We develop a method to infer community structure in directed networks where the groups are ordered in a latent one-dimensional hierarchy that determines the preferred edge direction. Our nonparametric Bayesian approach is based on a modification of the stochastic block model (SBM), which can take advantage of rank alignment and coherence to produce parsimonious descriptions of networks that combine ordered hierarchies with arbitrary mixing patterns between groups. Since our model also includes directed degree correction, we can use it to distinguish nonlocal hierarchical structure from local in- and out-degree imbalance—thus, removing a source of conflation present in most ranking methods. We also demonstrate how we can reliably compare with the results obtained with the unordered SBM variant to determine whether a hierarchical ordering is statistically warranted in the first place. We illustrate the application of our method on a wide variety of empirical networks across several domains.

We report that the atomic-scale vibrational coupling at the solid-fluid interface can substantially alter the interfacial properties such as wettability and fluid slip. The wettability of water droplets on substrates subjected to various vibrational frequencies is studied using molecular dynamics simulation. The contact angle increases (i.e., becomes more hydrophobic) when the oscillation frequency of the substrate matches the intermolecular bending frequency of liquid water. We investigate the underlying mechanism by examining the dynamics of water molecules at the interface and find that the temporal contact between the solid and fluid is shorter when the frequencies match, resulting in weak solid-fluid adsorption. We further report that the vibrational match at the interface reduces wall-fluid friction and enhances water transport through the nanopore. Our findings demonstrate the importance of the atomic-scale vibrational coupling at the solid-fluid interface on the physicochemical behavior of nanodevices and biological nanochannels.

Linear and nonlinear characteristics of electrostatic waves are studied in a magnetized plasma consisting of spin-up ($n_{\uparrow }$) and spin-down ($n_{\downarrow }$) state populations with uniformly distributed static ions in the background. The linear analysis shows the existence of four modes. One of these modes, termed the separated spin electron cyclotron wave, is found to be due to the separated spin populations. The Zakharov-Kuznetsov equation is derived by the reductive perturbation technique. The instability growth rate $\gamma$ is obtained from the same equation. It is observed that the magnetized spin quantum plasma admits rarefactive soliton with constant amplitude but increasing width with the increasing strength of the applied magnetic field. It has also been observed that the amplitude of soliton decreases and its width increases with the increasing values of polarization ratio $\kappa$. The unstable region expands with the increase in polarization ratio and contracts with the increased plasma number density and magnetic-field strength. The (growth rate) $\gamma$ of instability reduces by increasing the $\kappa$ and is increasing when the density of the plasma and the strength of the magnetic field increasing. The model developed in this work finds its scope in studying degenerate electron gas and astrophysical systems such as pulsar magnetosphere and neutron stars.

We propose a method to mitigate heavy-tailed distributions in fermion quantum Monte Carlo simulations originating from zeros of the fermion determinant. In this case, the second moment of the observables might not be well defined, and we show that by merely changing the synchronization between local updates and computation of observables, one can reduce the prefactor of the heavy-tailed distribution, thus substantially suppressing statistical fluctuations of observables. We also show that the average, or the first moment, is well defined and hence is independent on our measuring scheme. The method is especially suitable for local observables similar to, e.g., double occupancy, where the resulting speedup can reach two orders of magnitude. For observables containing spatial correlators, the speedup is more moderate but still ranges between five and ten. Our results are independent on the nature of the auxiliary field, discrete or continuous, and pave the way to improve measurement strategies for hybrid Monte Carlo simulations.

Uncovering whether strong system-bath coupling can be an advantageous operation resource for energy conversion can facilitate the development of efficient quantum heat engines (QHEs). Yet, a consensus on this ongoing debate is still lacking owing to challenges arising from treating strong couplings. Here, we conclude the debate for optimal linear cyclic QHEs operated under a small temperature difference by revealing the detrimental role of strong system-bath coupling in their optimal operations. We analytically demonstrate that both the efficiency at maximum power and maximum efficiency of strong-coupling linear cyclic QHEs are upper bounded by their weak-coupling counterparts with the same degree of time-reversal symmetry breaking. Under strong time-reversal symmetry breaking, we further reveal a quadratic suppression of the optimal efficiencies relative to the Carnot limit when away from the weak-coupling regime, along with a quadratic enhancement of the mean entropy production rate.

