- Alternative boundary conditions for Monte Carlo simulations based on self-consistent correlations: Application to the two- and three-dimensional Ising models
Author(s): I. Etxebarria, C. Capillas, and L. Elcoro
An alternative to periodic boundary conditions is developed and tested in Monte Carlo simulations of the two- and three-dimensional Ising models. The boundary conditions are based on a mean-field approach that incorporates consistency constraints for the magnetization and correlations between neares...
[Phys. Rev. E 81, 036703] Published Fri Mar 12, 2010
- Retrieving the impulse response of the Earth due to random electromagnetic forcing
Author(s): Sharmin Shamsalsadati and Chester J. Weiss
A derivation is presented of Green’s function in an arbitrary, heterogeneous conductive medium subject to random, ambient, uncorrelated noise sources. The approach for extracting Green’s function is based on the correlation of time series of magnetic field components at two independent locations...
[Phys. Rev. E 81, 036603] Published Fri Mar 12, 2010
- Nonlinear wave propagation in strongly coupled dusty plasmas
Author(s): B. M. Veeresha, S. K. Tiwari, A. Sen, P. K. Kaw, and A. Das
The nonlinear propagation of low-frequency waves in a strongly coupled dusty plasma medium is studied theoretically in the framework of the phenomenological generalized hydrodynamic (GH) model. A set of simplified model nonlinear equations are derived from the original nonlinear integrodifferential ...
[Phys. Rev. E 81, 036407] Published Fri Mar 12, 2010
- Relativistic quantum corrections to laser wakefield acceleration
Author(s): Jun Zhu and Peiyong Ji
The influence of quantum effects on the interaction of intense laser fields with plasmas is investigated by using a hydrodynamic model based on the framework of the relativistic quantum theory. Starting from the covariant Wigner function and Dirac equation, the hydrodynamic equations for relativisti...
[Phys. Rev. E 81, 036406] Published Fri Mar 12, 2010
- Transitions in eigenvalue and wavefunction structure in (1+2) -body random matrix ensembles with spin
Author(s): Manan Vyas, V. K. B. Kota, and N. D. Chavda
Finite interacting Fermi systems with a mean-field and a chaos generating two-body interaction are modeled by one plus two-body embedded Gaussian orthogonal ensemble of random matrices with spin degree of freedom [called EGOE(1+2)-s ]. Numerical calculations are used to demonstrate that, as λ , the...
[Phys. Rev. E 81, 036212] Published Fri Mar 12, 2010
- Infrared spectroscopy study of structural changes in glass-forming salol
Author(s): J. Baran and N. A. Davydova
We report the investigation of glass-forming salol upon different courses of the temperature changes from liquid to glass state and back using FT-IR spectroscopy measurements in the wide spectral and temperature ranges. The formation of the ordered clusters in supercooled liquid salol has been obser...
[Phys. Rev. E 81, 031503] Published Fri Mar 12, 2010
- Directed d -mer diffusion describing the Kardar-Parisi-Zhang-type surface growth
Author(s): Géza Ódor, Bartosz Liedke, and Karl-Heinz Heinig
We show that d+1 -dimensional surface growth models can be mapped onto driven lattice gases of d -mers. The continuous surface growth corresponds to one dimensional drift of d -mers perpendicular to the (d−1) -dimensional “plane” spanned by the d -mers. This facilitates efficient bit-coded alg...
[Phys. Rev. E 81, 031112] Published Fri Mar 12, 2010
- 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)]
Author(s): Frank Haußer and Axel Voigt
[Phys. Rev. E 81, 039901] Published Thu Mar 11, 2010
- Dependence on pulse duration and foil thickness in high-contrast-laser proton acceleration
Author(s): A. Flacco, F. Sylla, M. Veltcheva, M. Carrié, R. Nuter, E. Lefebvre, D. Batani, and V. Malka
Experimental measurements of proton acceleration with high intensity and high-contrast short laser pulses have been carried out over an order of magnitude range in target thickness and laser pulse duration. The dependence of the maximum proton energy with these parameters is qualitatively supported ...
[Phys. Rev. E 81, 036405] Published Thu Mar 11, 2010
- Negative effective mass of wave-driven classical particles in dielectric media
Author(s): A. I. Zhmoginov, I. Y. Dodin, and N. J. Fisch
For a classical particle undergoing nonlinear interaction with a wave in dielectric medium, a perturbation theory is developed, showing that the particle motion can be described in terms of an effective parallel mass which can become negative. A relativistic particle interacting with a circularly po...
