The existence of low-frequency waveguide modes of electrostatic ion acoustic waves is demonstrated in magnetized plasmas for cases where the electron temperature is striated along magnetic field lines. For low frequencies, the temperature striation acts as waveguide that supports a trapped mode. For conditions where the ion cyclotron frequency is below the ion plasma frequency we find a dispersion relation having also a radiative frequency band, where waves can escape from the striation. Arguments for the formation and propagation of an equivalent of electrostatic shocks are presented and demonstrated numerically for these conditions. The shock represents here a balance between an external energy input maintained by ion injection and a dissipation mechanism in the form of energy leakage of the harmonics generated by nonlinear wave steepening. This is a reversible form for energy loss that can replace the time-irreversible losses in a standard Burgers equation.

From macroscopic to microscopic scales it is demonstrated that diffusion through membranes can be modeled using specific boundary conditions across them. The membranes are here considered thin in comparison to the overall size of the system. In a macroscopic scale the membrane is introduced as a transmission boundary condition, which enables an effective modeling of systems that involve multiple scales. In a mesoscopic scale, a numerical lattice-Boltzmann scheme with a partial-bounceback condition at the membrane is proposed and analyzed. It is shown that this mesoscopic approach provides a consistent approximation of the transmission boundary condition. Furthermore, analysis of the mesoscopic scheme gives rise to an expression for the permeability of a thin membrane as a function of a mesoscopic transmission parameter. In a microscopic model, the mean waiting time for a passage of a particle through the membrane is in accordance with this permeability. Numerical results computed with the mesoscopic scheme are then compared successfully with analytical solutions derived in a macroscopic scale, and the membrane model introduced here is used to simulate diffusive transport between the cell nucleus and cytoplasm through the nuclear envelope in a realistic cell model based on fluorescence microscopy data. By comparing the simulated fluorophore transport to the experimental one, we determine the permeability of the nuclear envelope of HeLa cells to enhanced yellow fluorescent protein.

Recent evidence points to the presence of torsion in FtsZ bonds. In addition, experiments with FtsZ mutants on surfaces resulted in new aggregates that cannot be explained by older models for FtsZ dynamics. We use an interaction model for FtsZ derived from molecular dynamics simulations and expand a fine-grained lattice model used to describe FtsZ aggregates on a surface. This new model includes different anchoring angles for the monomers and allows bond twist, two ingredients that oppose each other resulting in a more dynamic and interesting system. We study the role and importance of these conflicting elements and how the aggregates are characterized by the different interaction parameters.

Elongated and rodlike objects such as carbon nanotubes (CNTs) are studied when immersed in a nematic liquid crystal. Their interaction energy in a uniform nematic field depends on their orientation relative to the director $\mathit{n}$, and its minimum determines if they stabilize parallel or perpendicular to $\mathit{n}$. Using free energy calculations, we deduce the orientation at equilibrium that they choose in a uniform director field $\mathit{n}$ or when they are in contact with a splay-bend disclination line. Naturally, the CNT orientations also depend on the anchoring conditions at their surface. Essentially, three types of anchorings are considered, planar, homeotropic, and Janus anchorings in the cases of weak and strong anchoring strengths. In the presence of a splay-bend disclination line, they are attracted toward it and ultimately, they get out of the colloidal dispersion to stick on it. Their orientation relative to the line is found to be parallel or perpendicular to it, again depending on the anchoring conditions. When a sufficient number of particles are deposited on a disclination line, we finally obtain a micro- or nanonecklace in the shape of a thin thread or of a bottle brush, according to the CNTs being oriented parallel or perpendicular to the disclination line, respectively. The system exhibits a rich versatility even if up to now the weak anchorings appear to be difficult to control. As discussed in the associated experimental paper, these necklaces could be a step toward interesting applications for realizing nanowires self-connected in three dimensions to predesignated electrodes. This method could provide a way to increase the number of transistors that may be connected together on a small volume.

