Preview: Recent Articles in Phys. Rev. E
Recent Articles in Phys. Rev. E
Recent articles in Physical Review E
Published: 2016-10-21T16:19:23-04:00
Direct calculation of the critical Casimir force in a binary fluid
2016-10-21T10:00:00-04:00
Author(s): Francesco Puosi, David Lopes Cardozo, Sergio Ciliberto, and Peter C. W. Holdsworth
We show that critical Casimir effects can be accessed through direct simulation of a model binary fluid passing through the demixing transition. We work in the semi-grand-canonical ensemble, in slab geometry, in which the Casimir force appears as the excess of the generalized pressure, P_{⊥}−nμ. The…
[Phys. Rev. E 94, 040102(R)] Published Fri Oct 21, 2016
Liquid-liquid critical point in a simple analytical model of water
2016-10-21T10:00:00-04:00
Author(s): Tomaz Urbic
A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds…
[Phys. Rev. E 94, 042126] Published Fri Oct 21, 2016
Hamiltonian analogs of combustion engines: A systematic exception to adiabatic decoupling
2016-10-21T10:00:00-04:00
Author(s): Lukas Gilz, Eike Thesing, and James R. Anglin
Workhorse theories throughout all of physics derive effective Hamiltonians to describe slow time evolution, even though low-frequency modes are actually coupled to high-frequency modes. Such effective Hamiltonians are accurate because of adiabatic decoupling: the high-frequency modes “dress” the low…
[Phys. Rev. E 94, 042127] Published Fri Oct 21, 2016
Inverse Gaussian and its inverse process as the subordinators of fractional Brownian motion
2016-10-21T10:00:00-04:00
Author(s): A. Wyłomańska, A. Kumar, R. Połoczański, and P. Vellaisamy
In this paper we study the fractional Brownian motion (FBM) time changed by the inverse Gaussian (IG) process and its inverse, called the inverse to the inverse Gaussian (IIG) process. Some properties of the time-changed processes are similar to those of the classical FBM, such as long-range depende…
[Phys. Rev. E 94, 042128] Published Fri Oct 21, 2016
Stochastic Fokker-Planck equation in random environments
2016-10-21T10:00:00-04:00
Author(s): Paul C. Bressloff
We analyze the stochastic dynamics of a large population of noninteracting particles driven by a common environmental input in the form of an Ornstein-Uhlenbeck (OU) process. The density of particles evolves according to a stochastic Fokker-Planck (FP) equation with respect to different realizations…
[Phys. Rev. E 94, 042129] Published Fri Oct 21, 2016
Optimal inference strategies and their implications for the linear noise approximation
2016-10-21T10:00:00-04:00
Author(s): David Hartich and Udo Seifert
We study the information loss of a class of inference strategies that is solely based on time averaging. For an array of independent binary sensors (e.g., receptors, single electron transistors) measuring a weak random signal (e.g., ligand concentration, gate voltage) this information loss is up to …
[Phys. Rev. E 94, 042416] Published Fri Oct 21, 2016
Design of block-copolymer-based micelles for active and passive targeting
2016-10-21T10:00:00-04:00
Author(s): Jérôme G. J. L. Lebouille, Frans A. M. Leermakers, Martien A. Cohen Stuart, and Remco Tuinier
A self-consistent field study is presented on the design of active and passive targeting block-copolymeric micelles. These micelles form in water by self-assembly of triblock copolymers with a hydrophilic middle block and two hydrophobic outer blocks. A minority amount of diblock copolymers with the…
[Phys. Rev. E 94, 042503] Published Fri Oct 21, 2016
Bragg reflection band width and optical rotatory dispersion of cubic blue-phase liquid crystals
2016-10-21T10:00:00-04:00
Author(s): Hiroyuki Yoshida, Konkanok Anucha, Yasuhiro Ogawa, Yuto Kawata, Masanori Ozaki, Jun-ichi Fukuda, and Hirotsugu Kikuchi
The Bragg reflection band width and optical rotatory dispersion of liquid crystalline cholesteric blue phases (BPs) I and II are compared by numerical simulations. Attention is paid to the wavelength regions for which the reflection bands with lowest photon energies appear, i.e., the [110] direction…
