The critical behavior of ribonucleic acid (RNA) secondary structures with quenched sequence randomness is studied by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold-melting transition appears when the disorder strength induces competition between favorable and unfavorable base pairs. Our results suggest that the cold denaturation of RNA found experimentally might be triggered by quenched sequence disorder. We calculate hot- and cold-melting critical temperatures for competing favorable and unfavorable base-pair energies and present a folding phase diagram as a function of the loop exponent and temperature.

Dielectrophoresis (DEP) in a medium with anisotropic dielectric susceptibility is very different from typical DEP in an isotropic medium: The direction of particle actuation can be switched depending on the direction of the susceptibility tensor of the medium. However, the understanding of switchable DEP (SDEP) in an anisotropic medium is still in its infant stage. Here, we investigate SDEP using heat-generated isotropic droplets in a nematic liquid crystal (LC) medium. We demonstrate that the location of the generation of isotropic droplets can be partially controlled by controlling the temperature gradient within the LC cell using dielectric loss. The SDEP actuation of isotropic droplets is also highly dependent on the location of the isotropic droplets. Using this method, we fabricated different array patterns of isotropic and nematic phase separations under different applied signals.

We present simulation results for an intruder pulled through a two-dimensional granular system by a spring using a model designed to mimic the experiments described by Kozlowski et al. [Phys. Rev. E 100, 032905 (2019)]. In that previous study the presence of basal friction between the grains and the base was observed to change the intruder dynamics from clogging to stick-slip. Here we first show that our simulation results are in excellent agreement with the experimental data for a variety of experimentally accessible friction coefficients governing interactions of particles with each other and with boundaries. We then use simulations to explore a broader range of parameter space, focusing on the friction between the particles and the base. We consider both static and dynamic basal friction coefficients, which are difficult to vary smoothly in experiments. The simulations show that dynamic friction strongly affects the stick-slip behavior when the coefficient is decreased below 0.1, while static friction plays only a marginal role.

Most treatments of electron-electron correlations in dense plasmas either ignore them entirely (random phase approximation) or neglect the role of ions (jellium approximation). In this work, we go beyond both these approximations to derive a formula for the electron-electron static structure factor which properly accounts for the contributions of both ionic structure and quantum-mechanical dynamic response in the electrons. The result can be viewed as a natural extension of the quantum Ornstein-Zernike theory of ionic and electronic correlations, and it is suitable for dense plasmas in which the ions are classical and the conduction electrons are quantum-mechanical. The corresponding electron-electron pair distribution functions are compared with the results of path integral Monte Carlo simulations, showing good agreement whenever no strong electron resonance states are present. We construct approximate potentials of mean force which describe the effective screened interaction between electrons. Significant deviations from Debye-Hückel screening are present at temperatures and densities relevant to high-energy density experiments involving warm and hot dense plasmas. The presence of correlations between conduction electrons is likely to influence the electron-electron contribution to the electrical and thermal conductivity. It is expected that excitation processes involving the conduction electrons (e.g., free-free absorption) will also be affected.

We study the extinction risk of a fragmented population residing on a network of patches coupled by migration, where the local patch dynamics includes deterministic bistability. Mixing between patches is shown to dramatically influence the population's viability. We demonstrate that slow migration always increases the population's global extinction risk compared to the isolated case, while at fast migration synchrony between patches minimizes the population's extinction risk. Moreover, we discover a critical migration rate that maximizes the extinction risk of the population, and identify an early-warning signal when approaching this state. Our theoretical results are confirmed via the highly efficient weighted ensemble method. Notably, our theoretical formalism can also be applied to studying switching in gene regulatory networks with multiple transcriptional states.

