Riboswitches are RNA-structured elements that modulate gene expression through changing their conformation in response to specific metabolite binding. However, the regulation mechanisms of riboswitches by ligand binding are still not well understood. At present two possible ligand-binding mechanisms have been proposed: conformational selection and induced fit. Based on explicit-solvent molecular dynamics (MD) simulations, we have studied the process of the binding of ligands (adenines) to add adenine riboswitch aptamer (AARA) in detail. Our results show that the relative high flexibility of the junction J23 of AARA allows the ligands to be captured by the binding pocket of AARA in a near-native state, which may be driven by hydrophobic and base-stacking interactions. In addition, the binding of a ligand makes the stem P1 and the junction J23 of AARA more stable than in the absence of the ligand. Generally, our analyses show that the ligand-binding process of the add adenine riboswitch may be partially embodied by a conformational selection mechanism.

During typical early-stage embryo development, single-cell-thick tissues of tightly bound epithelial cells autonomously generate profound changes in their shape, forming the basis of organism anatomy. We report on a (covariant) active-hydrodynamic theory of such monolayer morphogenesis that is closed under its shape-changing dynamics—i.e., the degrees of freedom that encode monolayer geometry appear properly as broken-symmetry variables. In our theory, the salient physics of tissue-scale deformations emerges from a balance between the displacement and/or shear of a low-Reynolds-number embedding fluid (the “yolk”) and cell-autonomous stresses, themselves a result of combining apical contractile stresses with an elastic-like mechanical response under the constraint of constant cell volume. The leading-order hydrodynamic instabilities include both passive constrained-buckling and active deformation, which can be further categorized by cell shape changes that are either “squamous to columnar” or “regular-prism to truncated-pyramid.” The deformations resulting from the latter qualitatively reproduce in vivo observations of the onset of both mesoderm and posterior midgut invaginations, which take place during gastrulation in the model organism Drosophila melanogaster.

How does removal of sites by a random walk lead to blockage of percolation? To study this problem of correlated site percolation, we consider a random walk (RW) of $N=u{L}^d$ steps on a $d$-dimensional hypercubic lattice of size $L^d$ (with periodic boundaries). We systematically explore dependence of the probability ${\mathrm{\Pi }}_d(L,u)$ of percolation (existence of a spanning cluster) of sites not removed by the RW on $L$ and $u$. The concentration of unvisited sites decays exponentially with increasing $u$, while the visited sites are highly correlated—their correlations decaying with the distance $r$ as $1/r^{d-2}$ (in $d>2$). On increasing $L$, the percolation probability ${\mathrm{\Pi }}_d(L,u)$ approaches a step function, jumping from 1 to 0 when $u$ crosses a percolation threshold $u_c$ that is close to 3 for all $3\le d\le 6$. Within numerical accuracy, the correlation length associated with percolation diverges with exponents consistent with $\nu =2/(d-2)$. There is no percolation threshold at the lower critical dimension of $d=2$, with the percolation probability approaching a smooth function ${\mathrm{\Pi }}_2(\infty ,u)>0$.

A binary number-conserving cellular automaton is a discrete dynamical system that models the movement of particles in a $d$-dimensional grid. Each cell of the grid is either empty or contains a particle. In subsequent time steps the particles move between the cells, but in one cell there can be at most one particle at a time. In this paper, the von Neumann neighborhood is considered, which means that in each time step a particle can move to an adjacent cell only. It is proven that regardless of the dimension $d$, all of these cellular automata are trivial, as they are intrinsically one-dimensional. Thus, for given $d$, there are only $4d+1$ binary number-conserving cellular automata with the von Neumann neighborhood: the identity rule and the shift and traffic rules in each of the $2d$ possible directions.