[Phys. Rev. E 94, 042703] Published Fri Oct 21, 2016
Magnetically tunable selective reflection of light by heliconical cholesterics
2016-10-21T10:00:00-04:00
Author(s): S. M. Salili, J. Xiang, H. Wang, Q. Li, D. A. Paterson, J. M. D. Storey, C. T. Imrie, O. D. Lavrentovich, S. N. Sprunt, J. T. Gleeson, and A. Jákli
We present studies of chiral nematic liquid crystals composed of flexible dimer molecules subject to large dc magnetic fields between 0 and 31 T. We observe that these fields lead to selective reflection of light depending on temperature and magnetic field. The band of reflected wavelengths can be t…
[Phys. Rev. E 94, 042705] Published Fri Oct 21, 2016
Stability of thin liquid curtains
2016-10-21T10:00:00-04:00
Author(s): E. S. Benilov, R. Barros, and S. B. G. O'Brien
We investigate the stability of thin liquid curtains with respect to two-dimensional perturbations. The dynamics of perturbations with wavelengths exceeding (or comparable to) the curtain's thickness are examined using the lubrication approximation (or a kind of geometric optics). It is shown that, …
[Phys. Rev. E 94, 043110] Published Fri Oct 21, 2016
Improved dynamical scaling analysis using the kernel method for nonequilibrium relaxation
2016-10-21T10:00:00-04:00
Author(s): Yuki Echinaka and Yukiyasu Ozeki
The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results …
[Phys. Rev. E 94, 043312] Published Fri Oct 21, 2016
Revised Chapman-Enskog analysis for a class of forcing schemes in the lattice Boltzmann method
2016-10-21T10:00:00-04:00
Author(s): Q. Li, P. Zhou, and H. J. Yan
In the lattice Boltzmann (LB) method, the forcing scheme, which is used to incorporate an external or internal force into the LB equation, plays an important role. It determines whether the force of the system is correctly implemented in an LB model and affects the numerical accuracy. In this paper …
[Phys. Rev. E 94, 043313] Published Fri Oct 21, 2016
Equilibrium free-energy differences at different temperatures from a single set of nonequilibrium transitions
2016-10-20T10:00:00-04:00
Author(s): Puneet Kumar Patra and Baidurya Bhattacharya
Crook's fluctuation theorem (CFT) and Jarzynski equality (JE) are effective tools for obtaining free-energy difference ΔF(λ_{A}→λ_{B},T_{0}) through a set of finite-time protocol driven nonequilibrium transitions between two equilibrium states A and B [parametrized by the time-varying protocol λ(t)]…
[Phys. Rev. E 94, 040101(R)] Published Thu Oct 20, 2016
From network reliability to the Ising model: A parallel scheme for estimating the joint density of states
2016-10-20T10:00:00-04:00
Author(s): Yihui Ren, Stephen Eubank, and Madhurima Nath
Network reliability is the probability that a dynamical system composed of discrete elements interacting on a network will be found in a configuration that satisfies a particular property. We introduce a reliability property, Ising feasibility, for which the network reliability is the Ising model's …
[Phys. Rev. E 94, 042125] Published Thu Oct 20, 2016
Stochastic inference with spiking neurons in the high-conductance state
2016-10-20T10:00:00-04:00
Author(s): Mihai A. Petrovici, Johannes Bill, Ilja Bytschok, Johannes Schemmel, and Karlheinz Meier
The highly variable dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference but stand in apparent contrast to the deterministic response of neurons measured in vitro. Based on a propagation of the membrane autocorrelation acro…
[Phys. Rev. E 94, 042312] Published Thu Oct 20, 2016
Vibrational properties of quasi-two-dimensional colloidal glasses with varying interparticle attraction
2016-10-20T10:00:00-04:00
Author(s): Matthew D. Gratale, Xiaoguang Ma, Zoey S. Davidson, Tim Still, Piotr Habdas, and A. G. Yodh
