The orientational ordering and the tilt angle behavior of a one-dimensional fluid of hard zigzag needles are examined by means of transfer matrix method and Onsager theory. The centers of mass of the particles are restricted to a line, while the orientational unit vectors are allowed to rotate freely in two dimensions. It is shown that zigzag needles do not undergo an isotropic-nematic phase transition, but the system is always in an orientationally ordered phase where the order parameter increases with the density. For hard needles and any other kinds of particles with an axis of symmetry the orientational distribution function is symmetric around its maximum value and the nematic director is perpendicular to the layer. For zigzag needles, which have nonconvex shape without an axis of symmetry, the orientational order is anisotropic around its maximum value and the nematic director is density dependent even at very high densities, i.e., the structure of one-dimensional fluid is always tilted. It is found that the density dependence of the tilted structure depends strongly on the shape of the zigzags. Surprisingly, the Onsager theory produces quite accurate results for the order parameters and tilt angles even in very dense systems.

We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a generalized method, we study within a single framework different continuous models and different types of regulatory functions, and establish conditions under which the system can display stable oscillations. These conditions depend only on general features such as the ratio of the relevant time scales, the degree of cooperativity of the regulating interactions, and the logical structure of the interactions. Our results combine and generalize the findings of several disconnected previous studies.

An anisotropic macromolecule confined between two surfaces displays Brownian motion predominantly in the plane parallel to these surfaces. It can be expected that both the rotational and translational diffusion coefficients are strongly affected by hydrodynamic interactions with the walls. This work studies the more extreme case in which a rodlike particle comes into contact with a wall or in very close proximity (order of 100 nm). Experimental data have been gathered and analyzed demonstrating the rod tethering on a surface. This is compared with numerical simulations to allow estimates of proximity to the surface. The experimental data show that particle tethered motion is subject to varied degrees of constraining which imply subtle deviations in the Brownian dynamical behavior. The key finding is that a rotational-translational coupling occurs which is markedly different from the translational and rotational movements normally predicted for anisotropic macromolecules.

It is typically assumed, without justification, that a weak coupling between a system and a bath is a necessary condition for the equivalence of a canonical ensemble and a microcanonical ensemble. For instance, in a canonical ensemble, temperature emerges if the system and the bath are uncoupled or weakly coupled. We investigate the validity region of this weak-coupling approximation, using a coupled composite-spin system. Our results show that the spin coupling strength can be as large as the level spacing of the system, indicating that the weak-coupling approximation has a much wider region of validity than usually expected.

We propose an implementation of the nonperturbative renormalization group (NPRG) which applies to lattice models. Contrary to the usual NPRG approach where the initial condition of the RG flow is the mean-field solution, the lattice NPRG uses the (local) limit of decoupled sites as the (initial) reference system. In the long-distance limit, it is equivalent to the usual NPRG formulation and therefore yields identical results for the critical properties. We discuss both a lattice field theory defined on a $d$-dimensional hypercubic lattice and classical spin models. The simplest approximation, the local potential approximation, is sufficient to obtain the critical temperature and the magnetization of the three-dimensional Ising, $XY$, and Heisenberg models to an accuracy on the order of 1%. We show how the local potential approximation can be improved to include a nonzero anomalous dimension $\eta$ and discuss the Berezinskii-Kosterlitz-Thouless transition of the two-dimensional $XY$ model on a square lattice.

We consider a network of $N$ noisy bistable elements with global time-delayed couplings. In a two-state description, where elements are represented by Ising spins, the collective dynamics is described by an infinite hierarchy of coupled master equations which was solved at the mean-field level in the thermodynamic limit. When the number of elements is finite, as is the case in actual laser networks, an analytical description was deemed so far intractable and numerical studies seemed to be necessary. In this paper we consider the case of two interacting elements and show that a partial analytical description of the stationary state is possible if the stochastic process is time symmetric. This requires some relationship between the transition rates to be satisfied.

