We demonstrate, using the example of the dc$+$ac driven overdamped Frenkel-Kontorova model, that an easily calculable measure of complexity can be used for the examination of Shapiro steps in the presence of thermal noise. In real systems, thermal noise causes melting or even disappearance of Shapiro steps, which makes their analysis in the standard way from the response function difficult. Unlike in the conventional approach, here, by calculating the Kolmogorov complexity of certain areas in the response function, we were able to detect Shapiro steps, measure their size with the desired precision, and examine their temperature dependence. The aim of this work is to provide scientists, particularly experimentalists, with an unconventional, but practical and easy tool for examination of Shapiro steps in real systems.

The bulk of stochastic gene expression models in the literature do not have an explicit description of the age of a cell within a generation and hence they cannot capture events such as cell division and DNA replication. Instead, many models incorporate the cell cycle implicitly by assuming that dilution due to cell division can be described by an effective decay reaction with first-order kinetics. If it is further assumed that protein production occurs in bursts, then the stationary protein distribution is a negative binomial. Here we seek to understand how accurate these implicit models are when compared with more detailed models of stochastic gene expression. We derive the exact stationary solution of the chemical master equation describing bursty protein dynamics, binomial partitioning at mitosis, age-dependent transcription dynamics including replication, and random interdivision times sampled from Erlang or more general distributions; the solution is different for single lineage and population snapshot settings. We show that protein distributions are well approximated by the solution of implicit models (a negative binomial) when the mean number of mRNAs produced per cycle is low and the cell cycle length variability is large. When these conditions are not met, the distributions are either almost bimodal or else display very flat regions near the mode and cannot be described by implicit models. We also show that for genes with low transcription rates, the size of protein noise has a strong dependence on the replication time, it is almost independent of cell cycle variability for lineage measurements, and increases with cell cycle variability for population snapshot measurements. In contrast for large transcription rates, the size of protein noise is independent of replication time and increases with cell cycle variability for both lineage and population measurements.

If a static perturbation is applied to a liquid crystal, then the director configuration changes to minimize the free energy. If a shear flow is applied to a liquid crystal, then one might ask: Does the director configuration change to minimize any effective potential? To address that question, we derive the Leslie-Ericksen equations for dissipative dynamics and determine whether they can be expressed as relaxation toward a minimum. The answer may be yes or no, depending on the number of degrees of freedom. Using theory and simulations, we consider two specific examples, reverse tilt domains under simple shear flow and dowser configurations under plane Poiseuille flow, and we demonstrate that each example shows relaxation toward the minimum of an effective potential.

We use numerical simulations to study the flow of a bidisperse mixture of athermal, frictionless, soft-core two-dimensional spherocylinders driven by a uniform steady-state simple shear applied at a fixed volume and a fixed finite strain rate $\dot{\gamma }$. Energy dissipation is via a viscous drag with respect to a uniformly sheared host fluid, giving a simple model for flow in a non-Brownian suspension with Newtonian rheology. Considering a range of packing fractions $\varphi$ and particle asphericities $\alpha$ at small $\dot{\gamma }$, we study the angular rotation ${\dot{\theta }}_i$ and the nematic orientational ordering ${\mathbf{S}}_2$ of the particles induced by the shear flow, finding a nonmonotonic behavior as the packing $\varphi$ is varied. We interpret this nonmonotonic behavior as a crossover from dilute systems at small $\varphi$, where single-particle-like behavior occurs, to dense systems at large $\varphi$, where the geometry of the dense packing dominates and a random Poisson-like process for particle rotations results. We also argue that the finite nematic ordering ${\mathbf{S}}_2$ is a consequence of the shearing serving as an ordering field, rather than a result of long-range cooperative behavior among the particles. We arrive at these conclusions by consideration of (i) the distribution of waiting times for a particle to rotate by $\pi$, (ii) the behavior of the system under pure, as compared to simple, shearing, (iii) the relaxation of the nematic order parameter ${\mathbf{S}}_2$ when perturbed away from the steady state, and (iv) by construction, a numerical mean-field model for the rotational motion of a particle. Our results also help to explain the singular behavior observed when taking the $\alpha \to 0$ limit approaching circular disks.

We measure the local yield stress, at the scale of small atomic regions, in a deeply quenched two-dimensional glass model undergoing shear banding in response to athermal quasistatic deformation. We find that the occurrence of essentially a single plastic event suffices to bring the local yield stress distribution to a well-defined value for all strain orientations, thus essentially erasing the memory of the initial structure. It follows that in a well-relaxed sample, plastic events cause the abrupt (nucleation-like) emergence of a local softness contrast and thus precipitate the formation of a band, which, in its early stages, is measurably softer than the steady-state flow. Moreover, this postevent yield stress ensemble presents a mean value comparable to that of the inherent states of a supercooled liquid around the mode-coupling temperature $T_{\mathrm{MCT}}$. This, we argue, explains that the transition between brittle and ductile yielding in amorphous materials occurs around a comparable parent temperature. Our data also permit to capture quantitatively the contributions of pressure and density changes and demonstrate unambiguously that they are negligible compared with the changes of softness caused by structural rejuvenation.