The ratio of two consecutive level spacings has emerged as a very useful metric in investigating universal features exhibited by complex spectra. It does not require the knowledge of density of states and is therefore quite convenient to compute in analyzing the spectrum of a general system. The Wigner-surmise-like results for the ratio distribution are known for the invariant classes of Gaussian random matrices. However, for the crossover ensembles, which are useful in modeling systems with partially broken symmetries, corresponding results have remained unavailable so far. In this work, we derive exact results for the distribution and average of the ratio of two consecutive level spacings in the Gaussian orthogonal to unitary crossover ensemble using a $3\times 3$ random matrix model. This crossover is useful in modeling time-reversal symmetry breaking in quantum chaotic systems. Although based on a $3\times 3$ matrix model, our results can also be applied in the study of large spectra, provided the symmetry-breaking parameter facilitating the crossover is suitably scaled. We substantiate this claim by considering Gaussian and Laguerre crossover ensembles comprising large matrices. Moreover, we apply our result to investigate the violation of time-reversal invariance in the quantum kicked rotor system.

We study the origin of the log-normal popularity distribution of trending memes observed in many real social networks. Based on a biological analogy, we introduce a fitness of each meme, which is a natural assumption based on sociological reasons. From numerical simulations, we find that the relative popularity distribution of the trending memes becomes a log-normal distribution when the fitness of the meme increases exponentially. On the other hand, if the fitness grows slowly, then the distribution significantly deviates from the log-normal distribution. This indicates that the fast growth of fitness is the necessary condition for the trending meme. Furthermore, we also show that the popularity of the trending topic grows linearly. These results provide a clue to understand long-lasting questions, such as what causes some memes to become extremely popular and how such memes are exposed to the public much longer than others.

Soft solids like colloidal glasses exhibit a yield stress, above which the system starts to flow. The microscopic analogon in microrheology is the untrapping or depinning of a tracer particle subject to an external force exceeding a threshold value in a glassy host. We characterize this delocalization transition based on a bifurcation analysis of the corresponding mode-coupling theory equations. A schematic model that allows analytical progress is presented first, and the full physical model is studied numerically next. This analysis yields a continuous dynamic transition with a critical power-law decay of the probe correlation functions with exponent $-1/2$. To compare with simulations with a limited duration, a finite-time analysis is performed, which yields reasonable results for not-too-small wave vectors. The theoretically predicted findings are verified by Langevin dynamics simulations. For small wave vectors we find anomalous behavior for the probe position correlation function, which can be traced back to a wave-vector divergence of the critical amplitude. In addition, we propose and test three methods to extract the critical force from experimental data, which provide the same value of the critical force when applied to the finite-time theory or simulations.

In this paper, based on the molecular dynamics simulations of quasireal model systems, we propose a method for determination of the effective intermolecular potential for real materials. We show that in contrast to the simple liquids, the effective intermolecular potential for the studied systems depends on the thermodynamic conditions. Nevertheless, the previously established relationship for simple liquids between the exponent of the inverse power law approximation of intermolecular potential and the density-scaling exponent is still preserved when small enough intermolecular distances are considered. However, our studies show that molecules approach each other at these very short distances relatively rarely. Consequently, only sparse interactions between extremely close molecules determine the value of the scaling exponent and then strongly influence the connection between dynamics and thermodynamics of the whole system.

Disordered packings of colloidal spheres show angle-independent structural color when the particles are on the scale of the wavelength of visible light. Previous work has shown that the positions of the peaks in the reflectance spectra can be predicted accurately from a single-scattering model that accounts for the effective refractive index of the material. This agreement shows that the main color peak arises from short-range correlations between particles. However, the single-scattering model does not quantitatively reproduce the observed color: the main peak in the reflectance spectrum is much broader and the reflectance at low wavelengths is much larger than predicted by the model. We use a combination of experiment and theory to understand these features. We find that one significant contribution to the breadth of the main peak is light that is scattered, totally internally reflected from the boundary of the sample, and then scattered again. The high reflectance at low wavelengths also results from multiple scattering but can be traced to the increase in the scattering cross section of individual particles with decreasing wavelength. Both of these effects tend to reduce the saturation of the structural color, which limits the use of these materials in applications. We show that while the single-scattering model cannot reproduce the observed saturations, it can be used as a design tool to reduce the amount of multiple scattering and increase the color saturation of materials, even in the absence of absorbing components.

