Molecular dynamics (MD) simulations and quasielastic neutron scattering (QENS) experiments were conducted on two hydrated DNA dodecamers with distinct deformability: $5\prime \mathrm{CGCG}\underline{\mathrm{AATT}}\mathrm{CGCG}3\prime$ and $5\prime \mathrm{CGCG}\underline{\mathrm{TTAA}}\mathrm{CGCG}3\prime$. The former is known to be rigid and the latter to be flexible. The mean-square displacements of DNA dodecamers exhibit so-called dynamical transition around 200–240 K for both sequences. To investigate the DNA-sequence-dependent dynamics, the dynamics of DNA and hydration water above the transition temperature were examined using both MD simulations and QENS experiments. The fluctuation amplitude of the AATT central tetramer is smaller, and its relaxation time is longer, than that observed in TTAA, suggesting that the AT step is kinetically more stable than TA. The sequence-dependent local base pair step dynamics correlates with the kinetics of breaking the hydrogen bond between DNA and hydration water. The sequence-dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Together with these results, we conclude that DNA deformability is related to the local dynamics of the base pair steps, themselves coupled to hydration water in the minor groove.

Chimera states consisting of domains of coherently and incoherently oscillating identical oscillators with nonlocal coupling are studied. These states usually coexist with the fully synchronized state and have a small basin of attraction. We propose a nonlocal phase-coupled model in which chimera states develop from random initial conditions. Several classes of chimera states have been found: (a) stationary multicluster states with evenly distributed coherent clusters, (b) stationary multicluster states with unevenly distributed clusters, and (c) a single cluster state traveling with a constant speed across the system. Traveling coherent states are also identified. A self-consistent continuum description of these states is provided and their stability properties analyzed through a combination of linear stability analysis and numerical simulation.

We study the quantum critical behavior of the Dicke Hamiltonian with finite number of atoms and explore the signature of quantum chaos using measures like the ground-state fidelity and the Loschmidt echo and the time-averaged Loschmidt echo. We show that these quantities clearly point to the classically chaotic nature of the system in the superradiant (SR) phase. While the ground-state fidelity shows aperiodic oscillations as a function of the coupling strength, the echo shows aperiodic oscillations in time and decays rapidly when the system is in the SR phase. We clearly demonstrate how the time-averaged value of the echo already incorporates the information about the ground-state fidelity and stays much less than unity, indicating the classically chaotic nature of the model in the SR phase.

As an unusual type of anomalous diffusion behavior, (transient) superballistic transport is not well known but has been experimentally simulated recently. Quantum superballistic transport models to date are mainly based on connected sublattices which are constructed to have different properties. In this work, we show that both quantum and classical superballistic transport in the momentum space can occur in a simple periodically driven Hamiltonian system, namely, a relativistic kicked-rotor system with a nonzero mass term. The nonzero mass term essentially realizes a situation, now in the momentum space, in which two (momentum) sublattices with different dispersion relations (and hence different nature of on-site potential) are connected as a junction. It is further shown that the quantum and classical superballistic transport should occur under much different choices of the system parameters. The results are of interest to studies of anomalous transport, quantum and classical chaos, and the issue of quantum-classical correspondence.

We probe the onset and effect of contact changes in soft harmonic particle packings which are sheared quasistatically. We find that the first contact changes are the creation or breaking of contacts on a single particle. We characterize the critical strain, statistics of breaking versus making a contact, and ratio of shear modulus before and after such events, and explain their finite size scaling relations. For large systems at finite pressure, the critical strain vanishes but the ratio of shear modulus before and after a contact change approaches one: linear response remains relevant in large systems. For finite systems close to jamming the critical strain also vanishes, but here linear response already breaks down after a single contact change.

Bacteria are usually studied in free-swimming planktonic state or in sessile biofilm state. However, little is known about intermediate states where variability in the environmental conditions and/or energy supply to the flagellar propulsive system alter flagellar activity. In this Rapid Communication, we propose an idealized physical model to investigate the effects of flagellar activity on the hydrodynamic interactions among a population of microswimmers. We show that decreasing flagellar activity induces a hydrodynamically triggered transition in confined microswimmers from turbulentlike swimming to aggregation and clustering. These results suggest that the interplay between flagellar activity and hydrodynamic interactions provides a physical mechanism for coordinating collective behaviors in confined bacteria, with potentially profound implications on processes such as molecular diffusion and transport of oxygen and nutrients that mediate transitions in the bacteria physiological state.

We study the stability of toroidal droplets inside a yield stress material. Similar to toroidal droplets in a viscous liquid, the slenderness of the torus controls whether it breaks into spherical droplets or grows thicker towards its center to coalesce onto itself and form a single spherical droplet. However, unlike tori generated in a viscous liquid, the elasticity of the outer medium can prevent either or both of these instabilities; this depends on the slenderness of the torus. Interestingly, we find that the value of the tube radius needed to prevent breakup is always larger than the value of the radius of the handle to prevent growth. This reflects the different deformations experienced by the yield stress material in either process. A simple model balancing the surface tension stress, which drives the evolution of the torus, and the yield stress, which favors its stability, accounts for all of our observations.