The plasma sheath is the non-neutral space charge region that isolates bulk plasma from a boundary. Radio-frequency (RF) sheaths are formed when applying RF voltage to electrodes. Generally, applied bias is mainly consumed by a RF sheath, which shields an external field. Here we report evidence that an intense boundary emission destroys a normal RF sheath and establishes a type of RF plasma where external bias is consumed by bulk plasma instead of a sheath. Ions are naturally confined while plasma electrons are unobstructed, generating a strong RF current in the entire plasma, combined with a unique particle and energy balance. The proposed model offers the possibility for ion erosion mitigation of a plasma-facing component. It also inspires techniques for reaction rate control in plasma processing and wave mode conversion.

The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and this process is referred to as “translation” of the genetic message encoded in the sequence of mRNA transcript. In each successful chemomechanical cycle during the (protein) elongation stage, the ribosome elongates the protein by a single subunit, called amino acid, and steps forward on the template mRNA by three nucleotides called a codon. Therefore, a ribosome is also regarded as a molecular motor for which the mRNA serves as the track, its step size is that of a codon and two molecules of GTP and one molecule of ATP hydrolyzed in that cycle serve as its fuel. What adds further complexity is the existence of competing pathways leading to distinct cycles, branched pathways in each cycle, and futile consumption of fuel that leads neither to elongation of the nascent protein nor forward stepping of the ribosome on its track. We investigate a model formulated in terms of the network of discrete chemomechanical states of a ribosome during the elongation stage of translation. The model is analyzed using a combination of stochastic thermodynamic and kinetic analysis based on a graph-theoretic approach. We derive the exact solution of the corresponding master equations. We represent the steady state in terms of the cycles of the underlying network and discuss the energy transduction processes. We identify the various possible modes of operation of a ribosome in terms of its average velocity and mean rate of GTP hydrolysis. We also compute entropy production as functions of the rates of the interstate transitions and the thermodynamic cost for accuracy of the translation process.

Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned substrate. This phenomenon, known as topotaxis, has been extensively studied for topographical gradients at the subcellular scale, but can also occur in the presence of a spatially varying density of cell-sized features. Such a large-scale topotaxis has recently been observed in highly motile cells that persistently crawl within an array of obstacles with smoothly varying lattice spacing. We introduce a toy model of large-scale topotaxis, based on active Brownian particles. Using numerical simulations and analytical arguments, we demonstrate that topographical gradients introduce a spatial modulation of the particles' persistence, leading to directed motion toward regions of higher persistence. Our results demonstrate that persistent motion alone is sufficient to drive large-scale topotaxis and could serve as a starting point for more detailed studies on self-propelled particles and cells.

This study focuses on the three-dimensional (3D) electrohydrodynamic flow instability between two parallel electrodes driven by unipolar charge injection with and without cross flow. Lattice Boltzmann method with a two-relaxation time model is used to compute flow patterns. In the absence of cross flow, the base-state solution is hydrostatic, and the electric field is one-dimensional. With strong charge injection and high electrical Rayleigh number, the system exhibits electroconvective vortices. Disturbed by perturbation patterns, such as rolling pattern, square pattern, and hexagon pattern, the flow develops corresponding to the most unstable mode. The growth rate and pattern transitions are studied using dynamic mode decomposition of the transient numerical solutions. The interactions between cross flow and electroconvective vortices lead to suppression and disappearance of structures with velocity components in the direction of cross flow, while the other components are not affected. Surprisingly, the transition from a 3D to a 2D flow pattern enhances the convective charge transport, marked by an increase in the electric Nusselt number. Hysteresis in the 3D to 2D transition is characterized by the nondimensional parameter Y, a ratio of the electrical force term to the viscous term in the momentum equation.

We use the forced Ostrovsky equation to investigate the generation of internal waves excited by a constant background current flowing over localized topography in the presence of background rotation. As is now well known in the absence of background rotation, the evolution scenarios fall into three cases, namely subcritical, transcritical, and supercritical. Here an analysis of the linearized response divides the waves into steady and unsteady waves. In all three cases, steady waves occur downstream but no steady waves can occur upstream, while unsteady waves can arise upstream only when there is a negative minimum of the group velocity. The regions occupied by the steady and unsteady waves are determined by their respective group velocities. When the background current is increased, the wave number of the steady waves decreases. In addition, the concavity (canyon or sill), the topographic width, and the relative strength of the rotation play an important role in the generation mechanism. Nonlinear effects modulate the wave amplitude and lead to the emergence of coherent wave packets. All these findings are confirmed by numerical simulations.

