resistance of Zabarankin [Proc. R. Soc. A 463, 2329 (2007)].

Aggregation of colloidal particles under shear is studied in model systems using a Langevin dynamics model with an improved interparticle interaction potential. In the absence of shear, aggregates that form are characterized by compact structure at small scales and ramified structure at larger scales. This confirms the structural crossover mechanism previously suggested by Sorensen and coworkers, that colloidal aggregation occurs due to monomer addition at small scales and due to cluster-cluster aggregation at large scales. The fractal dimension of nonsheared aggregates is scale-dependent. Smaller aggregates have a higher fractal dimension than larger ones, but the radius of gyration where this crossover occurs is independent of potential well depth for sufficiently deep wells. When these aggregates are subjected to shear they become anisotropic and form extended cigar-like structures. The size of sheared anisotropic aggregates in the direction perpendicular to the shear flow is limited by shear-induced breakage because the shear force dominates interparticle attraction for sufficiently large aggregates. Anisotropic aggregates are not completely characterized by a single radius of gyration, but rather by an inertia ellipsoid. Consequently the fractal dimension is no longer an adequate metric to properly characterize them, and to identify changes in their structure from their nonsheared isotropic counterparts. We introduce a new compactness-anisotropy analysis that characterizes the structure of anisotropic aggregates and allows us to distinguish between aggregates from sheared and nonsheared systems. Finally, using the ratio of interparticle force to the shear force $f_{\mathrm{pot},\mathrm{sh}}$ we are able to characterize different outcomes of sheared aggregation as a function of dimensionless well depth and Péclet number.

The properties of glasses vary widely depending on the way they are prepared, even though their structures appear similar. We show that the local potential energy landscape (PEL) sensitively reflects the stability differences through simulation of local structural excitation in a model metallic glass. It is observed that the spectrum of local structural excitation develops a pseudogap at low energies as the glass becomes more stable. We also demonstrate that the spatial variation of the atomic level shear modulus, rather than the distribution of the magnitude of the single atom shear modulus, is more closely related to the nature of the PEL and the stabilities of glasses. In particular, local aggregation of atoms with low shear modulus greatly contributes to instability of the system.

Traffic congestion in isolated complex networks has been investigated extensively over the last decade. Coupled network models have recently been developed to facilitate further understanding of real complex systems. Analysis of traffic congestion in coupled complex networks, however, is still relatively unexplored. In this paper, we try to explore the effect of interconnections on traffic congestion in interconnected Barabási–Albert scale-free networks. We find that assortative coupling can alleviate traffic congestion more readily than disassortative and random coupling when the node processing capacity is allocated based on node usage probability. Furthermore, the optimal coupling probability can be found for assortative coupling. However, three types of coupling preferences achieve similar traffic performance if all nodes share the same processing capacity. We analyze interconnected Internet autonomous-system-level graphs of South Korea and Japan and obtain similar results. Some practical suggestions are presented to optimize such real-world interconnected networks accordingly.

Premelted water that is adsorbed to particle surfaces and confined to capillary regions remains in the liquid state well below the bulk melting temperature and can supply the segregated growth of ice lenses. Using macroscopic measurements of ice-lens initiation position in step-freezing experiments, we infer how the nanometer-scale thicknesses of premelted films depend on temperature depression below bulk melting. The interfacial interactions between ice, liquid, and soda-lime glass particles exhibit a power-law behavior that suggests premelting in our system is dominated by short-range electrostatic forces. Using our inferred film thicknesses as inputs to a simple force-balance model with no adjustable parameters, we obtain good quantitative agreement between numerical predictions and observed ice-lens thickness. Macroscopic observations of lensing behavior have the potential as probes of premelting behavior in other systems.

Blackbody radiation is reconsidered using the counterpart of the Bose-Einstein distribution in the $\kappa$ statistics arising from the Kaniadakis entropy. The generalized Planck radiation law is presented and compared to the usual law, to which it reduces in the limiting case $\kappa \to 0$. Effective Einstein's coefficients of emission and absorption are defined in terms of the Kaniadakis parameter $\kappa$. It is shown that the Kaniadakis statistics keeps unchanged the first Einstein coefficient $A$ while the second coefficient $B$ admits a generalized form within the present theoretical framework.