We experimentally demonstrate that a Brownian gyrator of a colloidal particle confined in a two-dimensional harmonic potential with different effective temperatures on orthogonal axes can work as an autonomous heat engine capable of extracting work from the heat bath, generated by an optical feedback trap. The results confirm the theoretically predicted thermodynamic currents and validate the attainability of Carnot efficiency as well as the trade-off relation between power and efficiency. We further show that current fluctuations and the entropy production rate are time independent in the steady state and their product near the Carnot efficiency is close to the lower bound of the thermodynamic uncertainty relation.

We analyze the instability of viscoelastic solid freestanding thin films under the influence of van der Waals forces using linear stability analysis and nonlinear simulations. Linear stability analysis shows that the zero-frequency elastic modulus governs the onset of instability and stabilizes the film beyond a critical value analogous to thin supported viscoelastic solid films. However, for freestanding solid films, the critical shear modulus is found to be independent of surface tension, unlike that of thin supported viscoelastic solid films. It is further shown that freestanding viscoelastic solid films with higher moduli can be destabilized for a given film thickness and Hamaker constant compared to supported solid films. In contrast to thin viscoelastic liquid films where the growth rate is enhanced due to elastic effects but length scale is unaltered, freestanding films with solidlike viscoelasticity show a retarded growth rate and enhanced length scale. The presence of solidlike viscoelasticity has a stabilizing effect and affects all the key aspects of instability such as critical wave number, dominant wave number, and maximum growth rate. We numerically solve the set of coupled nonlinear evolution equations for film thickness and tangential displacement in order to elucidate the dynamics of film rupture. Our simulations show that, consistent with the linear stability predictions, an increase in the elastic modulus delays film rupture. The dynamics exhibits self-similarity in the vicinity of film rupture and the film thins as ${(t_r-t)}^{3/4}$, where $t_r$ is the rupture time and $t_r-t$ is the time remaining until film rupture. The scaling exponent $3/4$ obtained for a thin freestanding viscoelastic solid film is significantly greater than the scaling exponent $(1/3)$ for a thin freestanding viscous film.

The radius-weighted lattice Boltzmann model has achieved great success in the simulation of axisymmetric flows. However, severe spurious currents near the axis are observed when this model is extended to simulate axisymmetric multiphase flows. In this study, to determine the origin of this singularity, we conducted a truncation error analysis based on high-order Taylor series expansion and identified the leading error terms through dimensionless analysis. By neglecting the error terms in proportion to the radius, we obtained the final forms of the singular terms in the axisymmetric lattice Boltzmann model. We proposed a modified model by including an additional correction term, to remove the singularity at the third order. We validated the proposed model using numerical tests for flat and spherical interfaces. Results showed that the present modified model reduced the spurious currents near the axis by two orders of magnitude compared with the original model. This modified model also has been successfully applied to predict bubble dynamics in an air-water system. Our numerical results are in excellent agreement with available experimental observations in terms of bubble shapes and terminal velocities.

The numerical solution of coupled nonlinear Klein-Gordon equations on unbounded domains is considered by applying the artificial boundary method. Based on the unified approach to overcome the coupled nonlinearity, local artificial boundary conditions are designed on the introduced artificial boundaries. The original problem is reduced to an initial boundary value problem on a bounded domain, which can be efficiently solved by the finite difference method. Some numerical examples are provided to verify the accuracy and effectiveness of the proposed method.

Subdiffusion equation and molecule survival equation, both with Caputo fractional time derivatives with respect to other functions $g_1$ and $g_2$, respectively, are used to describe diffusion of a molecule that can disappear at any time with a constant probability. The process can be interpreted as an “ordinary” subdiffusion and “ordinary” molecule survival process in which timescales are changed by the functions $g_1$ and $g_2$. We derive the first-passage time distribution for the process. The mutual influence of subdiffusion and molecule-vanishing processes can be included in the model when the functions $g_1$ and $g_2$ are related to each other. As an example, we consider the processes in which subdiffusion and molecule survival are highly related, which corresponds to the case of $g_1\equiv g_2$.