The efficiency of the internal combustion engine might be enhanced by employing spinning gas. A gas spinning at near sonic velocities has an effectively higher heat capacity, which allows practical fuel cycles, which are far from the Carnot efficiency, to approach more closely the Carnot efficiency. A remarkable gain in fuel efficiency is shown to be theoretically possible for the Otto and Diesel cycles. The use of a flywheel, in principle, could produce even greater increases in efficiency.

We consider a model introduced by Baker et al. [Phys. Rev. E 88, 042113 (2013)] of a single lattice random walker moving on a domain of allowed sites, surrounded by blocked sites. The walker enlarges the allowed domain by eroding the boundary at its random encounters with blocked boundary sites: attempts to step onto blocked sites succeed with a given probability and convert these sites to allowed sites. The model interpolates continuously between the Pólya random walker on the one-dimensional lattice and a “blind” walker who attempts freely, but always aborts, moves to blocked sites. We obtain some exact results about the walker's location and the rate of erosion.

It is shown that a two-component percolation model on a simple cubic lattice can explain an experimentally observed behavior [Savage et al., Sens. Actuators B 79, 17 (2001); Sens. Actuators B 72, 239 (2001).], namely, that a network built up by a mixture of sintered nanocrystalline semiconducting $n$ and $p$ grains can exhibit selective behavior, i.e., respond with a resistance increase when exposed to a reducing gas A and with a resistance decrease in response to another reducing gas B. To this end, a simple model is developed, where the $n$ and $p$ grains are simulated by overlapping spheres, based on realistic assumptions about the gas reactions on the grain surfaces. The resistance is calculated by random walk simulations with $nn$, $pp$, and $np$ bonds between the grains, and the results are found in very good agreement with the experiments. Contrary to former assumptions, the $np$ bonds are crucial to obtain this accordance.

The activity of growing living bacteria was investigated using real-time and in situ rheology—in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus—strain COL and its isogenic cell wall autolysis mutant, RUSAL9—were considered in this work. For low bacteria density, strain COL forms small clusters, while the mutant, presenting deficient cell separation, forms irregular larger aggregates. In the early stages of growth, when subjected to a stationary shear, the viscosity of the cultures of both strains increases with the population of cells. As the bacteria reach the exponential phase of growth, the viscosity of the cultures of the two strains follows different and rich behaviors, with no counterpart in the optical density or in the population's colony-forming units measurements. While the viscosity of strain COL culture keeps increasing during the exponential phase and returns close to its initial value for the late phase of growth, where the population stabilizes, the viscosity of the mutant strain culture decreases steeply, still in the exponential phase, remains constant for some time, and increases again, reaching a constant plateau at a maximum value for the late phase of growth. These complex viscoelastic behaviors, which were observed to be shear-stress-dependent, are a consequence of two coupled effects: the cell density continuous increase and its changing interacting properties. The viscous and elastic moduli of strain COL culture, obtained with oscillatory shear, exhibit power-law behaviors whose exponents are dependent on the bacteria growth stage. The viscous and elastic moduli of the mutant culture have complex behaviors, emerging from the different relaxation times that are associated with the large molecules of the medium and the self-organized structures of bacteria. Nevertheless, these behaviors reflect the bacteria growth stage.

The exciton dynamics in a disordered extended dendrimer is investigated numerically. Because a homogeneous dendrimer exhibits few highly degenerate energy levels, a dynamical localization arises when the exciton is initially located on the periphery. However, it is shown that the disorder lifts the degeneracy and favors a delocalization-relocalization transition. Weak disorder enhances the delocalized nature of the exciton and improves any quantum communication, whereas strong disorder prevents the exciton from propagating in accordance with the well-known Anderson theory.

We revisit a rogue wave in a two-mode nonlinear fiber whose dynamics is described by two-component coupled nonlinear Schrödinger equations. The relative frequency between two modes can induce different rogue wave patterns transition. In particular, we find a four-petaled flower structure rogue wave can exist in the two-mode coupled system, which possesses an asymmetric spectrum distribution. Furthermore, spectrum analysis is performed on these different type rogue waves, and the spectrum relations between them are discussed. We demonstrate qualitatively that different modulation instability gain distribution can induce different rogue wave excitation patterns. These results would deepen our understanding of rogue wave dynamics in complex systems.

We present results from direct numerical simulations of the Boussinesq equations in the presence of rotation and/or stratification, both in the vertical direction. The runs are forced isotropically and randomly at small scales and have spatial resolutions of up to ${1024}^3$ grid points and Reynolds numbers of $\approx 1000$. We first show that solutions with negative energy flux and inverse cascades develop in rotating turbulence, whether or not stratification is present. However, the purely stratified case is characterized instead by an early-time, highly anisotropic transfer to large scales with almost zero net isotropic energy flux. This is consistent with previous studies that observed the development of vertically sheared horizontal winds, although only at substantially later times. However, and unlike previous works, when sufficient scale separation is allowed between the forcing scale and the domain size, the kinetic energy displays a perpendicular (horizontal) spectrum with power-law behavior compatible with $\sim k_{\perp }^{-5/3}$, including in the absence of rotation. In this latter purely stratified case, such a spectrum is the result of a direct cascade of the energy contained in the large-scale horizontal wind, as is evidenced by a strong positive flux of energy in the parallel direction at all scales including the largest resolved scales.

