Physical Review E

Published by American Physical Society

Online ISSN: 1550-2376


Print ISSN: 1539-3755


Correlation effects in a simple small-world network
  • Article
  • Full-text available

April 2002


96 Reads


We analyze the effect of correlations in a simple model of a small-world network by obtaining exact analytical expressions for the distribution of shortest paths in the network. We enter correlations into a simple model with a distinguished site, by taking the random connections to this site from an Ising distribution. Our method shows how the transfer-matrix technique can be used in the new context of small-world networks.

Structure of a large social network

April 2004


104 Reads

We study a social network consisting of over 10(4) individuals, with a degree distribution exhibiting two power scaling regimes separated by a critical degree k(crit), and a power law relation between degree and local clustering. We introduce a growing random model based on a local interaction mechanism that reproduces the observed scaling features and their exponents. We suggest that the double power law originates from two very different kinds of networks that are simultaneously present in the human social network.

Critical structure factor in using systems.

September 2002


57 Reads

We perform a large-scale Monte Carlo simulation of the three-dimensional Ising model on simple cubic lattices of size L(3) with L=128 and 256. We determine the corresponding structure factor (Fourier transform of the two-point function) and compare it with several approximations and with experimental results. We also compute the turbidity as a function of the momentum of the incoming radiation, focusing in particular on the deviations from the Ornstein-Zernike expression of Puglielli and Ford.

Information flow and information production in a population system

July 2011


37 Reads

An approach aiming to quantify the dynamics of information within a population is developed based on the mapping of the processes underlying the system's evolution into a birth and death type stochastic process and the derivation of a balance equation for the information entropy. Information entropy flux and information entropy production are identified and their time-dependent properties, as well as their dependence on the parameters present in the problem, are analyzed. States of minimum information entropy production are shown to exist for appropriate parameter values. Furthermore, uncertainty and information production are transiently intensified when the population traverses the inflexion point stage of the logisticlike growth process.

Fifth-order corrected field descriptions of the Hermite-Gaussian (0,0) and (0,1) mode laser beam

January 2002


41 Reads

The work of Barton and Alexander on the fifth-order corrected field expressions for a Hermite-Gaussian (0,0) mode laser beam was extended to more general cases with adjustable parameters C1 and A1. The parametric dependence of the electron dynamics was studied by numerical methods. It was found that such dependence is mainly influenced by the beam width and comes from the second-order corrections in the expansions. Finally, the fifth-order corrected field equations for Hermite-Gaussian (0,1) mode were also detailed.

Invariance of conductivity relaxation under pressure and temperature variations at constant conductivity relaxation time in 0.4Ca(NO_{3})_{2}-0.6KNO_{3}

December 2014


26 Reads

The article reports the dependence of the conductivity relaxation on temperature T and pressure P in the canonical ionic glass former 0.4Ca(NO_{3})_{2}-0.6KNO_{3}(CKN). At constant conductivity relaxation time τ_{σ}, the entire conductivity relaxation spectra obtained at widely different combinations of T and P superpose almost perfectly, and thus it is the ion-ion interaction but not thermodynamics that determines the frequency dispersion. Moreover, on vitrifying CKN by either elevating P or decreasing T, changes of P or T dependence of τ_{σ} at the glass transition pressure P_{g} and temperature T_{g} are observed to occur at the same value, i.e., τ_{σ}(P_{g})=τ_{σ}(T_{g}), indicating that the relation between τ_{σ} and the structural relaxation time τ_{α} is also independent of P and T.

