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Physical Review. E

Romualdo Pastor-Satorras, Claudio Castellano
The generalized H(n) Hirsch index of order n has been recently introduced and shown to interpolate between the degree and the K-core centrality in networks. We provide a detailed analytic characterization of the properties of sets of nodes having the same H(n), within the annealed network approximation. The connection between the Hirsch indices and the degree is highlighted. Numerical tests in synthetic uncorrelated networks and real-world correlated ones validate the findings. We also test the use of the Hirsch index for the identification of influential spreaders in networks, finding that it is in general outperformed by the recently introduced nonbacktracking centrality...
February 2017: Physical Review. E
F P C Benetti, B Marcos
Systems of particles with long-range interactions present two important processes: first, the formation of out-of-equilibrium quasistationary states (QSS) and, second, the collisional relaxation towards Maxwell-Boltzmann equilibrium in a much longer time scale. In this paper, we study the collisional relaxation in the Hamiltonian mean-field model using the appropriate kinetic equations for a system of N particles at order 1/N: the Landau equation when collective effects are neglected and the Lenard-Balescu equation when they are taken into account...
February 2017: Physical Review. E
Michaël Fanuel, Carlos M Alaíz, Johan A K Suykens
Communities in directed networks have often been characterized as regions with a high density of links, or as sets of nodes with certain patterns of connection. Our approach for community detection combines the optimization of a quality function and a spectral clustering of a deformation of the combinatorial Laplacian, the so-called magnetic Laplacian. The eigenfunctions of the magnetic Laplacian, which we call magnetic eigenmaps, incorporate structural information. Hence, using the magnetic eigenmaps, dense communities including directed cycles can be revealed as well as "role" communities in networks with a running flow, usually discovered thanks to mixture models...
February 2017: Physical Review. E
Sandro M Reia, Sebastian Herrmann, José F Fontanari
The solution of today's complex problems requires the grouping of task forces whose members are usually connected remotely over long physical distances and different time zones. Hence, understanding the effects of imposed communication patterns (i.e., who can communicate with whom) on group performance is important. Here we use an agent-based model to explore the influence of the betweenness centrality of the nodes on the time the group requires to find the global maxima of NK-fitness landscapes. The agents cooperate by broadcasting messages, informing on their fitness to their neighbors, and use this information to copy the more successful agents in their neighborhood...
February 2017: Physical Review. E
Kerstin Demberg, Frederik Bernd Laun, Johannes Windschuh, Reiner Umathum, Peter Bachert, Tristan Anselm Kuder
Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging...
February 2017: Physical Review. E
Kaushik Das, Bijay Kumar Sah, Sarathi Kundu
A Langmuir monolayer can be considered as a two-dimensional (2D) sheet at higher surface pressure which structurally deform with mechanical compression depending upon the elastic nature of the monolayer. The deformed structures formed after a certain elastic limit are called collapsed structures. To explore monolayer collapses at lower surface pressure and to see the effect of ions on such monolayer collapses, out-of-plane structures and in-plane morphologies of stearic acid Langmuir monolayers have been studied both at lower (≈6...
February 2017: Physical Review. E
Patrick Figliozzi, Nishant Sule, Zijie Yan, Ying Bao, Stanislav Burov, Stephen K Gray, Stuart A Rice, Suriyanarayanan Vaikuntanathan, Norbert F Scherer
To date investigations of the dynamics of driven colloidal systems have focused on hydrodynamic interactions and often employ optical (laser) tweezers for manipulation. However, the optical fields that provide confinement and drive also result in electrodynamic interactions that are generally neglected. We address this issue with a detailed study of interparticle dynamics in an optical ring vortex trap using 150-nm diameter Ag nanoparticles. We term the resultant electrodynamically interacting nanoparticles a driven optical matter system...
February 2017: Physical Review. E
Pierre Meystre
No abstract text is available yet for this article.
February 2017: Physical Review. E
Róbert Juhász, Ferenc Iglói
We have studied the phase transition of the contact process near a multiple junction of M semi-infinite chains by Monte Carlo simulations. As opposed to the continuous transitions of the translationally invariant (M=2) and semi-infinite (M=1) system, the local order parameter is found to be discontinuous for M>2. Furthermore, the temporal correlation length diverges algebraically as the critical point is approached, but with different exponents on the two sides of the transition. In the active phase, the estimate is compatible with the bulk value, while in the inactive phase it exceeds the bulk value and increases with M...
February 2017: Physical Review. E
Subhadip Ghosh, Ignacio Pagonabarraga, Sudipto Muhuri
We study a two-filament driven lattice gas model with oppositely directed species of particles moving on two parallel filaments with filament-switching processes and particle inflow and outflow at filament ends. The filament-switching process is correlated with the occupation number of the adjacent site such that particles switch filaments with finite probability only when oppositely directed particles meet on the same filament. This model mimics some of the coarse-grained features observed in context of microtubule-(MT) based intracellular transport, wherein cellular cargo loaded and off-loaded at filament ends are transported on multiple parallel MT filaments and can switch between the parallel microtubule filaments...
February 2017: Physical Review. E
Wytse van Dijk, Trevor Vanderwoerd, Sjirk-Jan Prins
The generalized Crank-Nicolson method is employed to obtain numerical solutions of the two-dimensional time-dependent Schrödinger equation. An adapted alternating-direction implicit method is used, along with a high-order finite-difference scheme in space. Extra care has to be taken for the needed precision of the time development. The method permits a systematic study of the accuracy and efficiency in terms of powers of the spatial and temporal step sizes. To illustrate its utility the method is applied to several two-dimensional systems...