Multiwall carbon nanotube (CNT) colloids with different anchoring conditions are dispersed in pentyl-cyanobiphenyl (5CB), a thermotropic liquid crystal (LC) that exhibits a room-temperature nematic phase. The experiments make use of CNTs treated for strong planar, homeotropic, or Janus anchorings. Observations with a polarizing microscope show that the CNTs placed in a uniform nematic field stabilize parallel or perpendicular to $\mathit{n}$ depending on their anchoring conditions. In the presence of a splay-bend disclination line, they are first attracted toward it and ultimately, they get trapped on it. Their orientation relative to the line is then found to be parallel or perpendicular to it, again depending on the anchoring conditions. When a sufficient number of particles are deposited on a disclination line, they form a micro- or nanonecklace in the shape of a thin thread or of a bottle brush, with the CNTs being oriented parallel or perpendicular to the disclination line according to the anchoring treatment. The system exhibits a rich versatility, even if until now the weak anchorings appear to be difficult to control. In a next step, the necklaces may be glued by means of pyrrole electropolymerization. In this manner, we realize a true materialization of the disclination lines, and we obtain nanowires capable of conducting the electricity in the place of the initial disclinations that just worked as templates. The advantage of the method is that it finally provides nanowires that are automatically connected to predesignated three-dimensional (3D) electrodes. Such a 3D nanowiring could have important applications, as it could allow one to develop electronic circuits in the third dimension. They could thus help with increasing the transistor density per surface unit, although downsizing of integrated circuits will soon be limited to atomic sizes or so. In other words, the predicted limitation to Moore's law could be avoided. For the moment, the nanowires that we obtain are not completely satisfactory, particularly because they are thickened by aggregates in some places. However, the method is far from being optimized. A few electric charges deposited on the CNTs could remedy those aggregates.

In this study, we propose a two-dimensional (2D) theoretical model to explore the adhesion behavior of a tubular vesicle adhering between two rigid planes, which are constrained by a couple of forces. Based upon the free-energy functional of the system, the equations for the equilibrium shape are derived. The general solution for the system with zero pressure is obtained analytically and the stability of the corresponding equilibrium shapes is tested by numerical simulation. With the volume constraint, three kinds of typical stable shapes are obtained through scanning the parameter space numerically. The phase diagram is obtained and it is occupied mostly by nonsymmetrical shapes. The force-displacement curves obtained for our model are in agreement with experimental results. The catastrophe of force is found at a critical state, which reveals a huge expanding force will act on the two planes by the vesicle. It also implies that vesicles can spontaneously squeeze into a slit only due to adhesion.

The bending modulus of air-water interfaces covered by a monolayer of bidisperse particles is probed experimentally under quasistatic conditions via the compression of the monolayer, and under dynamical conditions studying capillary-wave propagation. Simple averaging of the modulus obtained solely with small or large particles fails to describe our data. Indeed, as observed in other configurations for monodisperse systems, bidisperse rafts have both a granular and an elastic character: chain forces and collective effects must be taken into account to fully understand our results.

Classical nucleation theory offers a good framework for understanding the common features of new phase formation processes in metastable homogeneous media at rest. However, nucleation processes in liquids are ubiquitously affected by hydrodynamic flow, and there is no satisfactory understanding of whether shear promotes or slows down the nucleation process. We developed a classical nucleation theory for sheared systems starting from the molecular level of the Becker-Doering master kinetic equation and we analytically derived a closed-form expression for the nucleation rate. The theory accounts for the effect of flow-mediated transport of molecules to the nucleus of the new phase, as well as for the mechanical deformation imparted to the nucleus by the flow field. The competition between flow-induced molecular transport, which accelerates nucleation, and flow-induced nucleus straining, which lowers the nucleation rate by increasing the nucleation energy barrier, gives rise to a marked nonmonotonic dependence of the nucleation rate on the shear rate. The theory predicts an optimal shear rate at which the nucleation rate is one order of magnitude larger than in the absence of flow.

In propagating wave systems, three- or four-wave resonant interactions constitute a classical nonlinear mechanism exchanging energy between the different scales. Here we investigate three-wave interactions for gravity-capillary surface waves in a closed laboratory tank. We generate two crossing wave trains and we study their interaction. Using two optical methods, a local one (laser doppler vibrometry) and a spatiotemporal one (diffusive light photography), a third wave of smaller amplitude is detected, verifying the three-wave resonance conditions in frequency and in wave number. Furthermore, by focusing on the stationary regime and by taking into account viscous dissipation, we directly estimate the growth rate of the resonant mode. The latter is then compared to the predictions of the weakly nonlinear triadic resonance interaction theory. The obtained results confirm qualitatively and extend previous experimental results obtained only for collinear wave trains. Finally, we discuss the relevance of three-wave interaction mechanisms in recent experiments studying gravity-capillary turbulence.

We study an ensemble of random walkers carrying internal noisy phase oscillators which are synchronized among the walkers by local interactions. Due to individual mobility, the interaction partners of every walker change randomly, hereby introducing an additional, independent source of fluctuations, thus constituting the intrinsic nonequilibrium nature of the temporal dynamics. We employ this paradigmatic model system to discuss how the emergence of order is affected by the motion of individual entities. In particular, we consider both normal diffusive motion and superdiffusion. A non-Hamiltonian field theory including multiplicative noise terms is derived which describes the nonequilibrium dynamics at the macroscale. This theory reveals a defect-mediated transition from incoherence to quasi-long-range order for normal diffusion of oscillators in two dimensions, implying a power-law dependence of all synchronization properties on system size. In contrast, superdiffusive transport suppresses the emergence of topological defects, thereby inducing a continuous synchronization transition to long-range order in two dimensions. These results are consistent with particle-based simulations.