Low-frequency transient dynamic clusters in simulated amorphous Ni 0.5 Zr 0.5 around the glass temperature

November 2008


20 Reads

Molecular dynamics results are reported concerning cooperatively rearranging regions in simulated Ni0.5Zr0.5 melts down to 700 K . Emphasis is laid on discriminating between clusters of mobile atoms (CMA) from low-frequency dynamics and the all-frequency case, where the former characterize fluctuations and relaxations on the scale of the late beta regime and alpha decay, while the latter include, in addition, reversible high-frequency vibrations. Separation of the low-frequency part of the dynamics is carried out by low-pass filtering, exploiting the separation of time scales below the critical temperature T{c} of the mode-coupling theory. With increasing temperature, the low-frequency and all-frequency dynamics merge in the range of T{c} when the separation of time scales disappears. In the low-frequency CMA, the average size of correlated clusters of connected atoms turns out to be nearly one order of magnitude larger than in the all-frequency CMA. The low-frequency CMA appear as local clusters propagating extremely slowly in space with characteristic time scale of mus at 700 K , the scale of the onset of alpha decay.

FIG. 1. Measured magnetic field incident laser intensity as determined from harmonic polarimetry. ͑ ᭝ ͒ : second harmonic; ͑ b ͒ : third harmonic; ͑ ᮀ ͒ : fourth harmonic; ͑ ࡗ ͒ : fifth harmonic; ͑ ᭿ ͒ : eleventh–thirteenth harmonics, open cross: peak magnetic field from PIC simulations ( OSIRIS ) ; dashed line: ponderomotive scaling “fit” to simulation results. 
FIG. 2. ( Color ) Setup for VUV polarimetry. Inset is shown as an example of raw data with eighth–25th harmonic ( wavelength increases left to right ) separated into s and p polarization components ( up/down ) . 
FIG. 3. Calculated magnetic field from experiment at I =9 10 19 W/cm 2 : note that this displays the 3 scaling (solid line) which is characteristic of the Cotton-Mouton effect.
FIG. 4. ( Color ) Simulation of high intensity interaction using 2D particle in cell code, OSIRIS , showing hole-boring effects and regions of 
Laboratory measurements of 0.7 GG magnetic fields generated during high-intensity laser interactions with dense plasmas

September 2004


311 Reads

U Wagner



A Gopal




We report measurements of ultrahigh magnetic fields produced during intense ( approximately 10(20) Wcm(-2) micro m(2) ) laser interaction experiments with solids. We show that polarization measurements of high-order vuv laser harmonics generated during the interaction (up to the 15th order) suggest the existence of magnetic field strengths of 0.7+/-0.1 GG in the overdense plasma. Measurements using higher order harmonics indicate that denser regions of the plasma can be probed. This technique may be useful for measurements of multi- GG level magnetic fields which are predicted to occur at even higher intensities.

Advanced spectroscopic analysis of 0.8—1.0-MA Mo x pinches and the influence of plasma electron beams on L -shell spectra of Mo ions

March 2003


123 Reads

This paper presents a detailed investigation of the temporal, spatial, and spectroscopic properties of L-shell radiation from 0.8 to 1.0 MA Mo x pinches. Time-resolved measurements of x-ray radiation and both time-gated and time-integrated spectra and pinhole images are presented and analyzed. High-current x pinches are found to have complex spatial and temporal structures. A collisional-radiative kinetic model has been developed and used to interpret L-shell Mo spectra. The model includes the ground state of every ionization stage of Mo and detailed structure for the O-, F-, Ne-, Na-, and Mg-like ionization stages. Hot electron beams generated by current-carrying electrons in the x pinch are modeled by a non-Maxwellian electron distribution function and have significant influence on L-shell spectra. The results of 20 Mo x-pinch shots with wire diameters from 24 to 62 microm have been modeled. Overall, the modeled spectra fit the experimental spectra well and indicate for time-integrated spectra electron densities between 2 x 10(21) and 2 x 10(22) cm(-3), electron temperatures between 700 and 850 eV, and hot electron fractions between 3% and 7%. Time-gated spectra exhibit wide variations in temperature and density of plasma hot spots during the same discharge.

