Deterioration in dynamical activities may come up naturally or due to environmental influences in a massive portion of biological and physical systems. Such dynamical degradation may have outright effect on the substantive network performance. This requires us to provide some proper prescriptions to overcome undesired circumstances. In this paper, we present a scheme based on external feedback that can efficiently revive dynamism in damaged networks of active and inactive oscillators and thus enhance the network survivability. Both numerical and analytical investigations are performed in order to verify our claim. We also provide a comparative study on the effectiveness of this mechanism for feedbacks to the inactive group or to the active group only. Most importantly, resurrection of dynamical activity is realized even in time-delayed damaged networks, which are considered to be less persistent against deterioration in the form of inactivity in the oscillators. Furthermore, prominence in our approach is substantiated by providing evidence of enhanced network persistence in complex network topologies taking small-world and scale-free architectures, which makes the proposed remedy quite general. Besides the study in the network of Stuart-Landau oscillators, affirmative influence of external feedback has been justified in the network of chaotic Rössler systems as well.

The outer membrane protein channel $\mathit{Ec}\mathrm{ChiP}$, associated with a silent gene in $E$. coli, is a monomeric chitoporin. In a glucose-deficient environment, $E$. coli can express the ChiP gene to exploit chitin degradation products. Single-channel small ion current measurements, which reveal the dynamics of single sugar molecules trapped in channel, are used here to study the exotic transport of chitosugars by $E$. coli. Molecules escape from the channel on multiple timescales. Voltage-dependent trapping rates observed for charged chitosan molecules, as well as model calculations, indicate that the rapid escape processes are those in which the molecule escapes back to the side of the membrane from which it originated. The probability that a sugar molecule is translocated through the membrane is thus estimated from the current data and the dependence of this translocation probability on the length of the chitosugar molecule and the applied voltage analyzed. The described method for obtaining the translocation probability and related molecular translocation current is applicable to other transport channels.

We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.

To better understand the velocity field and flowing layer structure, we have performed a detailed discrete element method study of the flow of monodisperse particles in a partially filled three-dimensional cylindrical rotating tumblers. Similar to what occurs near the poles in spherical and conical tumblers, recirculation cells (secondary flows) develop near the flat endwalls of a cylindrical tumbler in which particles near the surface drift axially toward the endwall, while particles deeper in the flowing layer drift axially toward the midlength of the tumbler. Another recirculation cell with the opposite sense develops next to each endwall recirculation cell, extending to the midlength of the tumbler. For a long enough tumbler, each endwall cell is about one quarter of the tumbler diameter in length. Endwall cells are insensitive to tumbler length and relatively insensitive to rotation speed (so long as the flowing layer remains flat and continuously flowing) or fill level (from 25% to 50% full). However, for shorter tumblers (0.5 to 1.0 length/diameter aspect ratio) the endwall cell size does not change much, while center cells reduce their size and eventually disappear for the shortest tumblers. For longer tumblers (length/diameter aspect ratio larger than 2), a stagnation zone appears in between the central cells. These results provide insight into the mixing of monodisperse particles in rotating cylindrical tumblers as well as the frictional effects of the tumbler endwalls.

Wave phenomena in vibrofluidized dry and partially wet granular materials confined in a quasi-two-dimensional geometry are investigated with numerical simulations considering individual particles as hard spheres. Short-ranged cohesive interactions arising from the formation of liquid bridges between adjacent particles are modeled by changing the velocity-dependent coefficient of restitution. Such a change effectively suppresses the formation of surface waves, in agreement with previous experimental observations. The difference in pattern creation arises from the suppressed momentum transfer due to wetting and it can be quantitatively understood from an analysis of binary impacts.

In this paper, we study how the permeability of solid foam is modified by the presence of membranes that close partially or totally the cell windows connecting neighboring pores. The finite element method (FEM) simulations computing the Stokes problem are performed at both pore and macroscopic scales. For foam with fully interconnected pores, we obtain a robust power-law relationship between permeability and aperture size. This result is due to the local pressure drop mechanism through the aperture as described by Sampson for fluid flow through a circular orifice in a thin plate. Based on this local law, pore-network simulation of simple flow is used and is shown to reproduce FEM results. Then this low computational cost method is used to study in detail the effect of an open window fraction on the percolation properties of the foam pore space. The results clarify the effect of membranes on foam permeability. Finally, Kirkpatrick's model is adapted to provide analytical expressions that allow for our simulation results to be successfully reproduced.

In this study a single laser pulse spatially shaped into a ring is focused into a thin water layer, creating an annular cavitation bubble and cylindrical shock waves: an outer shock that diverges away from the excitation laser ring and an inner shock that focuses towards the center. A few nanoseconds after the converging shock reaches the focus and diverges away from the center, a single bubble nucleates at the center. The inner diverging shock then reaches the surface of the annular laser-induced bubble and reflects at the boundary, initiating nucleation of a tertiary bubble cloud. In the present experiments, we have performed time-resolved imaging of shock propagation and bubble wall motion. Our experimental observations of single-bubble cavitation and collapse and appearance of ring-shaped bubble clouds are consistent with our numerical simulations that solve a one-dimensional Euler equation in cylindrical coordinates. The numerical results agree qualitatively with the experimental observations of the appearance and growth of large bubble clouds at the smallest laser excitation rings. Our technique of shock-driven bubble cavitation opens interesting perspectives for the investigation of shock-induced single-bubble or multibubble cavitation phenomena in thin liquids.