The seemingly regular and continuous motion of fluid displacement fronts in porous media at the macroscopic scale is propelled by numerous (largely invisible) pore-scale abrupt interfacial jumps and pressure bursts. Fluid fronts in porous media are characterized by sharp phase discontinuities and by rapid pore-scale dynamics that underlie their motion; both attributes challenge standard continuum theories of these flow processes. Moreover, details of pore-scale dynamics affect front morphology and subsequent phase entrapment behind a front and thereby shape key macroscopic transport properties of the unsaturated zone. The study presents a pore-throat network model that focuses on quantifying interfacial dynamics and interactions along fluid displacement fronts. The porous medium is represented by a lattice of connected pore throats capable of detaining menisci and giving rise to fluid-fluid interfacial jumps (the study focuses on flow rate controlled drainage). For each meniscus along the displacement front we formulate a local inertial, capillary, viscous, and hydrostatic force balance that is then solved simultaneously for the entire front. The model enables systematic evaluation of the role of inertia and boundary conditions. Results show that while displacement patterns are affected by inertial forces mainly by invasion of throats with higher capillary resistance, phase entrapment (residual saturation) is largely unaffected by inertia, limiting inertial effects on hydrological properties behind a front. Interfacial jump velocities are often an order of magnitude larger than mean front velocity, are strongly dependent on geometrical throat dimensions, and become less predictable (more scattered) when inertia is considered. Model simulations of the distributions of capillary pressure fluctuations and waiting times between invasion events follow an exponential distribution and are in good agreement with experimental results. The modeling approach provides insights into the rich pore-scale dynamics of displacement fronts; these insights not only improve the basic understanding of these ubiquitous processes, but could shed light on solute dispersion and colloids mobilization at fronts and the mechanical consequences of passing fronts.

A reconstruction methodology based on threshold energy based energy minimization (TA) and different-phase-neighbor (DPN)-based pixel swapping is presented. The TA method uses an energy threshold rather than probabilities as an acceptance criteria for annealing steps. The DPN-based pixel selection method gives priority to pixels which are segregated from clusters instead of random selection. An in-house solver has been developed to obtain two-dimensional reconstructions of heterogeneous two-phase mediums. Compared to conventional simulated annealing with random pixel swapping, the proposed method was found to achieve an optimal structure with up to an order of magnitude reduction in energy. When selecting a threshold tolerance value, the proposed method showed a 50% improvement in convergence time compared to conventional simulated annealing with random pixel swapping. The improved algorithm is used to study the effect of multiple correlation functions during the reconstruction. It was found that a combination of two-point correlation function and lineal path function for both phases results in most accurate reconstructions.

In the present work we show how the update rule of a diffusive cellular automaton with mutual exclusion can be exploited in off-lattice Monte Carlo simulations of hard spheres to obtain a synchronous Monte Carlo sampling that satisfies the detailed balance principle.

A system of interacting vortices is considered as an appropriate model for describing properties of type-II superconductors, and it has been shown lately to be deeply associated with nonextensive statistical mechanics. Herein we comment on a recent investigation of this model [M. Girotto, A. P. dos Santos, and Y. Levin, Phys. Rev. E 88, 032118 (2013)], which tried to contradict this assertion, based on a mean-field type of solution, compared with numerical-simulation data that correspond typically to a regime characterized by low concentrations of particles, as well as very high temperatures. It is shown that the physical situations analyzed differ significantly from those of a real superconducting phase. The analytical solution obtained from such a mean-field approximation shows a discrepancy with respect to the results of molecular-dynamics numerical simulations, which increases as the temperature is lowered towards the superconducting phase, as expected. We demonstrate that these results, when interpreted properly by means of an analytical solution within the framework of nonextensive statistical mechanics, present a remarkable agreement between molecular-dynamics simulations and theoretical results, for all temperatures, specially for those temperatures associated with the existence of type-II superconductivity.

We argue that contrary to recent suggestions, nonextensive statistical mechanics has no relevance for inhomogeneous systems of particles interacting by short-range potentials. We show that these systems are perfectly well described by the usual Boltzmann-Gibbs statistical mechanics.

Even though chiral nematic phases were the first liquid crystals experimentally observed more than a century ago, the origin of the thermodynamic stability of cholesteric states is still unclear. In this Rapid Communication we address the problem by means of a density functional theory for the equilibrium pitch of chiral particles. When applied to right-handed hard helices, our theory predicts an entropy-driven cholesteric phase, which can be either right or left handed, depending not only on the particle shape but also on the thermodynamic state. We explain the origin of the chiral ordering as an interplay between local nematic alignment and excluded-volume differences between left- and right-handed particle pairs.