Phase synchronization is a universal concept in macro- and microstate coupling of complex systems. In this Rapid Communication, we demonstrate the existence of phase synchronization dynamics in a wave-particle interaction process under the framework of a Vlasov-Poisson (VP) system. Starting from a random phase setup, it is shown that the phases of the electrons spontaneously develop coherent patterns in its velocity space. The most interesting finding is that, mediated by the long-wavelength electrostatic mode, the phases of the electrons tend to attract each other, condense into a mean phase, and form a chimera pattern. Due to the finite-time singularity of the mean phase, the phase pattern gets evaporated and recondenses into a different chimera pattern. For the scenario of a finite wavelength, the random phases rapidly condense to slashing lines, which become steeper and steeper through a sequence of evaporation-condensation processes. The slashing pattern drives the mixing of the distribution function in the velocity space, which then induces the damping of the electrostatic mode. This phase self-organization dynamics uncovers another aspect of wave-particle interaction physics, and sheds light onto the longstanding enigma of Landau damping.

We investigate the outcome of generalized Lotka-Volterra dynamics of ecological communities with random interaction coefficients and nonlinear feedback. We show in simulations that the saturation of nonlinear feedback stabilizes the dynamics. This is confirmed in an analytical generating-functional approach to generalized Lotka-Volterra equations with piecewise linear saturating response. For such systems we are able to derive self-consistent relations governing the stable fixed-point phase and to carry out a linear stability analysis to predict the onset of unstable behavior. We investigate in detail the combined effects of the mean, variance, and covariance of the random interaction coefficients, and the saturation value of the nonlinear response. We find that stability and diversity increases with the introduction of nonlinear feedback, where decreasing the saturation value has a similar effect to decreasing the covariance. We also find cooperation to no longer have a detrimental effect on stability with nonlinear feedback, and the order parameters mean abundance and diversity to be less dependent on the symmetry of interactions with stronger saturation.

Understanding stickiness and power-law behavior of Poincaré recurrence statistics is an open problem for higher-dimensional systems, in contrast to the well-understood case of systems with two degrees of freedom. We study such intermittent behavior of chaotic orbits in three-dimensional volume-preserving maps using the example of the Arnold-Beltrami-Childress map. The map has a mixed phase space with a cylindrical regular region surrounded by a chaotic sea for the considered parameters. We observe a characteristic overall power-law decay of the cumulative Poincaré recurrence statistics with significant oscillations superimposed. This slow decay is caused by orbits which spend long times close to the surface of the regular region. Representing such long-trapped orbits in frequency space shows clear signatures of partial barriers and reveals that coupled resonances play an essential role. Using a small number of the most relevant resonances allows for classifying long-trapped orbits. From this the Poincaré recurrence statistics can be divided into different exponentially decaying contributions, which very accurately explains the overall power-law behavior including the oscillations.

We compute the optimal temporal profile for an external driving force $F\left(t\right)$ that can maximize the energy absorption of any driven nonlinear oscillator. The technique is based on constraining the maximum amplitude of the force field such that optimal control theory can provide quasianalytical solutions. We illustrate this computational technique for the undamped Duffing oscillator as well as for a driven quantum mechanical two-level system. We find that under optimal force conditions the asymptotic time-dependence of the maximum amplitude growth is given by a power law $X\left(t\right)\sim t^{2/\alpha }$, where the (possibly noninteger) exponent is determined by the highest degree of the oscillator's nonlinearity $\alpha$. As a universal result, this predicts that the maximal energy absorption of any nonlinear oscillator grows (under an optimized force field) quadratically in time. We also find for the two-level system that—even under optimized excitation conditions—the maximally achievable inversion does not monotonically increase with the force amplitude. It is characterized by an interesting sequence of $n$-cycle thresholds as well as a self-termination of the growth.

We study the translocation of the ubiquitin molecule (Ubq) across a channel with a double section which constitutes a general feature of several transmembrane nanopores such as the $\alpha$-hemolysin ($\alpha \mathrm{HL}$). Our purpose is to establish the structure-dependent character of the Ubq translocation pathway. This implies to find the correspondence, if any, between the translocational unfolding steps and the Ubq native state. For this reason, it is convenient to apply a coarse-grained computational approach, where the protein is described only by the backbone and the force field only exploits the information contained in the native state (in the spirit of Gō-like models, or native-centric models). The $\alpha \mathrm{HL}$-like pore is portrayed as two coaxial confining cylinders: a larger one for the vestibule and a narrower one for the barrel (or stem). Such simplified approach allows a large number of translocation events to be collected by limited computational resources. The co-translocational unfolding of Ubq is described via a few collective variables that characterize the translocation progress. We find two translocation intermediates (stalled conformations) that can be associated with specific unfolding stages. In particular, in the earliest step, the strand S5 unfolds and enters the pore. This step splits the native conformation into two structural clusters packing against each other in the Ubq fold. A second stall occurs when the hairpin of the N terminal engages the stem region.