February 2017: Physical Review. E
Kengo Deguchi
Rayleigh's stability criterion describes the inviscid stability of rotating fluid flows. Despite the limitations of the criterion due to the assumptions used, it has been widely viewed as a general stability barrier in various rapidly rotating flows. However, contrary to previous belief, a linear instability is identified in Rayleigh-stable Taylor-Couette flow. The instability is found in cyclonic rapid rotation regime, for almost the entire range of the radius ratio of the cylinders.
February 2017: Physical Review. E
Takahiro Tanabe, Takashi Shimada, Nobuyasu Ito, Hiraku Nishimori
Using the discrete element method, we study the splash processes induced by the impact of a grain on a randomly packed bed. Good correspondence is obtained between our numerical results and the findings of previous experiments for the movement of ejected grains. Furthermore, the distributions of the ejection angle and ejection speed for individual grains vary depending on the relative timing at which the grains are ejected after the initial impact. Obvious differences are observed between the distributions of grains ejected during the earlier and later splash periods: the form of the vertical ejection-speed distribution varies from a power-law form to a lognormal form with time; this difference may determine grain trajectory after ejection...
February 2017: Physical Review. E
K Mouloudakis, I K Kominis
Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation so far constituting the theoretical foundation of spin chemistry violates fundamental bounds for the entropy of quantum systems, in particular the Ozawa bound. In contrast, a recently developed theory based on quantum measurements, quantum coherence measures, and quantum retrodiction, thus exemplifying the paradigm of quantum biology, satisfies the Ozawa bound as well as the Lanford-Robinson bound on information extraction...
February 2017: Physical Review. E
C Y Xie, J J Tao, Z L Sun, J Li
The Rayleigh-Taylor (RT) mixing induced by random interface disturbances between two incompressible viscous fluids is simulated numerically. The ensemble averaged spike velocity is found to be remarkably retarded when the random interface disturbances are superimposed with an optimized additional mode. The mode's wavenumber is selected to be large enough to avoid enhancing the dominance of long-wavelength modes, but not so large that its saturated spike and bubble velocities are too small to stimulate a growing effective density-gradient layer suppressing the long-wavelength modes...
February 2017: Physical Review. E
Flavio Stellino, Alberto Mazzoni, Marco Storace
The response of bursting neurons to fluctuating inputs is usually hard to predict, due to their strong nonlinearity. For the same reason, decoding the injected stimulus from the activity of a bursting neuron is generally difficult. In this paper we propose a method describing (for neuron models) a mechanism of phase coding relating the burst onsets with the phase profile of the input current. This relation suggests that burst onset may provide a way for postsynaptic neurons to track the input phase. Moreover, we define a method of phase decoding to solve the inverse problem and estimate the likelihood of burst onset given the input state...
February 2017: Physical Review. E
Laura de Sousa Oliveira, P Alex Greaney
The Green-Kubo method is a commonly used approach for predicting transport properties in a system from equilibrium molecular dynamics simulations. The approach is founded on the fluctuation dissipation theorem and relates the property of interest to the lifetime of fluctuations in its thermodynamic driving potential. For heat transport, the lattice thermal conductivity is related to the integral of the autocorrelation of the instantaneous heat flux. A principal source of error in these calculations is that the autocorrelation function requires a long averaging time to reduce remnant noise...
February 2017: Physical Review. E
E E Vogel, J F Valdes, W Lebrecht, A J Ramirez-Pastor, P Centres
The deposition of one-dimensional objects (such as polymers) on a one-dimensional lattice with the presence of impurities is studied in order to find saturation conditions in what is known as jamming. Over a critical concentration of k-mers (polymers of length k), no further depositions are possible. Five different nematic (directional) depositions are considered: baseline, irreversible, configurational, loose-packing, and close-packing. Correspondingly, five jamming functions are found, and their dependencies on the length of the lattice, L, the concentration of impurities, p=M/L (where M is the number of one-dimensional impurities), and the length of the k-mer (k) are established...
February 2017: Physical Review. E
D Wu, X T He, W Yu, S Fritzsche
A Monte Carlo approach to proton stopping in warm dense matter is implemented into an existing particle-in-cell code. This approach is based on multiple electron-electron, electron-ion, and ion-ion binary collision and accounts for both the free and the bound electrons in the plasmas. This approach enables one to calculate the stopping of particles in a more natural manner than existing theoretical treatment. In the low-temperature limit, when "all" electrons are bound to the nucleus, the stopping power coincides with the predictions from the Bethe-Bloch formula and is consistent with the data from the National Institute of Standard and Technology database...
February 2017: Physical Review. E
Somajit Dey, Jayashree Saha
Aggregation mesophases of self-assembling amphiphiles in water are highly important in the context of biology (biomembranes), therapy (liposomes), industry (polymer surfactants), and condensed-matter physics (lyotropic liquid crystals). Besides helping to increase fundamental understanding of collective molecular behavior, simulations of these lyotropic phases are pivotal to technological and medical developments such as smart drug carriers for gene therapy. Implicit-solvent, coarse-grained, low resolution modeling with a simple pair potential is the key to realizing the larger length and time scales associated with such mesoscopic phenomena during a computer simulation...
February 2017: Physical Review. E
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