In this paper, we deal with anisotropy in an idealized granular material made of a collection of frictional, elastic, contacting particles. We present a theoretical analysis for an aggregate of particles isotropically compressed and then sheared, in which two possible contacts laws between particles are considered: a linear contact law, where the contact stiffness is constant; and a nonlinear contact law, where the contact stiffness depends on the overlapping between particles. In the former case the anisotropy observed in the aggregate is associated with particle arrangement. In fact, although the aggregate is initially characterized by an isotropic network of contacts, during the loading, an anisotropic texture develops, which is measured by a fabric tensor. With a nonlinear contact law it is possible to develop anisotropy because contacting stiffnesses are different, depending on the orientation of the contact vectors with respect to the axis of the applied deformation. We find that before the peak load is reached, an aggregate made of particles with a linear contact law develops a much smaller anisotropy compared with that of an aggregate with a nonlinear law.

We study the elastic inversion of a right circular cone, in particular, the uniform shape of the narrow crease that divides its upright and inverted parts. Our methodology considers a cylindrical shell analogy for simplicity where the crease is the boundary layer deformation. Solution of its governing equation of deformation requires careful crafting of the underlying assumptions and boundary conditions in order to reveal an expression for the crease shape in closed form. We can then define the characteristic width of crease exactly, which is compared to a geometrically nonlinear, large displacement finite element analysis. This width is shown to be accurately predicted for shallow and steep cones, which imparts confidence to our original assumptions. Using the shape of crease, we compute the strain energy stored in the inverted cone, in order to derive an expression for the applied force of inversion by a simple energy method. Again, our predictions match finite element data very well. This study may complement other studies of creases traditionally formed in a less controlled manner, for example, during crumpling of lightweight sheets.

We perform computer simulations based on adhesive contact mechanics to demonstrate the clogging process of charged microparticles at the single-pore level. The effect of long-range Coulomb repulsion on clogging is characterized in terms of bulk permeability, the number of penetrating particles, and particle capture efficiency. Results indicate that the repulsion among particles delays or even totally prevents the formation of clogs. A clogging phase diagram, in the form of the driving pressure and a proposed charge parameter ${\kappa }_{\mathrm{q}}$, is constructed to quantify the clogging-nonclogging transition. In addition, a critical state, where the capture efficiency of particles decreases to its minimum, is identified as a clogging-nonclogging criterion for repulsive particles. The distributions of the local volume fraction show that the structure of clogs is mainly determined by short-range adhesion. With relatively strong adhesion, a loose clog will be formed and it is easier for particles to penetrate. Finally, a schematic representation of the clogging process, considering both long-range repulsion and adhesion, is proposed to show the relationship between the clogging results and the interparticle interactions.

The dynamics of granular medium in a liquid-filled horizontal cylinder with a time-varying rotation rate is experimentally studied. When the cylinder is purely rotated, the granular medium develops an annular layer near the cylindrical wall. The interface between fluid and sand is smooth and axisymmetric. The time variation of the rotation rate initiates the azimuthal oscillation of the liquid in the cylinder's frame of reference and provokes the onset of quasisteady relief in the form of regular dunes. The stability of the axisymmetric sand surface and dynamics of regular dunes are examined. It is found that the ripple formation is provoked by the quasisteady instability of the Stokes boundary layer. In the range of high Reynolds numbers, the ripple formation occurs at a constant critical Shields number ${\theta }_c\simeq 0.05$. The spatial period of the relief is not sensitive to the fluid viscosity and granule diameter; it is determined by the amplitude of oscillation and ratio between the oscillation frequency and mean rotation rate. Long-term experiments show that there are forward and backward azimuthal drifts of dunes. An initial analysis of the issues related to the dune migration is provided.

Interaction of relativistically intense axisymmetrically polarized (radially or azimuthally polarized) laser pulses (RIAPLP) with underdense plasma is shown experimentally and theoretically to be essentially different from the interaction of conventional Gaussian pulses. The difference is clearly observed in distinct spectra of the side-scattered laser light for the RIAPLP and Gaussian pulses, as well as in the appearance of a spatially localized strong side emission of second harmonic of the laser pulse in the case of RIAPLP. According to our analysis based on three-dimensional particle-in-cell simulations, this is a result of instability in the propagation of RIAPLP in uniform underdense plasma.

