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Physical Review. E

Shahar Amitai, Raphael Blumenfeld
We identify two orthogonal sources of structural entropy in rattler-free granular systems: affine, involving structural changes that only deform the contact network, and topological, corresponding to different topologies of the contact network. We show that a recently developed connectivity-based granular statistical mechanics separates the two naturally by identifying the structural degrees of freedom with spanning trees on the graph of the contact network. We extend the connectivity-based formalism to include constraints on, and correlations between, degrees of freedom as interactions between branches of the spanning tree...
May 2017: Physical Review. E
Daniel Vågberg, Peter Olsson, S Teitel
We report on numerical simulations of simple models of athermal, bidisperse, soft-core, massive disks in two dimensions, as a function of packing fraction ϕ, inelasticity of collisions as measured by a parameter Q, and applied uniform shear strain rate γ[over ̇]. Our particles have contact interactions consisting of normally directed elastic repulsion and viscous dissipation, as well as tangentially directed viscous dissipation, but no interparticle Coulombic friction. Mapping the phase diagram in the (ϕ,Q) plane for small γ[over ̇], we find a sharp first-order rheological phase transition from a region with Bagnoldian rheology to a region with Newtonian rheology, and show that the system is always Newtonian at jamming...
May 2017: Physical Review. E
Abdallah Daddi-Moussa-Ider, Maciej Lisicki, Stephan Gekle
In this paper, we derive analytical expressions for the leading-order hydrodynamic mobility of a small solid particle undergoing motion tangential to a nearby large spherical capsule whose membrane possesses resistance toward shearing and bending. Together with the results obtained in the first part [Daddi-Moussa-Ider and Gekle, Phys. Rev. E 95, 013108 (2017)2470-004510.1103/PhysRevE.95.013108], where the axisymmetric motion perpendicular to the capsule membrane is considered, the solution of the general mobility problem is thus determined...
May 2017: Physical Review. E
František Slanina
We investigate adjacency matrices of bipartite graphs with a power-law degree distribution. Motivation for this study is twofold: first, vibrational states in granular matter and jammed sphere packings; second, graphs encoding social interaction, especially electronic commerce. We establish the position of the mobility edge and show that it strongly depends on the power in the degree distribution and on the ratio of the sizes of the two parts of the bipartite graph. At the jamming threshold, where the two parts have the same size, localization vanishes...
May 2017: Physical Review. E
Lipo Wang, Yongxiang Huang
The active interaction between the bacteria and fluid generates turbulent structures even at zero Reynolds number. The velocity of such a flow obtained experimentally has been quantitatively investigated based on streamline segment analysis. There is a clear transition at about 16 times the organism body length separating two different scale regimes, which may be attributed to the different influence of the viscous effect. Surprisingly the scaling extracted from the streamline segment indicates the existence of scale similarity even at the zero Reynolds number limit...
May 2017: Physical Review. E
Hessam Malmir, Muhammad Sahimi, M Reza Rahimi Tabar
Polydisperse packings of cubic particles arise in several important problems. Examples include zeolite microcubes that represent catalytic materials, fluidization of such microcubes in catalytic reactors, fabrication of new classes of porous materials with precise control of their morphology, and several others. We present the results of detailed and extensive simulation and microstructural characterization of packings of nonoverlapping polydisperse cubic particles. The packings are generated via a modified random sequential-addition algorithm...
May 2017: Physical Review. E
Zhen Dong, Jianjun Wang, Xin Zhou
Antifreeze proteins (AFPs) are the key biomolecules that protect many species from suffering the extreme conditions. Their unique properties of antifreezing provide the potential of a wide range of applications. Inspired by the present experimental approaches of creating an antifreeze surface by coating AFPs, here we present a two-dimensional random-field lattice Ising model to study the effect of AFPs on heterogeneous ice nucleation. The model shows that both the size and the free-energy effect of individual AFPs and their surface coverage dominate the antifreeze capacity of an AFP-coated surface...
May 2017: Physical Review. E
Kentaro Hara, Ido Barth, Erez Kaminski, I Y Dodin, N J Fisch
The energy of plasma waves can be moved up and down the spectrum using chirped modulations of plasma parameters, which can be driven by external fields. Depending on whether the wave spectrum is discrete (bounded plasma) or continuous (boundless plasma), this phenomenon is called ladder climbing (LC) or autoresonant acceleration of plasmons. It was first proposed by Barth et al. [Phys. Rev. Lett. 115, 075001 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.075001] based on a linear fluid model. In this paper, LC of electron plasma waves is investigated using fully nonlinear Vlasov-Poisson simulations of collisionless bounded plasma...
May 2017: Physical Review. E
Jason Hindes, Ira B Schwartz
We study the extinction of long-lived epidemics on finite complex networks induced by intrinsic noise. Applying analytical techniques to the stochastic susceptible-infected-susceptible model, we predict the distribution of large fluctuations, the most probable or optimal path through a network that leads to a disease-free state from an endemic state, and the average extinction time in general configurations. Our predictions agree with Monte Carlo simulations on several networks, including synthetic weighted and degree-distributed networks with degree correlations, and an empirical high school contact network...
May 2017: Physical Review. E
S M J Khadem, I M Sokolov
A continuous time random walk (CTRW) model with waiting times following the Lévy-stable distribution with exponential cutoff in equilibrium is a simple theoretical model giving rise to normal, yet non-Gaussian, diffusion. The distribution of the particles' displacements is explicitly time dependent and does not scale. Since fluorescent correlation spectroscopy (FCS) is often used to investigate diffusion processes, we discuss the influence of this lack of scaling on the possible outcome of the FCS measurements and calculate the FCS autocorrelation curves for such equilibrated CTRWs...