The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, a molecular-dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks confined to long, narrow, structureless channels with hard walls in the no-passing regime. We show that the diffusion coefficient obtained from the mean-squared displacement can be mapped onto the exact results for the diffusion of the strictly-one-dimensional hard rod system through an effective occupied volume fraction obtained from either the equation of state or a geometric projection of the particle interaction diameters.

This paper is the continuation of work done in our previous papers [A. A. Doinikov et al., Phys. Rev. E 100, 033104 (2019); Phys. Rev. E 100, 033105 (2019)]. The overall aim of the study is to develop a theory for modeling the velocity field of acoustic microstreaming produced by nonspherical oscillations of an acoustically driven gas bubble. In our previous papers, general equations have been derived to describe the velocity field of acoustic microstreaming produced by modes $m$ and $n$ of bubble oscillations. After solving these general equations for some particular cases of modal interactions (cases 0-$n$, 1-1, and 1-$m$), in this paper the general equations are solved analytically for the case that acoustic microstreaming results from the self-interaction of an arbitrary surface mode $n\ge 1$. Solutions are expressed in terms of complex mode amplitudes, meaning that the mode amplitudes are assumed to be known and serve as input data for the calculation of the velocity field of acoustic microstreaming. No restrictions are imposed on the ratio of the bubble radius to the viscous penetration depth. The self-interaction results in specific streaming patterns: a large-scale cross pattern and small recirculation zones in the vicinity of the bubble interface. Particularly the spatial organization of the recirculation zones is unique for a given surface mode and therefore appears as a signature of the $n\text{−}n$ interaction. Experimental streaming patterns related to this interaction are obtained and good agreement is observed with the theoretical model.

The one-point distribution of the height for the continuum Kardar-Parisi-Zhang equation is determined numerically using the mapping to the directed polymer in a random potential at high temperature. Using an importance sampling approach, the distribution is obtained over a large range of values, down to a probability density as small as ${10}^{-1000}$ in the tails. The short-time behavior is investigated and compared with recent analytical predictions for the large-deviation forms of the probability of rare fluctuations, showing a spectacular agreement with the analytical expressions. The flat and stationary initial conditions are studied in the full space, together with the droplet initial condition in the half-space.

We study laminar chaos in an electronic experiment. A two-diode nonlinear circuit with delayed feedback shows chaotic dynamics similar to the Mackey-Glass or Ikeda delay systems. Clock modulation of a single delay line leads to a conservative variable delay, which with a second delay line is augmented to dissipative delays, leading to laminar chaotic regimes. We discuss the properties of this particular delay modulation and demonstrate experimental aspects of laminar chaos in terms of power spectra and return maps.

This paper introduces a general model of a single-lane roundabout, represented as a circular lattice that consists of $L$ cells, with Markovian traffic dynamics. Vehicles enter the roundabout via on-ramp queues that have stochastic arrival processes, remain on the roundabout a random number of cells, and depart via off-ramps. Importantly, the model does not oversimplify the dynamics of traffic on roundabouts, while various performance-related quantities (such as delay and queue length) allow an analytical characterization. In particular, we present an explicit expression for the marginal stationary distribution of each cell on the lattice. Moreover, we derive results that give insight on the dependencies between parts of the roundabout, and on the queue distribution. Finally, we find scaling limits that allow, for every partition of the roundabout in segments, to approximate (i) the joint distribution of the occupation of these segments by a multivariate Gaussian distribution, and (ii) the joint distribution of their total queue lengths by a collection of independent Poisson random variables. To verify the scaling limit statements, we develop a way to empirically assess convergence in distribution of random variables.

Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms, and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits has been increasingly used to test the fundamental principles of genetic network dynamics. While the “repressilator” was used to first demonstrate the proof of principle, a more recently developed dual-feedback, fast, tunable genetic oscillator has demonstrated a greater degree of robustness and control over oscillatory behavior by combining positive- and negative-feedback loops. This oscillator, combining lacI (negative-) and araC (positive-) feedback loops, was, however, modeled using multiple layers of differential equations to capture the molecular complexity of regulation, in order to explain the experimentally measured oscillations. In the search for design principles of such minimal oscillatory circuits, we have developed a reduced model of this dual-feedback loop oscillator consisting of just six differential equations, two of which are delay differential equations. The delay term is optimized, as the only free parameter, to fit the experimental dynamics of the oscillator period and amplitude tunability by the two inducers isopropyl $\beta$-D-1-thiogalactopyranoside (IPTG) and arabinose. We proceed to use our reduced and experimentally validated model to redesign the network by comparing the effect of asymmetry in gene expression at the level of (a) DNA copy numbers and the rates of (b) mRNA translation and (c) degradation, since experimental and theoretical work had predicted a need for an asymmetry in the copy numbers of activator (araC) and repressor (lacI) genes encoded on plasmids. We confirm that the minimal period of the oscillator is sensitive to DNA copy number asymmetry, and can demonstrate that while the asymmetry in the translation rate has an identical effect as the plasmid copy numbers, modulating the asymmetry in mRNA degradation can improve the tunability of the period and amplitude of the oscillator. Thus, our model predicts control at the level of translation can be used to redesign such networks, for improved tunability, while at the same time making the network robust to replication “noise” and the effects of the host cell cycle. Thus, our model predicts experimentally testable principles to redesign a potentially more robust oscillatory genetic network.

We consider a mixture of active solute molecules in a suspension of passive solvent particles comprising a thermal bath. The solute molecules are considered to be extended objects with two chemically distinct heads, one head of which having chemical affinity towards the solvent particles. The coupled Langevin equations for the solvent particles along with the equations governing the dynamics of active molecules are numerically simulated to show how the active molecules self-assemble to form clusters which remain in dynamic equilibrium with the free solute molecules. We observe an interesting crossover at an intermediate time in the variation of the order parameter with time when the temperature of the bath is changed signifying the differential behavior of clusterization below and above the crossover time associated with a transition between a thermodynamic and a quasithermodynamic regime. Enthalpy-entropy compensation in the formation of clusters below the crossover is demonstrated.

This paper studies the process of fluid injection driven fractures in granular packs where particles are held together by external confining stresses and weak intergrain cohesion. We investigate the process of fracture formations in soft sand confined into a radial Hele-Shaw cell. Two main regimes are well known for fluid injection in soft sand. For low fluid injection pressures it behaves as a solid porous material while for high enough injection pressures grain rearrangement takes place. Grain rearrangements lead to the formation of fluid channels or “fractures,” the structure and geometry of which depend on the material and fluid properties. Due to macroscopic grain displacements and the predominant role of dissipative frictional forces in granular system dynamics, these materials do not behave as conventional brittle, linear elastic materials and the transition between these two regimes cannot usually be described using poroelastic models. In this work we investigate the change in the minimum fluid pressure required to start grain mobilization as a function of the confining stresses applied to the system using a spatially resolved computational fluid dynamics–discrete element method numerical model. We show that this change is proportional to the applied stress when the confining stresses can be regarded as uniformly distributed among the particles in the system. A preliminary analytical expression for this change is presented.

It will be shown that for a solution of salt dissolved in water in contact with a metallic or dielectric wall, the concentration of salt ions (both positive and negative) near the wall can be large enough to exceed the salt's solubility limit, as a result of electrical image charge forces. In addition, since the dielectric constant of water increases from 2.1 at the wall to 81 at about 1 nm from a solid wall, there will be an attractive image potential near the plane on which this increase of the dielectric constant occurs. Such large ion concentrations could possibly be used in water desalination.