We study the directed Abelian sandpile model on a square lattice, with $K$ downward neighbors per site, $K>2$. The $K=3$ case is solved exactly, which extends the earlier known solution for the $K=2$ case. For $K>2$, the avalanche clusters can have holes and side branches and are thus qualitatively different from the $K=2$ case where avalanche clusters are compact. However, we find that the critical exponents for $K>2$ are identical with those for the $K=2$ case, and the large-scale structure of the avalanches for $K>2$ tends to the $K=2$ case.

We investigate the $\text{O}\left(n\right)$ nonintersecting loop model on the square lattice under the constraint that the loops consist of 90-deg bends only. The model is governed by the loop weight $n$, a weight $x$ for each vertex of the lattice visited once by a loop, and a weight $z$ for each vertex visited twice by a loop. We explore the $(x,z)$ phase diagram for some values of $n$. For $0<n<1$, the diagram has the same topology as the generic $\text{O}\left(n\right)$ phase diagram with $n<2$, with a first-order line when $z$ starts to dominate and an $\text{O}\left(n\right)$-like transition when $x$ starts to dominate. Both lines meet in an exactly solved higher critical point. For $n>1$, the $\text{O}\left(n\right)$-like transition line appears to be absent. Thus, for $z=0$, the $(n,x)$ phase diagram displays a line of phase transitions for $n\le 1$. The line ends at $n=1$ in an infinite-order transition. We determine the conformal anomaly and the critical exponents along this line. These results agree accurately with a recent proposal for the universal classification of this type of model, at least in most of the range $-1\le n\le 1$. We also determine the exponent describing crossover to the generic $\text{O}\left(n\right)$ universality class, by introducing topological defects associated with the introduction of “straight” vertices violating the 90-deg-bend rule. These results are obtained by means of transfer-matrix calculations and finite-size scaling.

Interdependent networks are more fragile under random attacks than simplex networks, because interlayer dependencies lead to cascading failures and finally to a sudden collapse. This is a hybrid phase transition (HPT), meaning that at the transition point the order parameter has a jump but there are also critical phenomena related to it. Here we study these phenomena on the Erdős-Rényi and the two-dimensional interdependent networks and show that the hybrid percolation transition exhibits two kinds of critical behaviors: divergence of the fluctuations of the order parameter and power-law size distribution of finite avalanches at a transition point. At the transition point global or “infinite” avalanches occur, while the finite ones have a power law size distribution; thus the avalanche statistics also has the nature of a HPT. The exponent ${\beta }_m$ of the order parameter is $1/2$ under general conditions, while the value of the exponent ${\gamma }_m$ characterizing the fluctuations of the order parameter depends on the system. The critical behavior of the finite avalanches can be described by another set of exponents, ${\beta }_a$ and ${\gamma }_a$. These two critical behaviors are coupled by a scaling law: $1-{\beta }_m={\gamma }_a$.

We study a three-state (leftist, rightist, centrist) model that couples the dynamics of social balance with an external deradicalizing field. The mean-field analysis shows that there exists a critical value of the external field $p_c$ such that for a weak external field ($p<p_c$), the system exhibits a metastable fixed point and a saddle point in addition to a stable fixed point. However, if the strength of the external field is sufficiently large ($p>p_c$), there is only one (stable) fixed point, which corresponds to an all-centrist consensus state (absorbing state). In the weak-field regime, the convergence time to the absorbing state is evaluated using the quasistationary distribution and is found to be in agreement with the results obtained by numerical simulations.

We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.

We study the emergence and coherence of stochastic oscillations in star networks of excitable elements in which peripheral nodes receive independent random inputs. A biophysical model of a distal branch of sensory neuron in which peripheral nodes of Ranvier are coupled to a central node by myelinated cable segments is used along with a generic model of networked stochastic active rotators. We show that coherent oscillations can emerge due to stochastic synchronization of peripheral nodes and that the degree of coherence can be maximized by tuning the coupling strength and the size of the network. Analytical results are obtained for the strong-coupling regime of the active rotator network. In particular, we show that in the strong-coupling regime, the network dynamics can be described by an effective single active rotator with rescaled parameters and noise.