We investigate macroscopic two-fluid effects in magnetorheological fluids generalizing a one-fluid model studied before. In the bulk of the paper we use a model in which the carrier fluid, with density ${\rho }_1$, moves with velocity ${\mathit{v}}_1$, while the magnetic component (density ${\rho }_2$) and, therefore, the magnetization and the magnetic-field-induced relaxing strain field move with velocity ${\mathit{v}}_{\mathit{2}}$. In the framework of macroscopic dynamics we find, in particular, reversible dynamic and dissipative cross-coupling terms between the magnetization and the velocity difference. Experiments to detect some of these cross-coupling terms are suggested. We also compare the results of the two-fluid model presented here with two-fluid models available for electrorheological fluids. In two appendices we discuss the simplifying assumptions made to arrive at the model used in this paper and we also outline how to detect potential deviations from this model.

The evolution of dissolved species in a porous medium is determined by its adsorption on the porous matrix through the classical advection-diffusion processes. The extent to which the adsorption affects the solute propagation in applications related to chromatography and contaminant transport is largely dependent upon the adsorption isotherm. Here, we examine the influence of a nonlinear Langmuir adsorbed solute on its propagation dynamics. Interfacial deformations can also be induced by classical viscous fingering (VF) instability that develops when a less viscous fluid displaces a more viscous one. We present numerical simulations of an initially step-up concentration profile of the solute that capture a rarefaction/diffusive wave solution due to the nonlinearity introduced through Langmuir adsorption and variety of pattern-forming behaviors of the solute dissolved in the displaced fluid. The fluid velocity is governed by Darcy's law, coupled with the advection-diffusion equation that determines the evolution of the solute concentration controlling the viscosity of the fluids. Numerical simulations are performed using the Fourier pseudospectral method to investigate and illustrate the role played by VF and Langmuir adsorption in the development of the patterns of the interface. We show that the solute transport proceeds by the formation of a rarefaction wave results in the enhanced spreading of the solute. Interestingly we obtained a nonmonotonic behavior in the onset of VF, which depends on the adsorption parameters and existence of an optimal value of such adsorption constant is obtained near $b=1$, for which the most delayed VF is observed. Hence, it can be concluded that the rarefaction wave formation stands out to be an effective tool for controlling the VF dynamics.

We study the joint probability distributions of separation $R$ and radial component of the relative velocity $V_R$ of particles settling under gravity in a turbulent flow. We also obtain the moments of these distributions and analyze their anisotropy using spherical harmonics. We find that the qualitative nature of the joint distributions remains the same as no-gravity case. Distributions of $V_R$ for fixed values of $R$ show a power-law dependence on $V_R$ for a range of $V_R$; the exponent of the power law depends on the gravity. Effects of gravity are also manifested in the following ways: (a) Moments of the distributions are anisotropic; degree of anisotropy depends on particle's Stokes number, but does not depend on $R$ for small values of $R$. (b) Mean velocity of collision between two particles is decreased for particles having equal Stokes numbers but increased for particles having different Stokes numbers. For the later, collision velocity is set by the difference in their settling velocities.

Electronic parametric instabilities of an ultrarelativistic circularly polarized laser pulse propagating in underdense plasmas are studied by numerically solving the dispersion relation which includes the effect of the radiation reaction force in laser-driven plasma dynamics. Emphasis is placed on studying the different modes in the laser-plasma system and identifying the absolute and convective nature of the unstable modes in a parameter map spanned by the normalized laser vector potential and the plasma density. Implications for the ultraintense laser-plasma experiments are pointed out.

The unique spatial and temporal properties of relativistic high harmonics generated from a laser-driven plasma surface allow them to be coherently focused to an extremely high intensity reaching the Schwinger limit. The ultimately achievable intensity is limited by the harmonic wavefront distortions during the interactions. Here we demonstrate experimentally that the harmonic divergence can be controlled by an optically shaped plasma surface with a prepulse that has the same spatial and temporal distribution as the main laser pulse. Simulations are also performed to explain the experimental observation, and we find that the harmonic wavefront curvature from a dented surface can be precompensated by a convex plasma. Our work suggests an active approach to control the harmonic divergence and wavefront by an optically shaped target. This can be critical for further high harmonics applications.