May 2017: Physical Review. E
Jianhua Zeng, Boris A Malomed
Recent studies have demonstrated that defocusing cubic nonlinearity with local strength growing from the center to the periphery faster than r^{D}, in space of dimension D with radial coordinate r, supports a vast variety of robust bright solitons. In the framework of the same model, but with a weaker spatial-growth rate ∼r^{α} with α≤D, we test here the possibility to create stable localized continuous waves (LCWs) in one-dimensional (1D) and 2D geometries, localized dark solitons (LDSs) in one dimension, and localized dark vortices (LDVs) in two dimensions, which are all realized as loosely confined states with a divergent norm...
May 2017: Physical Review. E
D J Tweten, P V Bayly, A E Carlsson
Clathrin-mediated endocytosis in yeast is driven by a protein patch containing close to 100 different types of proteins. Among the proteins are 5000-10000 copies of polymerized actin, and successful endocytosis requires growth of the actin network. Since it is not known exactly how actin network growth drives endocytosis, we calculate the spatial distribution of actin growth required to generate the force that drives the process. First, we establish the force distribution that must be supplied by actin growth, by combining membrane-bending profiles obtained via electron microscopy with established theories of membrane mechanics...
May 2017: Physical Review. E
Yuriy Shevchenko, Konstantin Nefedev, Yutaka Okabe
We use a Monte Carlo simulation to study the diluted antiferromagnetic Ising model on frustrated lattices including the pyrochlore lattice to show the dilution effects. Using the Wang-Landau algorithm, which directly calculates the energy density of states, we accurately calculate the entropy of the system. We discuss the nonmonotonic dilution concentration dependence of residual entropy for the antiferromagnetic Ising model on the pyrochlore lattice, and compare it to the generalized Pauling approximation proposed by Ke et al...
May 2017: Physical Review. E
Amihai Horesh, Matvey Morozov, Ofer Manor
We study the thinning and drainage of the intermediate liquid film between a bubble and a solid surface at close proximity in the presence of a surface acoustic wave (SAW) in the solid. Specifically, we employ the diffraction of light to observe a long air bubble confined in a solid rectangular channel filled with silicone oil. This setup, constituting a two-dimensional physical model of thin film drainage, allows us to analyze the influence of a SAW on the rate of thinning of the micron-thick liquid film separating the bubble and the solid substrate...
May 2017: Physical Review. E
Pratik Mullick, Parongama Sen
We consider the zero-temperature coarsening in the Ising model in two dimensions where the spins interact within the Moore neighborhood. The Hamiltonian is given by H=-∑_{〈i,j〉}S_{i}S_{j}-κ∑_{〈i,j^{'}〉}S_{i}S_{j^{'}}, where the two terms are for the first neighbors and second neighbors, respectively, and κ≥0. The freezing phenomenon, already noted in two dimensions for κ=0, is seen to be present for any κ. However, the frozen states show more complicated structure as κ is increased; e.g., local antiferromagnetic motifs can exist for κ>2...
May 2017: Physical Review. E
Rick Keesman, Jules Lamers
We perform a numerical study of the F model with domain-wall boundary conditions. Various exact results are known for this particular case of the six-vertex model, including closed expressions for the partition function for any system size as well as its asymptotics and leading finite-size corrections. To complement this picture we use a full lattice multicluster algorithm to study equilibrium properties of this model for systems of moderate size, up to L=512. We compare the energy to its exactly known large-L asymptotics...
May 2017: Physical Review. E
Simone Zuccher, Renzo L Ricca
By numerically solving the three-dimensional Gross-Pitaevskii equation we analyze the cascade process associated with the evolution and decay of a pair of linked vortex rings. The system decays through a series of reconnections to produce finally three unlinked, unfolded, almost planar vortex loops. Total helicity, initially zero, remains unchanged throughout the process. The gradual transfer from writhe (due to initial linking) to twist helicity, followed by a continuous relaxation of twist across scales during the evolution is shown to be a generic mechanism that consistently takes place on each individual component...
May 2017: Physical Review. E
Debarshi Basu, Joydip Nandi, A M Jayannavar, Rahul Marathe
Miniaturized heat engines constitute a fascinating field of current research. Many theoretical and experimental studies are being conducted that involve colloidal particles in harmonic traps as well as bacterial baths acting like thermal baths. These systems are micron-sized and are subjected to large thermal fluctuations. Hence, for these systems average thermodynamic quantities, such as work done, heat exchanged, and efficiency, lose meaning unless otherwise supported by their full probability distributions...
May 2017: Physical Review. E
Maxim Kuznetsov, Andrey Kolobov, Andrey Polezhaev
We investigate numerically the behavior of a two-component reaction-diffusion system of Fitzhugh-Nagumo type before the onset of subcritical Turing bifurcation in response to local rigid perturbation. In a large region of parameters, the initial perturbation evolves into a localized structure. In a part of that region, closer to the bifurcation line, this structure turns out to be unstable and covers all the available space over the course of time in a process of self-completion. Depending on the parameter values in two-dimensional (2D) space, this process happens either through generation and evolution of new peaks on oscillatory tails of the initial pattern, or through the elongation, deformation, and rupture of initial structure, leading to space-filling nonbranching snakelike patterns...
May 2017: Physical Review. E
C A Plata, A Prados
In kinetic theory, a system is usually described by its one-particle distribution function f(r,v,t), such that f(r,v,t)drdv is the fraction of particles with positions and velocities in the intervals (r,r+dr) and (v,v+dv), respectively. Therein, global stability and the possible existence of an associated Lyapunov function or H theorem are open problems when nonconservative interactions are present, as in granular fluids. Here, we address this issue in the framework of a lattice model for granularlike velocity fields...
May 2017: Physical Review. E
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