Oscillatory systems with long-range or global coupling offer promising insight into the interplay between high-dimensional (or microscopic) chaotic motion and collective interaction patterns. Within this paper, we use Lyapunov analysis to investigate whether chimera states in globally coupled Stuart-Landau (SL) oscillators exhibit collective degrees of freedom. We compare two types of chimera states, which emerge in SL ensembles with linear and nonlinear global coupling, respectively, the latter introducing a constraint that conserves the oscillation of the mean. Lyapunov spectra reveal that for both chimera states the Lyapunov exponents split into several groups with different convergence properties in the limit of large system size. Furthermore, in both cases the Lyapunov dimension is found to scale extensively and the localization properties of covariant Lypunov vectors manifest the presence of collective Lyapunov modes. Here, however, we find qualitative differences between the two types of chimera states: Whereas the ones in the system under nonlinear global coupling exhibit only slow collective modes corresponding to Lyapunov exponents equal or close to zero, those which experience the linear mean-field coupling exhibit also faster collective modes associated with Lyapunov exponents with large positive or negative values. Furthermore, for the fastest collective mode we showed that it spreads across both synchonous and incoherent oscillators.

In this paper we explore the evolution of transport capacity on networks with stochastic incidence of damage and accumulation of faults in their connections. For each damaged configuration of the network, we analyze a Markovian random walker that hops over weighted links that quantify the capacity of transport of each connection. The weights of the links in the network evolve due to randomly occurring damage effects that reduce gradually the transport capacity of the structure. We introduce a global measure to determine the functionality of each configuration and how the system ages due to the accumulation of damage that cannot be repaired completely. Then, by assuming a minimum value of the functionality required for the system to be “alive,” we explore the statistics of the lifetimes for several realizations of this process in different types of networks. Finally, we analyze the characteristic longevity of such a system and its relation with the “complexity” of the network structure. One finding is that systems with greater complexity live longer. Our approach introduces a model of aging processes relating the reduction of functionality with the accumulation of “misrepairs” and the lifetime of a complex system.

We consider a two-layer multiplex network of diffusively coupled FitzHugh-Nagumo (FHN) neurons in the excitable regime. We show that the phenomenon of coherence resonance (CR) in one layer can not only be controlled by the network topology, the intra- and interlayer time-delayed couplings, but also by another phenomenon, namely, self-induced stochastic resonance (SISR) in the other layer. Numerical computations show that when the layers are isolated, each of these noise-induced phenomena is weakened (strengthened) by a sparser (denser) ring network topology, stronger (weaker) intralayer coupling forces, and longer (shorter) intralayer time delays. However, CR shows a much higher sensitivity than SISR to changes in these control parameters. It is also shown, in contrast to SISR in a single isolated FHN neuron, that the maximum noise amplitude at which SISR occurs in the network of coupled FHN neurons is controllable, especially in the regime of strong coupling forces and long time delays. In order to use SISR in the first layer of the multiplex network to control CR in the second layer, we first choose the control parameters of the second layer in isolation such that in one case CR is poor and in another case, nonexistent. It is then shown that a pronounced SISR can not only significantly improve a poor CR, but can also induce a pronounced CR, which was nonexistent in the isolated second layer. In contrast to strong intralayer coupling forces, strong interlayer coupling forces are found to enhance CR, while long interlayer time delays, just as long intralayer time delays, deteriorate CR. Most importantly, we find that in a strong interlayer coupling regime, SISR in the first layer performs better than CR in enhancing CR in the second layer. But in a weak interlayer coupling regime, CR in the first layer performs better than SISR in enhancing CR in the second layer. Our results could find novel applications in noisy neural network dynamics and engineering.

So far, most studies on evolutionary game dynamics in finite populations have concentrated on a single update rule. However, given the impacts of the environment and individual cognition, individuals may use different update rules to change their current strategies. In light of this, the current paper reports on a study that constructed a mixed stochastic evolutionary game dynamic by combining the imitation and aspiration-driven update processes. The target was to clarify the influences of the aspiration-driven process on the evolution of the level of cooperation by considering the behavior of a population in which individuals have two strategies available: cooperation and defection. Through a numerical analysis of unstructured populations and simulation analyses of structured populations and of the random-matching model, the following results were found. First, the mean fraction of cooperators varied alongside the probability with which the individual adopted the aspiration-driven update rule. In the Prisoner's Dilemma and coexistence games, the aspiration-driven update process promoted cooperation in the well-mixed population but inhibited it in structured ones and the random-matching model; however, in the coordination game, the aspiration-driven update process was seen to exert the opposite effect on cooperation by inhibiting the latter in a homogeneously mixed population but promoting it in structured ones and in the random-matching model. Second, the mean fraction of cooperators changed with the aspiration level in the differently structured populations and random-matching model, and there appeared a phase transition point. Third, the evolutionary characteristics of the mean fraction of cooperators maintained robustness in the differently structured populations and random-matching model. These results extend evolutionary game theory.