Coarsening effect on island-size scaling: The model case InAs/GaAs(001)

December 2012


77 Reads

The distributions of the size of islands and of the capture zones are discussed comparatively, both experimentally and numerically, for the case of a sudden nucleation process with and without coarsening. The experiments were performed by growing InAs islands on GaAs(001) and the coarsening was altered by varying the temperature. In the two-dimensional kinetic Monte Carlo simulations a single-species diffusing adatom was taken into account, and the coarsening was altered in this case by modifying the binding energy between adatoms and islands. The results show that size and capture zone distributions overlap only when coarsening can be disregarded.

FIG. 1: Snapshot of a Si(001) surface at T = 580 K. Open squares represent the initial positions, solid circles the positions after 10 6 MCS. Dashed lines indicate anti-phase domains walls.
FIG. 5: 
Hybrid Monte Carlo-molecular dynamics algorithm for the study of islands and step edges on semiconductor surfaces: Application to Si/Si(001)

October 2004


141 Reads

A classical, hybrid Monte Carlo-molecular dynamic (MC-MD) algorithm is introduced for the study of phenomena like two-dimensional (2D) island stability or step-edge evolution on semiconductor surfaces. This method presents the advantages of working off lattice and utilizing bulk-fitted potentials. It is based on the introduction of collective moves, such as dimer jumps, in the MC algorithm. MD-driven local relaxations are considered as trial moves for the MC. The algorithm is applied to the analysis of 2D Si islands on Si(001). Results on early stages of island formation, island stability versus temperature and system size, and step-edge evolution are presented. In all cases good qualitative agreement with experimental results is found.

UW/PT-01-07 Monte Carlo simulation of O(2) φ 4 field theory in three dimensions

December 2001


179 Reads

Using standard numerical Monte Carlo lattice methods, we study non-universal properties of the phase transition of three-dimensional straight phi(4) theory of a two-component real field phi=(phi(1),phi(2)) with O(2) symmetry. Specifically, we extract the renormalized values of <phi(2)>/u and r/u(2) at the phase transition, where the continuum action of the theory is integral d(3)x[1/2/inverted Delta phi/(2) + 1 2r phi(2)+(u/4!)phi(4)]. These values have applications to calculating the phase-transition temperature of dilute or weakly interacting Bose gases (both relativistic and nonrelativistic). In passing, we also provide perturbative calculations of various O(a) lattice-spacing errors in three-dimensional O(N) scalar field theory, where a is the lattice spacing.

Retraction: Geometric Ginzburg-Landau theory for faceted crystals in one dimension: From coarsening to chaos through a driving force [Phys. Rev. E 79 , 011115 (2009)]

February 2009


28 Reads

We consider the dynamic behavior in driven phase transitions dominated either by attachment-detachment or by surface diffusion mass transport mechanisms. As the driving force increases, we numerically demonstrate for both cases that the spatiotemporal faceted structure of the surface undergoes a sequential transition from slow coarsening turning to accelerated coarsening followed by fixed length scale structures before finally becoming spatiotemporally chaotic. For the attachment-detachment dominated phase transition problem we compare in the accelerated coarsening regime the simulation results with an intrinsic dynamical system governing the leading-order piecewise-affine dynamic surface (PADS), which can be obtained through a matched asymptotic analysis. The PADS predicts the numerically observed coarsening law for the growth in time of the characteristic morphological length scale L_{M} . In particular we determine the prefactor of the scaling law which allows for quantitative predictions necessary for any use of the theory in preparing patterned surfaces through modifications of the driving force.