We study a Feynman-like thermal Brownian motor, in which the asymmetric corrugated cylinder as the ratchet is coupled with a corrugated plate by the noncontact Casimir interaction between them. The source of driving of the system is the thermal fluctuations and its dynamic evolution is described by a set of Langevin equations. Further, the mean velocity and thermal efficiency of the motor in the overdamped limit are studied in detail as a function of the temperature of the baths, external load applied, magnitude of the Casimir interaction, and other relevant parameters by the numerical stimulation. The transport properties attained here and the essential roles of the Casimir interaction can be explicitly demonstrated by designing a Casimir Brownian motor with present nanotechnology.

We study photon diffusion in a one-dimensional model foam composed of thin films and Plateau borders. Each thin film or Plateau border is characterized by its own intensity transmittance. We relate $l_{\text{Foam}}^{\ast }$, the transport-mean-free path of photons diffusing in the foam, to the foam microstructure. Denoting by $l_{\text{Film}}^{\ast }$ $\left(l_{\text{PB}}^{\ast }\right)$ the transport-mean-free path of photons in a medium composed only of thin films (Plateau borders), we find $1/l_{\text{Foam}}^{\ast }={\phi }_F/l_{\text{Film}}^{\ast }+{\phi }_P/l_{\text{PB}}^{\ast }$. Here ${\phi }_F$ and ${\phi }_P=1-{\phi }_F$ are the fraction of films and Plateau borders, respectively.

Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard spheres, thus retaining all features of the porous confinement while limiting the control parameters to the packing fraction of the matrix, ${\varphi }_{\text{m}}$, and that of the fluid, ${\varphi }_{\text{f}}$. We conduct detailed investigations on several dynamic properties, including the tagged-particle and collective intermediate scattering functions, the mean-squared displacement, and the van Hove function. We show the confining obstacles to profoundly impact the relaxation pattern of various quantifiers pertinent to the fluid. Varying the type of quantifier (tagged-particle or collective) as well as ${\varphi }_{\text{m}}$ and ${\varphi }_{\text{f}}$, we unveil both discontinuous and continuous arrest scenarios. Furthermore, we discover subdiffusive behavior and demonstrate its close connection to the matrix structure. Our findings partly confirm the various predictions of a recent extension of mode-coupling theory to the quenched-annealed protocol.

The energetically driven Ehrlich-Schwoebel barrier had been generally accepted as the primary cause of the growth instability in the form of quasiregular moundlike structures observed on the surface of thin film grown via molecular-beam epitaxy (MBE) technique. Recently the second mechanism of mound formation was proposed in terms of a topologically induced flux of particles originating from the line tension of the step edges which form the contour lines around a mound. Through large-scale simulations of MBE growth on a variety of crystalline lattice planes using limited-mobility, solid-on-solid models introduced by Wolf-Villain and Das Sarma–Tamborenea in $2+1$ dimensions, we show that there exists a topological uphill particle current with strong dependence on specific lattice crystalline structure. Without any energetically induced barriers, our simulations produce spectacular mounds very similar, in some cases, to what have been observed in many recent MBE experiments. On a lattice where these currents cease to exist, the surface appears to be scale invariant, statistically rough as predicted by the conventional continuum growth equation.

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

We study onset and control of stochastic resonance (SR) phenomenon in two driven bistable systems, mutually coupled and subjected to independent noises, taking into account the influence of both the inertia and the coupling. In the absence of coupling, we found two critical damping parameters: one for the onset of SR and another for which SR is optimum. We then show that in weakly coupled systems, emergence of SR is governed by chaos. A strong coupling between the two oscillators induces coherence in the system; however, the systems do not synchronize no matter what the coupling is. Moreover, a specific coupling parameter is found for which the SR of each subsystem is optimum. Finally, a scheme for controlling SR in such coupled systems is proposed by introducing a phase difference between the two coherent driving forces.