[Phys. Rev. E 81, 036404] Published Thu Mar 11, 2010
- Two-dimensional point singularity model of a low-Reynolds-number swimmer near a wall
Author(s): Darren G. Crowdy and Yizhar Or
This paper studies a simple two-dimensional model of a swimmer at low-Reynolds-number near a no-slip wall by utilizing methods of complex analysis. The swimmer is propelled by purely tangential surface deformations and is modeled by moving point singularities. The nonlinear dynamics of the swimmer i...
[Phys. Rev. E 81, 036313] Published Thu Mar 11, 2010
- Pumping by flapping in a viscoelastic fluid
Author(s): On Shun Pak, Thibaud Normand, and Eric Lauga
In a world without inertia, Purcell’s scallop theorem states that in a Newtonian fluid a time-reversible motion cannot produce any net force or net flow. Here we consider the extent to which the nonlinear rheological behavior of viscoelastic fluids can be exploited to break the constraints of the ...
[Phys. Rev. E 81, 036312] Published Thu Mar 11, 2010
- Spanning traceroutes over modular networks and general scaling degree distributions
Author(s): Alberto Lovison, Gianmarco Manzini, Amos Maritan, Mario Putti, and Andrea Rinaldo
We analyze the class of networks characterized by modular structure where a sequence of ℓ Erdös-Renyi random networks of size N⪢ℓ with random average degrees is joined by links whose structure must remain immaterial. We find that traceroutes spanning the entire macronetwork exhibit scaling de...
[Phys. Rev. E 81, 036105] Published Thu Mar 11, 2010
- Effective zero-thickness model for a conductive membrane driven by an electric field
Author(s): Falko Ziebert, Martin Z. Bazant, and David Lacoste
The behavior of a conductive membrane in a static (dc) electric field is investigated theoretically. An effective zero-thickness model is constructed based on a Robin-type boundary condition for the electric potential at the membrane, originally developed for electrochemical systems. Within such a f...
[Phys. Rev. E 81, 031912] Published Thu Mar 11, 2010
- Self-consistent approach for neutral community models with speciation
Author(s): Bart Haegeman and Rampal S. Etienne
Hubbell’s neutral model provides a rich theoretical framework to study ecological communities. By incorporating both ecological and evolutionary time scales, it allows us to investigate how communities are shaped by speciation processes. The speciation model in the basic neutral model is particula...
[Phys. Rev. E 81, 031911] Published Thu Mar 11, 2010
- Microtubule length distributions in the presence of protein-induced severing
Author(s): Simon H. Tindemans and Bela M. Mulder
Microtubules are highly regulated dynamic elements of the cytoskeleton of eukaryotic cells. One of the regulation mechanisms observed in living cells is the severing by the proteins katanin and spastin. We introduce a model for the dynamics of microtubules in the presence of randomly occurring sever...
[Phys. Rev. E 81, 031910] Published Thu Mar 11, 2010
- Growth kinetics of colloidal chains and labyrinths
Author(s): Mark D. Haw
Particles interacting by a combination of isotropic short-range attraction and long-range repulsion have been shown to form complex phases despite the apparent simplicity of the interparticle potential. Using computer simulations we study the behavior of two-dimensional systems of colloids with such...
[Phys. Rev. E 81, 031402] Published Thu Mar 11, 2010
- Return probabilities and hitting times of random walks on sparse Erdös-Rényi graphs
Author(s): O. C. Martin and P. Šulc
We consider random walks on random graphs, focusing on return probabilities and hitting times for sparse Erdös-Rényi graphs. Using the tree approach, which is expected to be exact in the large graph limit, we show how to solve for the distribution of these quantities and we find that these distrib...
[Phys. Rev. E 81, 031111] Published Thu Mar 11, 2010
- Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations
Author(s): Stephen D. Hicks and C. L. Henley
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamic...
[Phys. Rev. E 81, 030903] Published Thu Mar 11, 2010
- Optimizing transport efficiency on scale-free networks through assortative or dissortative topology
Author(s): Yu-hua Xue, Jian Wang, Liang Li, Daren He, and Bambi Hu
We find that transport on scale-free random networks depends strongly on degree-correlated network topologies whereas transport on Erdös-Rényi networks is insensitive to the degree correlation. An approach for the tuning of scale-free network transport efficiency through assortative or dissortativ...