FIG. 7. Fractal dimension of the aggregates of DPPC liposomes at different concentration of La 3+ calculated by scattering intensity 
FIG. 9. TEM photograph of DPPC liposomes in the presence of 0.2 M of La 3+ . RCLA clusters with closed and compact structures. 
FIG. 11. Variation of the number of liposomes aggregated with the concentration of La 3+ ions. The insets represent the secondary 
Erratum: Aggregation of liposomes in presence of La3+: A study of the fractal dimension [Phys. Rev. E 76, 011408 (2007)]

July 2007


102 Reads

A study of the fractal dimension of the aggregation of three different types of large unilamellar vesicles, formed by egg yolk phosphatidylcholine (EYPC), dimyristoyl-phosphocholine (DMPC), and dipalmitoyl-phosphocholine (DPPC), in the presence of La3+, is presented. Aggregate liposome fractal dimensions were calculated by two methods, aggregation kinetics, using the approaches diffusion-limited cluster aggregation (DLCA) and reaction-limited cluster aggregation (RLCA) and angle-scattering light dispersion. Electrophoretic measurements show a similar variation of the zeta potential (zeta potential) for EYPC and DPPC, with a small increase of initial positive values. However, the zeta potential of DMPC changes from a initial negative value to near zero with increasing La3+ concentration. The evolution of the aggregate sizes was followed by light scattering. DPPC and DMPC show a RLCA regimen growth at low La3+ concentrations and a DLCA regimen at higher concentrations. In the case of EYPC, the final size of aggregation strongly depends on La3+ concentration. The calculated fractal dimension is in the range 1.8 to 2.1.

Dynamics of a bouncing ball in human performance. Phys Rev E 63:011902-1-011902-8

February 2001


321 Reads

On the basis of a modified bouncing-ball model, we investigated whether human movements utilize principles of dynamic stability in their performance of a similar movement task. Stability analyses of the model provided predictions about conditions indicative of a dynamically stable period-one regime. In a series of experiments, human subjects bounced a ball rhythmically on a racket and displayed these conditions supporting that they attuned to and exploited the dynamic stability properties of the task.

Erratum: Long-range correlations in the electric signals that precede rupture [Phys. Rev. E 66 , 011902 (2002)]

August 2002


114 Reads

The Smoluchowski-Chapman-Kolmogorov functional equation is applied to the electric signals that precede rupture. The results suggest a non-Markovian character of the analyzed data. The rescaled range Hurst and detrended fluctuation analyses, as well as that related with the "mean distance a walker spanned," lead to power-law exponents, which are consistent with the existence of long-range correlations. A "universality" in the power spectrum characteristics of these signals emerges, if an analysis is made (not in the conventional time frame, but) in the "natural" time domain. Within this frame, it seems that certain power spectrum characteristics of ion current fluctuations in membrane channels distinguish them from the electric signals preceding rupture. The latter exhibit a behavior compatible with that expected from a model based on the random field Ising Hamiltonian at the critical point.

Erratum: Opening of nucleic-acid double strands by helicases: Active versus passive opening [Phys. Rev. E 71, 011904 (2005)]

February 2005


21 Reads

Helicase proteins move along double-stranded nucleic-acid molecules and unwind the double helix. This paper presents a theoretical study of the coupling between helicase translocation and duplex unwinding. Two different cases-active and passive opening-are usually distinguished. In active opening, the helicase directly destabilizes the double-stranded nucleic acid (dsNA) to promote opening. Passive opening implies that the helicase binds ssNA available when a thermal fluctuation partially opens the dsNA. We formulate a discrete model for helicase motion. An interaction potential describes how the helicase affects duplex unwinding when near a junction between single-stranded and double-stranded NA. Different choices of the potential correspond to the cases of active and passive opening. An optimal choice of interaction potential leads to a helicase which can unwind NA as rapidly as it translocates on single strands.