We study Chebyshev-polynomial expansion of the inverse localization length of Hermitian and non-Hermitian random chains as a function of energy. For Hermitian models, the expansion produces this energy-dependent function numerically in one run of the algorithm. This is in strong contrast to the standard transfer-matrix method, which produces the inverse localization length for a fixed energy in each run. For non-Hermitian models, as in the transfer-matrix method, our algorithm computes the inverse localization length for a fixed (complex) energy. We also find a formula of the Chebyshev-polynomial expansion of the density of states of non-Hermitian models. As explained in detail, our algorithm for non-Hermitian models may be the only available efficient algorithm for finding the density of states of models with interactions.

In the absence of a fermion sign problem, auxiliary-field (or determinantal) quantum Monte Carlo (DQMC) approaches have long been the numerical method of choice for unbiased, large-scale simulations of interacting many-fermion systems. More recently, the conceptual scope of this approach has been expanded by introducing ingenious schemes to compute entanglement entropies within its framework. On a practical level, these approaches, however, suffer from a variety of numerical instabilities that have largely impeded their applicability. Here we report on a number of algorithmic advances to overcome many of these numerical instabilities and significantly improve the calculation of entanglement measures in the zero-temperature projective DQMC approach, ultimately allowing us to reach similar system sizes as for the computation of conventional observables. We demonstrate the applicability of this improved DQMC approach by providing an entanglement perspective on the quantum phase transition from a magnetically ordered Mott insulator to a band insulator in the bilayer square lattice Hubbard model at half filling.

We present an exact mathematical framework able to describe site-percolation transitions in real multiplex networks. Specifically, we consider the average percolation diagram valid over an infinite number of random configurations where nodes are present in the system with given probability. The approach relies on the locally treelike ansatz, so that it is expected to accurately reproduce the true percolation diagram of sparse multiplex networks with negligible number of short loops. The performance of our theory is tested in social, biological, and transportation multiplex graphs. When compared against previously introduced methods, we observe improvements in the prediction of the percolation diagrams in all networks analyzed. Results from our method confirm previous claims about the robustness of real multiplex networks, in the sense that the average connectedness of the system does not exhibit any significant abrupt change as its individual components are randomly destroyed.

Endocytosis is among the most common transport mechanisms which cells employ to receive macromolecules, the so-called cargo, from its extra cellular environment. Clathrin-mediated endocytosis (CME), in particular, involves the cytoplasmic protein clathrin which induces formation and internalization of clathrin-coated membrane buds that contain extra-cellular cargo. Decades of experimental work have established that the morphology of the clathrin coat evolves with time and induces its curvature on the membrane bud; but energetics of the process remain unclear. Recent experiments by Avinoam et al. [Science 348, 1369 (2015)] reported that the area of the clathrin coat remains fixed while its curvature increases with time and also the clathrin molecules in the coat turn over rapidly. We show that these observations challenge existing models of coated membrane bud formation. We analyze their data to bring out certain features consistent with the underlying lattice structure of the coat. We hypothesize that membrane curvature inhibits clathrin deposition and propose a kinetic model that explains the area distribution of clathrin coats. We also show that their data on shape evolution of the coated membrane bud can be approximately understood from simple geometric considerations. However, the energetics of the coat formation which controls the kinetics of the process remains a puzzle.

The Landau-Ginzburg-Wilson paradigm is applied to model the low-temperature crystallographic $\mathrm{C}\alpha$ backbone structure of sperm whale myoglobin. The Glauber protocol is employed to simulate its response to an increase in ambient temperature. The myoglobin is found to unfold from its native state by a succession of $\alpha$-helical intermediates, fully in line with the observed folding and unfolding patterns in denaturation experiments. In particular, a molten globule intermediate is identified with experimentally correct attributes. A detailed, experimentally testable contact map is constructed to characterize the specifics of the unfolding pathway, including the formation of long-range interactions. The results reveal how the unfolding process of a protein is driven by the interplay between, and a successive melting of, its modular secondary structure components.