[Phys. Rev. E 81, 037101] Published Wed Mar 10, 2010
- General solution of lattices for Cartesian lattice Bhatanagar-Gross-Krook models
Author(s): Xiaowen Shan (单肖文)
We give the general solutions of lattices, i.e., velocity sets and weights, for the lattice Bhatanagar-Gross-Krook (LBGK) models on two- and three-dimensional Cartesian grids. The solutions define the necessary and sufficient conditions so that the resulting LBGK model can accurately capture the dyn...
[Phys. Rev. E 81, 036702] Published Wed Mar 10, 2010
- Taming turbulence in the complex Ginzburg-Landau equation
Author(s): Meng Zhan, Wei Zou, and Xu Liu
Taming turbulence in the complex Ginzburg-Landau equation (CGLE) by using a global feedback control method and choosing traveling-wave solutions as our target state is investigated. The problem of optimal control for the smallest driving strength is studied by systematically comparing the stabilitie...
[Phys. Rev. E 81, 036211] Published Wed Mar 10, 2010
- Reconstructing the Hopfield network as an inverse Ising problem
Author(s): Haiping Huang
We test four fast mean-field-type algorithms on Hopfield networks as an inverse Ising problem. The equilibrium behavior of Hopfield networks is simulated through Glauber dynamics. In the low-temperature regime, the simulated annealing technique is adopted. Although performances of these network reco...
[Phys. Rev. E 81, 036104] Published Wed Mar 10, 2010
- Exact moment scaling from multiplicative noise
Author(s): Giacomo Bormetti and Danilo Delpini
For a general class of diffusion processes with multiplicative noise, describing a variety of physical as well as financial phenomena, mostly typical of complex systems, we obtain the analytical solution for the moments at all times. We allow for a nontrivial time dependence of the microscopic dynam...
[Phys. Rev. E 81, 032102] Published Wed Mar 10, 2010
- Dynamics of electroencephalogram entropy and pitfalls of scaling detection
Author(s): M. Ignaccolo, M. Latka, W. Jernajczyk, P. Grigolini, and B. J. West
In recent studies a number of research groups have determined that human electroencephalograms (EEG) have scaling properties. In particular, a crossover between two regions with different scaling exponents has been reported. Herein we study the time evolution of diffusion entropy to elucidate the sc...
[Phys. Rev. E 81, 031909] Published Wed Mar 10, 2010
- All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein
Author(s): Eric C. Dykeman and Reidun Twarock
Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymme...
[Phys. Rev. E 81, 031908] Published Wed Mar 10, 2010
- Nonlinear dynamics of capacitive charging and desalination by porous electrodes
Author(s): P. M. Biesheuvel and M. Z. Bazant
The rapid and efficient exchange of ions between porous electrodes and aqueous solutions is important in many applications, such as electrical energy storage by supercapacitors, water desalination and purification by capacitive deionization, and capacitive extraction of renewable energy from a salin...
[Phys. Rev. E 81, 031502] Published Wed Mar 10, 2010
- Gas-liquid critical parameters of asymmetric models of ionic fluids
Author(s): O. V. Patsahan and T. M. Patsahan
The effects of size and charge asymmetry on the gas-liquid critical parameters of a primitive model (PM) of ionic fluids are studied within the framework of the statistical field theory based on the collective variables method. Recently, this approach has enabled us to obtain the correct trends of t...
[Phys. Rev. E 81, 031110] Published Wed Mar 10, 2010
- Nonequilibrium stationary state of a truncated stochastic nonlinear Schrödinger equation: Formulation and mean-field approximation
Author(s): Philippe Mounaix, Pierre Collet, and Joel L. Lebowitz
We investigate the stationary state of a model system evolving according to a modified focusing truncated nonlinear Schrödinger equation used to describe the envelope of Langmuir waves in a plasma. We restrict the system to have a finite number of normal modes each of which is in contact with a Lan...
[Phys. Rev. E 81, 031109] Published Wed Mar 10, 2010
- Role of anisotropy for protein-protein encounter
Author(s): Jakob Schluttig, Christian B. Korn, and Ulrich S. Schwarz
Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a Brownian dynamics approach and extensive computer simulations, we...
[Phys. Rev. E 81, 030902] Published Wed Mar 10, 2010
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