We analyze the frequency dependence of the force between ac-voltage-biased plates in electrolyte solutions. To this end we solve analytically the Poisson-Nernst-Planck transport model in the dilute concentration and low voltage regime for a 1:1 symmetric electrolyte with blocking electrodes under a dc+ac applied voltage. The total force, which is the resultant of the electric and osmotic forces, shows a complex dependence on plate separation, frequency, ion concentration, and compact layer properties, different from that predicted from electrostatic current models or equivalent circuit models, due to the relevance of the osmotic force contribution in almost the whole range of frequencies. For the total dc force, we show that it decays at fixed ion concentration, linearly with plate separation for separations larger than a few times the Debye screening length. This linear dependence is due to the assumption about the conservation of the number of ions in the system. Moreover, the 1ω and 2ω ac harmonics of the total force show a broad peak at intermediate frequencies; it is centered at about the inverse of the charging time of the double layer capacitance, and covers the frequency range between the inverse of the diffusion time and the inverse of the electrolyte dielectric relaxation time. Finally, the 1ω ac harmonic component attains its high frequency asymptotic value at frequencies much higher than the inverse of the electrolyte dielectric relaxation time due to the very slow relaxation of the osmotic 1ω harmonic component at high frequencies. The derived analytical expressions for the total force remain valid up to voltages of the order of the thermal voltage, as has been assessed by means of numerical calculations. The numerical calculations are also used to explore the onset of higher force harmonics for larger applied voltages. Understanding the frequency dependence of the force acting on voltage-biased plates in electrolyte solutions can be of relevance for electrical actuation strategies in microelectromechanical systems and for the interpretation of some emerging electric scanning probe force microscopy techniques operating in electrolyte solutions.

The Janssen model of stress redistribution within laterally bounded particulate assemblies is a longstanding and valuable theoretical framework, widely used in the design of industrial systems. However, the model relies on the assumption of a static packing of particles and has never been tested in a truly dynamic regime nor for a constraining system whose geometry is dynamically altered. In this paper, we explore the pressure distributions of granular beds housed within a container possessing a laterally mobile sidewall, allowing the depth, height, and cross-sectional areas of the systems studied to be dynamically altered, thus, inducing particle rearrangements and flow in the particulate system constrained thereby. We demonstrate that the systems studied can be successfully described by the Janssen model across a wide range of system expansion rates, including those for which liquidlike flow is clearly observed and propose an extension to the model allowing for an improved characterization of constrained dynamic systems.

A high level of mixing by passive means is a desirable feature in microchannels for various applications, and use of flexible obstacles (or plates) is one of the prime choices in that regard. To gain further insight, we carry out two-dimensional numerical simulations for flow past one or two flexible plates anchored to a channel's opposite walls using a fluid-structure interaction framework. For the inlet flow Reynolds number vs the Strouhal number plane, we observe a sudden flow change from a laminar to a time-periodic vortex shedding state when flexible plates are present in the channel. We found the critical Reynolds number to be ${\mathrm{Re}}_{\mathrm{cr}}\approx 370$ when a single plate is anchored on the channel wall and ${\mathrm{Re}}_{\mathrm{cr}}\approx 290$ or even lower when two plates are anchored. With an increase in the inlet flow Reynolds number (up to 3200), we found that vortices detach regularly at the plates' tips, which causes the flow to meander in the channel. In a two-plate anchored configuration, primary vortices generated at the first plate are constrained by the second plate and result in an energetic secondary vortex generation in the downstream side. The overall flow features and the energy dissipation in the channel are mainly controlled by the separation gap between the plates. At high-inlet-flow Reynolds numbers ($\ge 1600$), the probability density function ($\mathcal{F}$) of the kinetic energy dissipation in a flexible plate configuration shows a stretched exponential shape in the form $\mathcal{F}\left(Z\right)\sim \frac{1}{\sqrt{Z}}{e}^{-p{Z}^q}$, where $Z$ is the normalized kinetic energy dissipation and the constants $p=0.89$ and $q=0.86$. The observed increase in energy dissipation comes at the cost of an increase in pressure loss in the channel, and we found that the loss is inversely related to the plates' separation gap. From our simulations, we found that if high mixing levels are desired, then two flexible plates anchored to the channel walls is a better choice than a channel flow without obstacles or flow past a single plate. The two-plate configuration with zero separation gap between the plates is best suited to achieve a high mixing level.