Artificial phoretic particles swim using self-generated gradients in chemical species (self-diffusiophoresis) or charges and currents (self-electrophoresis). These particles can be used to study the physics of collective motion in active matter and might have promising applications in bioengineering. In the case of self-diffusiophoresis, the classical physical model relies on a steady solution of the diffusion equation, from which chemical gradients, phoretic flows, and ultimately the swimming velocity may be derived. Motivated by disk-shaped particles in thin films and under confinement, we examine the extension to two dimensions. Because the two-dimensional diffusion equation lacks a steady state with the correct boundary conditions, Laplace transforms must be used to study the long-time behavior of the problem and determine the swimming velocity. For fixed chemical fluxes on the particle surface, we find that the swimming velocity ultimately always decays logarithmically in time. In the case of finite Péclet numbers, we solve the full advection-diffusion equation numerically and show that this decay can be avoided by the particle moving to regions of unconsumed reactant. Finite advection thus regularizes the two-dimensional phoretic problem.

Theory that predicts the phase behavior of interacting Yukawa spheres in a solution containing nonadsorbing polymer is presented. Our approach accounts for multiple overlap of depletion zones. It is found that additional Yukawa interactions beyond hard core interactions strongly affect the location and presence of coexistence regions and phase states. The theoretical phase diagrams are compared with Monte Carlo simulations. The agreement between the two approaches supports the validity of the theoretical approximations made and confirms that, by choosing the parameters of the interaction potentials, tuning of the binodals is possible. The critical end point characterizes the phase diagram topology. It is demonstrated how an additional Yukawa interaction shifts this point with respect to the hard sphere case. Provided a certain depletant-to-colloid size ratio for which a stable colloidal gas-liquid phase coexistence takes place for hard spheres, added direct interactions turn this into a metastable gas-liquid equilibrium. The opposite case, the induction of a stable gas-liquid coexistence where only fluid-solid was present for hard spheres, is also reported.

Using discrete element methods, the effects of the grain size distribution on the density and the shear strength of frictionless disk packings are analyzed. Specifically, two recent findings on the relationship between the system's grain size distribution and its rheology are revisited, and their validity is tested across a broader range of distributions than what has been used in previous studies. First, the effects of the distribution on the solid fraction are explored. It is found that the distribution that produces the densest packing is not the uniform distribution by volume fractions as suggested in a recent publication. In fact, the maximal packing fraction is obtained when the grading curve follows a power law with an exponent close to 0.5 as suggested by Fuller and Thompson in 1907 and 1919 [Trans Am. Soc. Civ. Eng. 59, 1 (1907) and A Treatise on Concrete, Plain and Reinforced (1919), respectively] while studying mixtures of cement and stone aggregates. Second, the effects of the distribution on the shear strength are analyzed. It is confirmed that these systems exhibit a small shear strength, even if composed of frictionless particles as has been shown recently in several works. It is also found that this shear strength is independent of the grain size distribution. This counterintuitive result has previously been shown for the uniform distribution by volume fractions. In this paper, it is shown that this observation keeps true for different shapes of the grain size distribution.

We investigate numerically the Princeton magnetorotational instability (MRI) experiment and the effect of conducting axial boundaries or endcaps. MRI is identified and found to reach a much higher saturation than for insulating endcaps. This is probably due to stronger driving of the base flow by the magnetically rather than viscously coupled boundaries. Although the computations are necessarily limited to lower Reynolds numbers ($\mathrm{Re}$) than their experimental counterparts, it appears that the saturation level becomes independent of $\mathrm{Re}$ when $\mathrm{Re}$ is sufficiently large, whereas it has been found previously to decrease roughly as ${\mathrm{Re}}^{-1/4}$ with insulating endcaps. The much higher saturation levels will allow for the positive detection of MRI beyond its theoretical and numerical predictions.