Normal functioning in many realistic complex dynamical systems, such as neural networks, requires coherence and synchronization for collective actions of network components. However, strong synchronization of the whole network is often related to pathological situations. A regime in between enabling both segregation in subsystems and integration as a whole is thus desirable. Here, we characterize this regime by complexity of synchronization patterns and study its relationship to heterogeneous and modular architecture in complex network of oscillators. We show that these networks possess a broad range of high complexity associated with the formation of dynamical clusters and the coordination between the clusters. In realistic networks of C. elegans and cat cortex, the complexity is reduced when the original network is rewired in various ways, reflecting that the neural systems are organized to provide a combination of segregation and integration with the coexistence of various complex network features, especially modularity and heterogeneity. Our work can stimulate further studies on structure-function relationships in neural systems through the inquiry of the specific functional roles of the intermediate dynamical regime.

This paper reports some experimental results on two-phase flows in model two-dimensional porous media. Standard microfluidic techniques are used to fabricate networks of straight microchannels and to control the throat size distribution. We analyze both the invasion mechanism of the medium by a nonwetting fluid and the drainage after the percolation for capillary numbers lying between ${10}^{-7}$ and ${10}^{-2}$. We propose a crude model allowing a description of the observed capillary fingering that captures its scaling properties. This model is supported by numerical simulations based on a pore-network model. Numerical simulations and experiments agree quantitatively.

We have studied a model of a random walk in a quenched random environment. In addition to featuring anomalous diffusion and localization, for special regimes of disorder parameters the particle density decomposes into multi-Gaussian structure while its cumulative distribution is normal. We explain the observed fine structure of the density and point out its significance to experiments.

The microstructure and melting dynamics of the two-dimensional mesoscopic Coulomb crystal with $1/r$-type mutual interaction force and parabolic transverse confining potential, under different degrees of incommensurability, are investigated through molecular-dynamics simulation. To tune the degree of incommensurability, $N_a$ extra particles are added into the commensurate uniform triangular lattice which has seven-layer structure and 40 particles in each layer with the periodic longitudinal boundary condition, until the system reaches another commensurate packing with eight-layer structure at $N_a=40$. It is found that the increasing incommensurability with the increasing $N_a$ or $40-N_a$ gradually deteriorates the structural order with the presence of intrinsic defects and the anisotropic bond-length distribution, except for the defect-free configurations at a few magic $N_a$’s. The system prefers the seven- and the eight-layer single structures through the entire crystal for the low- and the high-$N_a$ regimes, respectively, and the configurations with seven- and eight-layer domain mixtures for $18\le N_a\le 24$. The increasing strain or the worse local particle interlocking around the intrinsic defects with the increasing incommensurability also causes the easier structural rearrangement associated with the easier particle hopping and the earlier onset of melting transition. The transverse confinement suppresses the transverse motion, induces nonuniform melting, and sustains the layered structure after melting.

We report a mechanism by which nanoscale filaments self-assemble into asymmetric aggregates by elastocapillary action. Specifically, capillary rise of liquid into an asymmetric pattern of vertically aligned filaments causes the filaments to deflect laterally during elastocapillary densification. We quantitatively show that the lateral deflection can be controlled precisely by the pattern shape and the coupling strength among the filaments. We exploit this mechanism to fabricate asymmetric micropillars and multidirectional bridges of densely packed carbon nanotubes. Analogous behavior occurs as biological filaments interact with liquids, and these findings enable scalable fabrication of anisotropic filament assemblies for manipulating surface interactions between solids and liquids.

Evidence of the existence of a transient surface tension between two miscible fluid phases is given. This is done by making use of a density matched free of gravity perturbations, binary liquid of isobutyric acid and water, which presents a miscibility gap and is studied by light scattering. The experiment is performed very near the critical point of the binary liquid, where the diffusion of phases is extremely slow. The surface tension is deduced from the evolution of the structure factor obtained from low angle light scattering. The latter evolution is successfully analyzed in terms of a local equilibrium diffusive approach that makes explicit how the surface tension decreases with time.