The laminar-turbulent transition induced by two-dimensional steplike roughness is investigated focusing on the pattern of breakdown. The statistics of the turbulent burst rate is found to be significantly different from the prediction of the classical theory. A systematic investigation of the pattern of breakdown is motivated by this phenomenon. It is identified with heuristic analysis that a pattern of distributed breakdown is responsible for the deviation, in contrast to the concentrated breakdown hypothesis in the classical theory. The pattern indicates that the steps probably induced a bypass transition in present experimental setup, which is different from the current understanding about the step-induced transition. Cellular-automaton simulations are carried out to validate the heuristic analysis. The influences of quasiconcentration and non-Poisson process in spot generation on the breakdown statistics are also discussed based on the simulation results.

We study the statistics of fluid (gas) density and concentration of passive tracer particles (dust) in compressible turbulence. As $\mathrm{Ma}$ increases from small or moderate values, the density and the concentration in the inertial range go through a phase transition from a finite continuous smooth distribution to a singular multifractal spatial distribution. Multifractality is associated with scaling, which would not hold if the solenoidal and the potential components of the flow scaled differently, producing transport which is not self-similar. Thus, we propose that the transition occurs when the difference of the scaling exponents of the components, decreasing with $\mathrm{Ma}$, becomes small. Under the smallness assumption, the particles' volumes obey a power-law evolution. That, by the use of conservation of the total volume of the flow, entails the volumes' shrinking to zero with probability 1 and formation of a singular distribution. We discuss various concepts of multifractality and propose a way to calculate fractal dimensions from numerical or experimental data. We derive a simple expression for the spectrum of fractal dimensions of isothermal turbulence and describe limitations of lognormality. The expression depends on a single parameter: the scaling exponent of the density spectrum. We demonstrate that the pair-correlation function of the tracer concentration has the Markov property. This implies applicability of the compressible version of the Kraichnan turbulence model. We use the model to derive an explicit expression for the tracer pair correlation that demonstrates their smooth transition to multifractality and confirms the transition's mechanism. The obtained fractal dimension explains previous numerical observations. Our results have potentially important implications for astrophysical problems such as star formation as well as technological applications such as supersonic combustion. As an example, we demonstrate the strong increase of planetesimal formation rate at the transition. We prove that finiteness of internal energy implies vanishing of the sum of Lyapunov exponents in the dissipation range. Our study leads to the question of whether the fluid density which is an active field that reacts back on the transporting flow and the passive concentration of tracers must coincide in the steady state. This is demonstrated to be crucial both theoretically and experimentally. The fields' coincidence is provable at small Mach numbers; however, at finite Mach numbers, the assumption of mixing is needed, which we demonstrate to be not self-evident because of the possibility of self-organization.

A mechanism for removal of salt from salt water is discussed, which results from friction due to Ohm's law heating, resulting from motion of an electron charge induced in the tube walls by the water molecules’ dipoles and the ions’ charges. The desalination occurs because this friction is larger for salt ions than for water molecules. Friction due to Ohm's law heating might also provide an explanation for the observation by Secchi et al. [Nature 537, 210 (2016)] that the flow velocity of water in carbon nanotubes for a given pressure gradient increases rapidly as the tube radius decreases from 50 to 15 nm, which does not occur for boron nitride nanotubes, which are insulators. This friction can have the right magnitude to produce the slip lengths reported by Secchi et al. One possibility is that the nanotubes in this experiment were metallic, and their conductivity becomes large as their radius decreases, due to ballistic conduction. Another possibility is that when the tube circumference drops below the electron mean-free path, the wall switches from behaving as a two-dimensional conductor to behaving as a one-dimensional conductor for which the electrons are more strongly localized. When the conductivity is sufficiently small, small displacements of the localized electron states can provide the dominant contribution to the motion of the induced charge, rather than current flow, thus reducing the friction due to Ohm's law heating.