The hybrid Vlasov-Maxwell system of equations is suitable to describe a magnetized plasma at scales on the order of or larger than proton kinetic scales. An exact stationary solution is presented by revisiting previous results with a uniform-density shear flow, directed either parallel or perpendicular to a uniform magnetic field, and by adapting the solution to the hybrid Vlasov-Maxwell model. A quantitative characterization of the equilibrium distribution function is provided by studying both analytically and numerically the temperature anisotropy and gyrotropy and the heat flux. In both cases, in the shear region, the velocity distribution significantly departs from local thermodynamical equilibrium. A comparison between the time behavior of the usual “fluidlike” equilibrium shifted Maxwellian and the exact stationary solutions is carried out by means of numerical simulations of the hybrid Vlasov-Maxwell equations. These hybrid equilibria can be employed as unperturbed states for numerous problems which involve sheared flows, such as the wave propagation in an inhomogeneous background and the onset of the Kelvin-Helmholtz instability.

While historically many quantum-mechanical simulations of molecular dynamics have relied on the Born-Oppenheimer approximation to separate electronic and nuclear behavior, recently a great deal of interest has arisen in quantum effects in nuclear dynamics as well. Due to the computational difficulty of solving the Schrödinger equation in full, these effects are often treated with approximate methods. In this paper, we present an algorithm to tackle these problems using an extension to the many-interacting-worlds approach to quantum mechanics. This technique uses a kernel function to rebuild the probability density, and therefore, in contrast with the approximation presented in the original paper, it can be naturally extended to $n$-dimensional systems. This opens up the possibility of performing quantum ground-state searches with steepest-descent methods, and it could potentially lead to real-time quantum molecular-dynamics simulations. The behavior of the algorithm is studied in different potentials and numbers of dimensions and compared both to the original approach and to exact Schrödinger equation solutions whenever possible.

We present a general framework for constructing trans-scale discrete Boltzmann models (DBMs) for high-speed compressible flows ranging from continuum to transition regime. This is achieved by designing a higher-order discrete equilibrium distribution function that satisfies additional nonhydrodynamic kinetic moments. To characterize the thermodynamic nonequilibrium (TNE) effects and estimate the condition under which the DBMs at various levels should be used, two measures are presented: (i) the relative TNE strength, describing the relative strength of the ($N+1$)th order TNE effects to the $N\mathrm{th}$ order one; (ii) the TNE discrepancy between DBM simulation and relevant theoretical analysis. Whether or not the higher-order TNE effects should be taken into account in the modeling and which level of DBM should be adopted is best described by the relative TNE intensity and/or the discrepancy rather than by the value of the Knudsen number. As a model example, a two-dimensional DBM with 26 discrete velocities at Burnett level is formulated, verified, and validated.

We introduce an alternative solution to Glauber multispin dynamics on random graphs. The solution is based on the recently introduced cavity master equation (CME), a time-closure turning the, in principle, exact dynamic cavity method into a practical method of analysis and of fast simulation. Running CME once is of comparable computational complexity as one Monte Carlo run on the same problem. We show that CME correctly models the ferromagnetic $p$-spin Glauber dynamics from high temperatures down to and below the spinoidal transition. We also show that CME allows an alternative exploration of the low-temperature spin-glass phase of the model.

A quantum error correcting protocol can be substantially improved by taking into account features of the physical noise process. We present an efficient decoder for the surface code which can account for general noise features, including coherences and correlations. We demonstrate that the decoder significantly outperforms the conventional matching algorithm on a variety of noise models, including non-Pauli noise and spatially correlated noise. The algorithm is based on an approximate calculation of the logical channel using a tensor-network description of the noisy state.

Tracking tracer particles in heterogeneous environments plays an important role in unraveling material properties. These heterogeneous structures are often static and depend on the sample realizations. Sample-to-sample fluctuations of such disorder realizations sometimes become considerably large. When we investigate the sample-to-sample fluctuations, fundamental averaging procedures are a thermal average for a single disorder realization and the disorder average for different disorder realizations. Here we report on non-self-averaging phenomena in quenched trap models with finite system sizes, where we consider the periodic and the reflecting boundary conditions. Sample-to-sample fluctuations of diffusivity greatly exceed trajectory-to-trajectory fluctuations of diffusivity in the corresponding annealed model. For a single disorder realization, the time-averaged mean square displacement and position-dependent observables converge to constants because of the existence of the equilibrium distribution. This is a manifestation of ergodicity. As a result, the time-averaged quantities depend neither on the initial condition nor on the thermal histories but depend crucially on the disorder realization.