FIG. 6: Dynamic range as a function of the system size L for p = q = 1. Lines are just guides to the eye. 
FIG. 8: Experimental response curves (normalized firing rate vs. light intensity) of retinal on-center ganglion cells in linearlog (main plot) and log-log (inset) scales (data extracted from Fig. 6 of Ref. [4]). Filled (open) circles are for WT (Cx36KO) mice, solid (dashed) lines show the results of the pair approximation, thus L → ∞, with p = q = 1 (p = q = 0). Upper curves are for n = 10, lower curves are for n = 3. The dot-dashed line corresponds to simulations with n = 10, p = q = 1 and L = 20. 
Furtado, L. S. & Copelli, M. Response of electrically coupled spiking neurons: a cellular automaton approach. Phys. Rev. E 73, 011907

February 2006


82 Reads

Experimental data suggest that some classes of spiking neurons in the first layers of sensory systems are electrically coupled via gap junctions or ephaptic interactions. When the electrical coupling is removed, the response function (firing rate vs. stimulus intensity) of the uncoupled neurons typically shows a decrease in dynamic range and sensitivity. In order to assess the effect of electrical coupling in the sensory periphery, we calculate the response to a Poisson stimulus of a chain of excitable neurons modeled by n-state Greenberg-Hastings cellular automata in two approximation levels. The single-site mean field approximation is shown to give poor results, failing to predict the absorbing state of the lattice, while the results for the pair approximation are in good agreement with computer simulations in the whole stimulus range. In particular, the dynamic range is substantially enlarged due to the propagation of excitable waves, which suggests a functional role for lateral electrical coupling. For probabilistic spike propagation the Hill exponent of the response function is alpha=1, while for deterministic spike propagation we obtain alpha=1/2, which is close to the experimental values of the psychophysical Stevens exponents for odor and light intensities. Our calculations are in qualitative agreement with experimental response functions of ganglion cells in the mammalian retina.

Erratum: Disordered asymmetric simple exclusion process: Mean-field treatment [Phys. Rev. E 70 , 016108 (2004)]

February 2004


29 Reads

We provide two complementary approaches to the treatment of disorder in a fundamental nonequilibrium model, the asymmetric simple exclusion process. First, a mean-field steady-state mapping is generalized to the disordered case, where it provides a mapping of probability distributions and demonstrates how disorder results in a new flat regime in the steady-state current-density plot for periodic boundary conditions. This effect was earlier observed by Phys. Rev. E 58, 1911 (1998)] but we provide a treatment for more general distributions of disorder, including both numerical results and analytic expressions for the width 2 Delta(C) of the flat section. We then apply an argument based on moving shock fronts [Europhys. Lett. 48, 257 (1999)]] to show how this leads to an increase in the high-current region of the phase diagram for open boundary conditions. Second, we show how equivalent results can be obtained easily by taking the continuum limit of the problem and then using a disordered version of the well-known Cole-Hopf mapping to linearize the equation. Within this approach we show that adding disorder induces a localization transformation (verified by numerical scaling), and Delta(C) maps to an inverse localization length, helping to give a physical interpretation to the problem.

Bornholdt, S.: Statistical Mechanics of Community Detection. Physics Review E 74(1), 016110

August 2006


998 Reads

Starting from a general ansatz, we show how community detection can be interpreted as finding the ground state of an infinite range spin glass. Our approach applies to weighted and directed networks alike. It contains the ad hoc introduced quality function from [J. Reichardt and S. Bornholdt, Phys. Rev. Lett. 93, 218701 (2004)] and the modularity Q as defined by Newman and Girvan [Phys. Rev. E 69, 026113 (2004)] as special cases. The community structure of the network is interpreted as the spin configuration that minimizes the energy of the spin glass with the spin states being the community indices. We elucidate the properties of the ground state configuration to give a concise definition of communities as cohesive subgroups in networks that is adaptive to the specific class of network under study. Further, we show how hierarchies and overlap in the community structure can be detected. Computationally efficient local update rules for optimization procedures to find the ground state are given. We show how the ansatz may be used to discover the community around a given node without detecting all communities in the full network and we give benchmarks for the performance of this extension. Finally, we give expectation values for the modularity of random graphs, which can be used in the assessment of statistical significance of community structure.