Molecular dynamic simulations are performed to reveal the long-time behavior of the velocity autocorrelation function (VAF) by utilizing the finite-size effect in a Lennard-Jones binary mixture. Whereas in normal liquids the classical positive $t^{-3/2}$ long-time tail is observed, we find in supercooled liquids a negative tail. It is strongly influenced by the transfer of the transverse current wave across the period boundary. The $t^{-5/2}$ decay of the negative long-time tail is confirmed in the spectrum of VAF. Modeling the long-time transverse current within a generalized Maxwell model, we reproduce the negative long-time tail of the VAF, but with a slower algebraic $t^{-2}$ decay.

A calorimetric measurement has recently been proposed as a promising technique to measure thermodynamic quantities in a dissipative superconducting qubit. These measurements rely on the fact that the system is projected into energy eigenstates whenever energy is exchanged with the environment. This requirement imposes a restriction on the class of systems that can be measured in this way. Here we extend the calorimetric protocol to the measurement of work in a driven quantum harmonic oscillator. We employ a scheme based on a two-level approximation that makes use of an experimentally accessible quantity and show how it relates to the work obtained through the standard two-measurement protocol. We find that the average work is well approximated in the underdamped regime for short driving times and, in the overdamped regime, for any driving time. However, this approximation fails for the variance and higher moments of work at finite temperatures. Furthermore, we show how to relate the work statistics obtained through this scheme to the work statistics given by the two-measurement protocol.

$k$-core percolation has served as a paradigmatic model of discontinuous percolation for a long time. Recently it was revealed that the order parameter of $k$-core percolation of random networks additionally exhibits critical behavior. Thus $k$-core percolation exhibits a hybrid phase transition. Unlike the critical behaviors of ordinary percolation that are well understood, those of hybrid percolation transitions have not been thoroughly understood yet. Here, we investigate the critical behavior of $k$-core percolation of Erdős-Rényi networks. We find numerically that the fluctuations of the order parameter and the mean avalanche size diverge in different ways. Thus, we classify the critical exponents into two types: those associated with the order parameter and those with finite avalanches. The conventional scaling relations hold within each set, however, these two critical exponents are coupled. Finally we discuss some universal features of the critical behaviors of $k$-core percolation and the cascade failure model on multiplex networks.

The behavior of a thin plasma target irradiated by two counterpropagating laser pulses of ultrahigh intensity is studied in the framework of one- and two-dimensional particle-in-cell simulations. It is found that above an intensity threshold, radiative trapping can focus electrons in the peaks of the electromagnetic field. At even higher intensities, the trapping effect cannot be maintained according to the increasing influence of electron-positron pair production on the laser-plasma dynamics.

R. Garcia-Millan et al. [Phys. Rev. E 91, 042122 (2015)] reported a universal finite-size scaling form of the survival probability in discrete time branching processes. In this comment, we generalize the argument to a wide range of continuous time branching processes. Owing to the continuity, the resulting differential (rather than difference) equations can be solved in closed form, rendering some approximations by R. Garcia-Millan et al. superfluous, although we work along similar lines. In the case of binary branching, our results are in fact exact. Demonstrating that discrete time and continuous time models have their leading order asymptotics in common, raises the question to what extent corrections are identical.

We investigate perturbative thermodynamic geometry of nonextensive ideal classical, Bose, and Fermi gases. We show that the intrinsic statistical interaction of nonextensive Bose (Fermi) gas is attractive (repulsive) similar to the extensive case but the value of thermodynamic curvature is changed by a nonextensive parameter. In contrary to the extensive ideal classical gas, the nonextensive one may be divided to two different regimes. According to the deviation parameter of the system to the nonextensive case, one can find a special value of fugacity, $z^{*}$, where the sign of thermodynamic curvature is changed. Therefore, we argue that the nonextensive parameter induces an attractive (repulsive) statistical interaction for $z<z^{*}$ ($z>z^{*}$) for an ideal classical gas. Also, according to the singular point of thermodynamic curvature, we consider the condensation of nonextensive Boson gas.