In this paper we provide a comprehensive analysis of a structural model for the dynamics of prices of assets traded in a market which takes the form of an interacting generalization of the geometric Brownian motion model. It is formally equivalent to a model describing the stochastic dynamics of a system of analog neurons, which is expected to exhibit glassy properties and thus many metastable states in a large portion of its parameter space. We perform a generating functional analysis, introducing a slow driving of the dynamics to mimic the effect of slowly varying macroeconomic conditions. Distributions of asset returns over various time separations are evaluated analytically and are found to be fat-tailed in a manner broadly in line with empirical observations. Our model also allows us to identify collective, interaction-mediated properties of pricing distributions and it predicts pricing distributions which are significantly broader than their noninteracting counterparts, if interactions between prices in the model contain a ferromagnetic bias. Using simulations, we are able to substantiate one of the main hypotheses underlying the original modeling, viz., that the phenomenon of volatility clustering can be rationalized in terms of an interplay between the dynamics within metastable states and the dynamics of occasional transitions between them.

We have investigated the nonthermal effect of 10 GHz/22 dBm microwave radiation on hen egg-white lysozyme (HEWL) over different irradiation times, ranging from 2 min to 1 h. To ensure a control over the radiation parameters, a pair of microwave rectangular waveguides is used to irradiate the samples. Optical spectroscopic measurements, which include UV-visible absorption spectroscopy, Raman spectroscopy, and far UV CD spectroscopy, reveal the exposure of the buried tryptophan (Trp) residues of the native molecule between 15 and 30 min of radiation. The higher duration of the perturbation leads to a compact structure of the protein and Trp residues are buried again. Interestingly, we do not find any change in the secondary structure of the protein even for 1 h duration of radiation. The relaxation dynamics of the irradiated molecules also has been discussed. We have shown that the molecules relax to their native configuration in 7–8 h after the radiation field is turned off. The structural rearrangement over the above timescale has further been probed by a model calculation, based on a modified Langevin equation. Our coarse-grained simulation approach utilizes the mean of atomic positions and net atomic charge of each amino acid of native HEWL to mimic the initial conformation of the molecule. The modified positions of the residues are then calculated for the given force fields. The simulation results reveal the nonmonotonous change in overall size of the molecule, as observed experimentally. The radiation parameters used in our experiments are very similar to those of some of the electronic devices we often come across. Thus, we believe that the results of our studies on a simple protein structure may help us in understanding the effect of radiation on complex biological systems as well.

We revisit a classical problem of theoretical electrochemistry: the response of an electric double-layer capacitor (EDLC) subject to a small, suddenly applied external potential. We solve the Debye-Falkenhagen equation to obtain exact expressions for key EDLC quantities: the ionic charge density, the ionic current density, and the electric field. In contrast to earlier works, our results are not restricted to the long-time asymptotics of those quantities. The solutions take the form of infinite sums whose successive terms all decay exponentially with increasingly short relaxation times. Importantly, this set of relaxation times is the same among all aforementioned EDLC quantities; this property is demanded on physical grounds but not generally achieved within approximation schemes. The scaling of the largest relaxation timescale ${\tau }_1$, that determines the long-time decay, is in accordance with earlier results: Depending on the Debye length, ${\lambda }_D$, and the electrode separation, $2L$, it amounts to ${\tau }_1\simeq {\lambda }_{D}L/D$ for $L\gg {\lambda }_D$ and ${\tau }_1\simeq 4L^2/\left({\pi }^{2}D\right)$ for $L\ll {\lambda }_D$, respectively (with $D$ being the ionic diffusivity).

When a spatially uniform system that displays a liquid-crystal ordering on a two-dimensional surface is confined inside a rectangular box, the liquid crystal direction field develops inhomogeneous textures accompanied by topological defects because of the geometric frustrations. We show that the rich variety of nematic textures and defect patterns found in recent experimental and theoretical studies can be classified by the solutions of the rather fundamental, extended Onsager model. This is critically examined based on the determined free energies of different defect states, as functions of a few relevant, dimensionless geometric parameters.

Based on the Langevin equation of Brownian motion, we present a simple model that emulates a typical mode in incompressible magnetohydrodynamic turbulence, providing a demonstration of several key properties. The model equation is consistent with von Kármán decay law and Kolmogorov's symmetries. We primarily focus on the behavior of inertial range modes, although we also attempt to include some properties of the large-scale modes. Dissipation scales are not considered. Results from the model are compared with results from published direct numerical simulations.

We show that the direction of directed particle transport in a two-dimensional ac-driven lattice can be dynamically reversed by changing the structure of the lattice in the direction perpendicular to the applied driving force. These structural changes introduce dimensional coupling effects, the strength of which governs the timescale of the current reversals. The underlying mechanism is based on the fact that dimensional coupling allows the particles to explore regions of phase space which are inaccessible otherwise. The experimental realization for cold atoms in ac-driven optical lattices is discussed.