We study magnetic polymers, defined as self-avoiding walks where each monomer $i$ carries a “spin” $s_i$ and interacts with its first neighbor monomers, let us say $j$, via a coupling constant $J(s_i,s_j)$. Ising-like $[s_i=\pm 1$, with $J(s_i,s_j)=\varepsilon s_i{s}_j]$ and Potts-like $[s_i=1,...,q$, with $J(s_i,s_j)=\varepsilon \left(s_i\right)\delta (s_i,s_j)]$ models are investigated. Some particular cases of these systems have recently been studied in the continuum and on regular lattices and are related to interesting applications. Here, we solve these models on Bethe lattices of branching number $\sigma$, focusing on the ferromagnetic case in zero external magnetic field. In most cases, the phase diagrams present a nonpolymerized (NP) and two polymerized phases: a paramagnetic (PP) and a ferromagnetic (FP) one. However, quite different thermodynamic properties are found depending on $q$ in the Potts-like polymers and on whether one uses the Ising or Potts coupling in the two-state systems. For instance, for the standard Potts model [where $\varepsilon \left(1\right)=\cdots =\varepsilon \left(q\right)]$ with $q=2$, beyond the $\theta$-point (where the critical and discontinuous NP-PP transition lines meet), a second tricritical point connecting a critical and a discontinuous transition line between the PP-FP phases is found in the system. A triple point where the NP-PP, NP-FP, and PP-FP first-order transition lines meet is also present in the phase diagram. For $q\ge 3$ the PP-FP transition is always discontinuous, and the scenario with the triple and $\theta$ points appears for $q\le 6$. Interestingly, for $q\ge 7$, as well as for the Ising-like model the $\theta$ point becomes metastable and the critical NP-PP transition line ends at a critical end point (CEP), where it meets the NP-FP and PP-FP coexistence lines. Importantly, these results indicate that when $q\le 6$ the spin ordering transition is preceded by the polymer collapse transition, whereas for $q\ge 7$ and in the Ising case these transitions happen together at the CEPs. Some interesting nonstandard Potts models are also studied, such as the lattice version of the model for epigenetic marks in the chromatin introduced by Michieletto et al. [Phys. Rev. X 6, 041047 (2016)]. In addition, the solution of the dilute Ising and dilute Potts models on the Bethe lattice are also presented here, since they are important to understand the PP-FP transitions.

External driving of bath temperatures with a phase difference of a nonequilibrium quantum engine leads to the emergence of geometric effects on the thermodynamics. In this work we modulate the amplitude of the external driving protocols by introducing envelope functions and study the role of geometric effects on the flux, noise, and efficiency of a four-level driven quantum heat engine coupled with two thermal baths and a unimodal cavity. We observe that having a finite width of the modulation envelope introduces an additional control knob for studying the thermodynamics in the adiabatic limit. The optimization of the flux as well as the noise with respect to thermally induced quantum coherences becomes possible in the presence of geometric effects, which hitherto has not been possible with sinusoidal driving without an envelope. We also report the deviation of the slope and generation of an intercept in the standard expression for efficiency at maximum power as a function of Carnot efficiency in the presence of geometric effects under the amplitude modulation. Further, a recently developed universal bound on the efficiency obtained from the thermodynamic uncertainty relation is shown not to hold when a small width of the modulation envelope along with a large value of cavity temperature is maintained.

We calculate density profiles for self-gravitating clusters of an ideal Fermi-Dirac gas with nonrelativistic energy-momentum relation and macroscopic mass at thermal equilibrium. Our study includes clusters with planar symmetry in dimensions $\mathcal{D}=1,2,3$, clusters with cylindrical symmetry in $\mathcal{D}=2,3$, and clusters with spherical symmetry in $\mathcal{D}=3$. Wall confinement is imposed where needed for stability against escape. The length scale and energy scale in use render all results independent of total mass and prove adequate at all temperatures. We present exact analytic expressions for (fully degenerate) $T=0$ density profiles in four of the six combinations of symmetry and dimensionality. Our numerical results for $T>0$ describe the emergence, upon quasistatic cooling, of a core with incipient degeneracy surrounded by a more dilute halo. The equilibrium macrostates are found to depend more strongly on the cluster symmetry than on the space dimensionality. We demonstrate the mechanical and thermal stability of spherical clusters with coexisting phases.

Real world networks contain multiple layers of links whose interactions can lead to extraordinary collective dynamics, including synchronization. The fundamental problem of assessing how network topology controls synchronization in multilayer networks remains open due to serious limitations of the existing stability methods. Towards removing this obstacle, we propose an approximation method which significantly enhances the predictive power of the master stability function for stable synchronization in multilayer networks. For a class of saddle-focus oscillators, including Rössler and piecewise linear systems, our method reduces the complex stability analysis to simply solving a set of linear algebraic equations. Using the method, we analytically predict surprising effects due to multilayer coupling. In particular, we prove that two coupling layers—one of which would alone hamper synchronization and the other would foster it—reverse their roles when used in a multilayer network. We also analytically demonstrate that increasing the size of a globally coupled layer, that in isolation would induce stable synchronization, makes the multilayer network unsynchronizable.