Three important kinetic phenomena have been cataloged by Kovacs in the investigation of molecular glasses during structural recovery or physical aging. These are responses to temperature-jump histories referred to as intrinsic isotherms, asymmetry of approach, and memory effect. Here we use a thermosensitive polystyrene-poly ($N$-isopropylacrylamide)-poly (acrylic acid) core-shell particle-based dispersion as a colloidal model and by working at a constant number concentration of particles we use temperature changes to create volume-fraction changes. This imposes conditions similar to those defined by Kovacs on the colloidal system. We use creep experiments to probe the physical aging and structural recovery behavior of colloidal glasses in the Kovacs-type histories and compare the results with those seen in molecular glasses. We find that there are similarities in aging dynamics between molecular glasses and colloidal glasses, but differences also persist. For the intrinsic isotherms, the times $t_{\mathrm{eq}}$ needed for relaxing or evolving into the equilibrium (or stationary) state are relatively insensitive to the volume fraction and the values of $t_{\mathrm{eq}}$ are longer than the $\alpha$-relaxation time ${\tau }_{\alpha }$ at the same volume fraction. On the other hand, both of these times grow at least exponentially with decreasing temperature in molecular glasses. For the asymmetry of approach, similar nonlinear behavior is observed for both colloidal and molecular glasses. However, the equilibration time $t_{\mathrm{eq}}$ is the same for both volume-fraction up-jump and down-jump experiments, different from the finding in molecular glasses that it takes longer for the structure to evolve into equilibrium for the temperature up-jump condition than for the temperature down-jump condition. For the two-step volume-fraction jumps, a memory response is observed that is different from observations of structural recovery in two-step temperature histories in molecular glasses. The concentration dependence of the dynamics of the colloidal dispersions is also examined in the equilibrium state and we find that the dynamic fragility index $m$ is sensitive to the degree of softness of the soft colloidal dispersion, indicating that soft colloids make stronger glasses. Finally, we compare the present results with prior findings for similar thermoresponsive systems obtained with diffusing wave spectroscopy and discuss similarities and differences.

Magnetohydrodynamic Rayleigh-Bénard convection was studied experimentally using a liquid metal inside a box with a square horizontal cross section and aspect ratio of five. Systematic flow measurements were performed by means of ultrasonic velocity profiling that can capture time variations of instantaneous velocity profiles. Applying a horizontal magnetic field organizes the convective motion into a flow pattern of quasi-two-dimensional rolls arranged parallel to the magnetic field. The number of rolls has the tendency to decrease with increasing Rayleigh number Ra and to increase with increasing Chandrasekhar number $Q$. We explored convection regimes in a parameter range, at $2\times {10}^3<Q<{10}^4$ and $5\times {10}^3<\mathrm{Ra}<3\times {10}^5$, thus extending the regime diagram provided by Yanagisawa et al. [T. Yanagisawa et al., Phys. Rev. E 88, 063020 (2013)]. Three regimes were identified, of which the regime of regular flow reversals in which five rolls periodically change the direction of their circulation with gradual skew of the roll axes can be considered as the most remarkable one. The regime appears around a range of $\mathrm{Ra}/Q=10$, where irregular flow reversals were observed in Yanagisawa et al. We performed the proper orthogonal decomposition (POD) analysis on the spatiotemporal velocity distribution and detected that the regular flow reversals can be interpreted as a periodic emergence of a four-roll state in a dominant five-roll state. The POD analysis also provides the definition of the effective number of rolls as a more objective approach.

Ionic transport coefficients for dense plasmas have been numerically computed using an effective Boltzmann approach. We have developed a simplified effective potential approach that yields accurate fits for all of the relevant cross sections and collision integrals. Our results have been validated with molecular-dynamics simulations for self-diffusion, interdiffusion, viscosity, and thermal conductivity. Molecular dynamics has also been used to examine the underlying assumptions of the Boltzmann approach through a categorization of behaviors of the velocity autocorrelation function in the Yukawa phase diagram. Using a velocity-dependent screening model, we examine the role of dynamical screening in transport. Implications of these results for Coulomb logarithm approaches are discussed.

The traditional algorithm for computing the complex travel time, e.g., dynamic ray tracing method, is based on the paraxial ray approximation, which exploits the second-order Taylor expansion. Consequently, the computed results are strongly dependent on the width of the ray tube and, in regions with dramatic velocity variations, it is difficult for the method to account for the velocity variations. When solving the complex eikonal equation, the paraxial ray approximation can be avoided and no second-order Taylor expansion is required. However, this process is time consuming. In this case, we may replace the global computation of the whole model with local computation by taking both sides of the ray as curved boundaries of the evanescent wave. For a given ray, the imaginary part of the complex travel time should be zero on the central ray. To satisfy this condition, the central ray should be taken as a curved boundary. We propose a nonuniform grid-based finite difference scheme to solve the curved boundary problem. In addition, we apply the limited-memory Broyden-Fletcher-Goldfarb-Shanno technology for obtaining the imaginary slowness used to compute the complex travel time. The numerical experiments show that the proposed method is accurate. We examine the effectiveness of the algorithm for the complex travel time by comparing the results with those from the dynamic ray tracing method and the Gauss-Newton Conjugate Gradient fast marching method.