We introduce a scheme to perform Monte Carlo renormalization group with the coupling constants of the system Hamiltonian encoded in a tensor network. With this scheme we compute the tangent space to the manifold of the critical Hamiltonians representable by a tensor network at the nearest-neighbor critical coupling for three models: the two- and three-dimensional Ising models and the two-dimensional three-state Potts model.

In their recent paper [Phys. Rev. E 99, 032134 (2019)], Oikonomou and Bagci have argued that Rényi entropy is ill suited for inference purposes because it is not consistent with the Shore-Johnson axioms of statistical estimation theory. In this Comment we seek to clarify the latter statement by showing that there are several issues in Oikonomou's and Bagci's reasonings which lead to erroneous conclusions. When all these issues are properly accounted for, no violation of Shore-Johnson axioms is found.

We reply to the preceding Comment by Jizba and Korbel [Jizba and Korbel, Phys. Rev. E 100, 026101 (2019)] by first pointing out that the Schur concavity proposed by them falls short of identifying the correct intervals of normalization for the optimum probability distribution even though normalization is a necessary ingredient in the entropy maximization procedure. Second, their treatment of the subset independence axiom requires a modification of the Lagrange multipliers one begins with, thereby rendering the optimization less trustworthy. We also explicitly demonstrate that the Rényi entropy violates the subset independence axiom and compare it with the Shannon entropy. Third, the composition rule offered by Jizba and Korbel is shown to yield probability distributions even without a need for the entropy maximization procedure at the expense of creating artificial bias in the data.

We study the statistical properties of the long-time dynamics of the rule 54 reversible cellular automaton (CA), driven stochastically at its boundaries. This CA can be considered as a discrete-time and deterministic version of the Fredrickson-Andersen kinetically constrained model (KCM). By means of a matrix product ansatz, we compute the exact large deviation cumulant generating functions for a wide range of time-extensive observables of the dynamics, together with their associated rate functions and conditioned long-time distributions over configurations. We show that for all instances of boundary driving the CA dynamics occurs at the point of phase coexistence between competing active and inactive dynamical phases, similar to what happens in more standard KCMs. We also find the exact finite size scaling behavior of these trajectory transitions, and provide the explicit “Doob-transformed” dynamics that optimally realizes rare dynamical events.

We describe a platform developed on the LULI2000 laser facility to investigate the evolution of Rayleigh-Taylor instability (RTI) in scaled conditions relevant to young supernova remnants (SNRs) up to 200 years. An RT unstable interface is imaged with a short-pulse laser-driven (PICO2000) x-ray source, providing an unprecedented simultaneous high spatial ($24\mu \mathrm{m}$) and temporal (10 ps) resolution. This experiment provides relevant data to compare with astrophysical codes, as observational data on the development of RTI at the early stage of the SNR expansion are missing. A comparison is also performed with FLASH radiative magnetohydrodynamic simulations.

We investigate the critical behavior of three-dimensional ferromagnetic ${\mathrm{CP}}^{N-1}$ models, which are characterized by a global $\mathrm{U}(N$) and a local U(1) symmetry. We perform numerical simulations of a lattice model for $N=2$, 3, and 4. For $N=2$ we find a critical transition in the Heisenberg O(3) universality class, while for $N=3$ and 4 the system undergoes a first-order transition. For $N=3$ the transition is very weak and a clear signature of its discontinuous nature is only observed for sizes $L\gtrsim 50$. We also determine the critical behavior for a large class of lattice Hamiltonians in the large-$N$ limit. The results confirm the existence of a stable large-$N{\mathrm{CP}}^{N-1}$ fixed point. However, this evidence contradicts the standard picture obtained in the Landau-Ginzburg-Wilson (LGW) framework using a gauge-invariant order parameter: The presence of a cubic term in the effective LGW field theory for any $N\ge 3$ would usually be taken as an indication that these models generically undergo first-order transitions.