Many systems in nature exhibit avalanche dynamics with scale-free features. A general scaling theory has been proposed for critical avalanche profiles in crackling noise, predicting the collapse onto a universal avalanche shape, as well as the scaling behavior of the activity power spectrum as Brown noise. Recently, much attention has been given to the profile of neuronal avalanches, measured in neuronal systems in vitro and in vivo. Although a universal profile was evidenced, confirming the validity of the general scaling theory, the parallel study of the power spectrum scaling under the same conditions was not performed. The puzzling observation is that in the majority of healthy neuronal systems the power spectrum exhibits a behavior close to $1/f$, rather than Brown, noise. Here we perform a numerical study of the scaling behavior of the avalanche shape and the power spectrum for a model of integrate and fire neurons with a short-term plasticity parameter able to tune the system to criticality. We confirm that, at criticality, the average avalanche size and the avalanche profile fulfill the general avalanche scaling theory. However, the power spectrum consistently exhibits Brown noise behavior, for both fully excitatory networks and systems with 30% inhibitory networks. Conversely, a behavior closer to $1/f$ noise is observed in systems slightly off criticality. Results suggest that the power spectrum is a good indicator to determine how close neuronal activity is to criticality.

Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e., over- or underwound. They are ubiquitous in cellular DNA, and their physical properties have attracted significant interest both from the experimental side and from the modeling side. In this paper, we investigate fluctuations of the end-point distance $z$ of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched phase and a plectonemic phase. A variety of mechanisms are found to contribute to extension fluctuations, characterized by the variance $\langle \mathrm{\Delta }{z}^2\rangle$. We find the dominant contribution to $\langle \mathrm{\Delta }{z}^2\rangle$ to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the twistable wormlike chain and analyze the fluctuation of various quantities, the results of which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.

Limbless crawling is ubiquitous in biology, from cells to organisms. We develop and analyze a model for the dynamics of one-dimensional elastic crawlers, subject to active stress and deformation-dependent friction with the substrate. We find that the optimal active stress distribution that maximizes the crawler's center-of-mass displacement given a fixed amount of energy input is a traveling wave. This theoretical optimum corresponds to peristalsislike extension-contraction waves observed in biological organisms, possibly explaining the prevalence of peristalsis as a convergent gait across species. Our theory elucidates key observations in biological systems connecting the anchoring phase of a crawler to the retrograde and prograde distinction seen in peristaltic waves among various organisms. Using our optimal gait solution, we derive a scaling relation between the crawling speed and body mass, explaining experiments on earthworms with three orders of magnitude body mass variations. Our results offer insights and tools for optimal bioinspired crawling robots design with finite battery capacity.

We investigate the behavior of a magnetorheological (MR) fluid annulus, bounded by a nonmagnetic fluid and confined in a Hele-Shaw cell, under the simultaneous effect of in-plane, external radial and azimuthal magnetic fields. A second-order mode-coupling theory is used to study the early nonlinear stage of the pattern-forming dynamics. We examine changes in the morphology of the MR fluid annular structure as a function of its magnetic-field-tunable rheological properties, as well as the combined magnetic field's intensities, and thickness of the ring. Our weakly nonlinear perturbative results show that, depending on the system control parameters, the MR fluid annulus adopts various stationary shapes. These equilibrium annular structures present slightly bent, asymmetric fingered protrusions which may emerge on the inner, outer, or even on both boundaries of the magnetic fluid ring. On top of these morphological changes, we find that the resulting permanent shape patterns rotate with a well defined angular velocity. We focus on analyzing how the overall shape of the fingered patterns, in particular their sharpness and asymmetric form, as well as the number of resulting fingers are impacted by the magnetic-field-dependent yield stress of the MR fluid annulus. The influence of the magnetically controlled rheological properties of the MR fluid on the angular velocity of the rotating annulus is also scrutinized.

A developing supercritical collisionless shock propagating in a homogeneously magnetized plasma of ambient gas origin having higher uniformity than the previous experiments is formed by using high-power laser experiment. The ambient plasma is not contaminated by the plasma produced in the early time after the laser shot. While the observed developing shock does not have stationary downstream structure, it possesses some characteristics of a magnetized supercritical shock, which are supported by a one-dimensional full particle-in-cell simulation taking the effect of finite time of laser-target interaction into account.