Universality class of absorbing transitions with continuously varying critical exponents (vol E 69, art no 016122, 2004)

February 2004


206 Reads

The well-established universality classes of absorbing critical phenomena are directed percolation (DP) and directed Ising (DI) classes. Recently, the pair contact process with diffusion (PCPD) has been investigated extensively and claimed to exhibit a different type of critical phenomenon distinct from both DP and DI classes. Noticing that the PCPD possesses a long-term memory effect, we introduce a generalized version of the PCPD (GPCPD) with a parameter controlling the memory strength. The GPCPD connects the DP fixed point to the PCPD point continuously. Monte Carlo simulations strongly suggest that the GPCPD displays, to our knowledge, novel critical phenomena which are characterized by continuously varying critical exponents. The same critical behaviors are also observed in models where two species of particles are coupled cyclically. We present one possible scenario that the long-term memory may serve as a marginal perturbation to the ordinary DP fixed point.

Perc, M.: Spatial coherence resonance in excitable media. Phys. Rev. E 72, 016207

August 2005


51 Reads

We study the phenomenon of spatial coherence resonance in a two-dimensional model of excitable media with FitzHugh-Nagumo local dynamics. In particular, we show that there exists an optimal level of additive noise for which an inherent spatial scale of the excitable media is best pronounced. We argue that the observed phenomenon occurs due to the existence of a noise robust excursion time that is characteristic for the local dynamics whereby the diffusion constant, representing the rate of diffusive spread, determines the actual resonant spatial frequency. Additionally, biological implications of presented results in the field of neuroscience are outlined.

Pumping of water with AC electric fields applied to asymmetric pairs of microelectrods. Phys Rev E 63:016305

February 2001


147 Reads

Bulk fluid flow induced by an ac electric potential with a peak voltage below the ionization potential of water is described. The potential is applied to an ionic solution with a planar array of electrodes arranged in pairs so that one edge of a large electrode is close to an opposing narrow electrode. During half the cycle, the double layer on the surface of the electrodes charges as current flows between the electrodes. The electrodes charge in a nonuniform manner producing a gradient in potential parallel to the surface of the electrodes. This gradient drives the ions in the double layer across the surface of the electrode and this in turn drags the fluid across the electrode surface. The anisotropic nature of the pairs of electrodes is used to produce a net flow of fluid. The flow produced is approximately uniform at a distance from the electrodes that is greater than the periodicity of the electrode array. The potential and frequency dependence of this flow is reported and compared to a simple model. This method of producing fluid flow differs from electrical and thermal traveling-wave techniques as only a low voltage is required and the electrode construction is much simpler.

Publisher's Note: Patterns of sound radiation behind pointlike charged obstacles in plasma flows [Phys. Rev. E 78 , 016401 (2008)]

July 2008


33 Reads

The electrostatic potential and plasma density variations around a pointlike charged object in a plasma flow are studied. These objects can represent small charged dust particles, for instance. The radiation patterns can be interpreted as the result of sound waves being radiated by the obstacle. Two limits are considered: one where the electron-ion temperature ratio is large, Te>Ti , and one where Te/Ti approximately 1 . The former limit can be described by a simple model based on geometrical optics, while the latter requires a kinetic model in order to account for the effects of ion Landau damping. The results are illustrated by numerical simulation using a particle-in-cell code, where the electrons are treated as an isothermal massless fluid, giving a nonlinear Poisson equation. The analytical results are in good agreement with the numerical simulations.

Erratum: Generalization of super-transition-array methods to hot dense plasmas by using optimum independent particle reference systems [Phys. Rev. E. 65, 016403 (2002)]

February 2002


45 Reads

The computation of superconfiguration partition functions relies upon independent electron statistics, with electron-electron contributions included as an average first-order correction factor. The decomposition into a first-order correction and reference independent electron system has degrees of freedom not exploited by current methods. We present a derivation for the conventional choice of decomposition and propose a different method for obtaining an optimal decomposition for each superconfiguration. This constitutes an alternative procedure to recomputing self-consistent fields for the refinement of superconfiguration partition functions. Numerical results are presented and discussed.

Top-cited authors