We measure the vibrational modes and particle dynamics of quasi-two-dimensional colloidal glasses as a function of interparticle interaction strength. The interparticle attractions are controlled via a temperature-tunable depletion interaction. Specifically, the interparticle attraction energy is in…
[Phys. Rev. E 94, 042606] Published Thu Oct 20, 2016
Energy rectification in quantum graded spin chains: Analysis of the XXZ model
2016-10-19T10:00:00-04:00
Author(s): Lucas Schuab, Emmanuel Pereira, and Gabriel T. Landi
In this work, with focus on the energy-transport properties in quantum, low-dimensional, graded materials, we address the investigation of the energy (and spin) current in XXZ open chains with graded inner structures and driven out of equilibrium by magnetization pumping applied at the ends. We stud…
[Phys. Rev. E 94, 042122] Published Wed Oct 19, 2016
Comparing the influence of distinct kinds of temporal disorder in a low-dimensional absorbing transition model
2016-10-19T10:00:00-04:00
Author(s): C. M. D. Solano, M. M. de Oliveira, and C. E. Fiore
Recently it was stated that temporal disorder constitutes a relevant perturbation in absorbing phase transitions for all dimensions. However, its effect on systems other than the standard contact process (CP), its competition with other ingredients (e.g., particle diffusion), and other kinds of diso…
[Phys. Rev. E 94, 042123] Published Wed Oct 19, 2016
Grand-canonical condensate fluctuations in weakly interacting Bose-Einstein condensates of light
2016-10-19T10:00:00-04:00
Author(s): Christoph Weiss and Jacques Tempere
Grand-canonical fluctuations of Bose-Einstein condensates of light are accessible to state-of-the-art experiments [J. Schmitt et al., Phys. Rev. Lett. 112, 030401 (2014).]. We phenomenologically describe these fluctuations by using the grand-canonical ensemble for a weakly interacting Bose gas at t…
[Phys. Rev. E 94, 042124] Published Wed Oct 19, 2016
Yielding of glass under shear: A directed percolation transition precedes shear-band formation
2016-10-19T10:00:00-04:00
Author(s): Gaurav Prakash Shrivastav, Pinaki Chaudhuri, and Jürgen Horbach
Under external mechanical loading, glassy materials, ranging from soft matter systems to metallic alloys, often respond via formation of inhomogeneous flow patterns, during yielding. These inhomogeneities can be precursors to catastrophic failure, implying that a better understanding of their underl…
[Phys. Rev. E 94, 042605] Published Wed Oct 19, 2016
Chaos of energetic positron orbits in a dipole magnetic field and its potential application to a new injection scheme
2016-10-19T10:00:00-04:00
Author(s): H. Saitoh, Z. Yoshida, Y. Yano, M. Nishiura, Y. Kawazura, J. Horn-Stanja, and T. Sunn Pedersen
We study the behavior of high-energy positrons emitted from a radioactive source in a magnetospheric dipole field configuration. Because the conservation of the first and second adiabatic invariants is easily destroyed in a strongly inhomogeneous dipole field for high-energy charged particles, the p…
[Phys. Rev. E 94, 043203] Published Wed Oct 19, 2016
Solution to sign problems in models of interacting fermions and quantum spins
2016-10-19T10:00:00-04:00
Author(s): Emilie Huffman and Shailesh Chandrasekharan
We show that solutions to fermion sign problems that are found in the formulation where the path integral is expanded in powers of the interaction in continuous time can be extended to systems involving fermions interacting with dynamical quantum spins. While these sign problems seem unsolvable in t…
[Phys. Rev. E 94, 043311] Published Wed Oct 19, 2016
Effects of time-delayed feedback on the properties of self-sustained oscillators
2016-10-18T10:00:00-04:00
Author(s): S. Risau-Gusman
Most self-sustained oscillations in biological systems and in technical applications are based on a feedback loop, and it is usually important to know how they will react when an external oscillatory force is applied. Here we investigate the effects that the introduction of a time delay in the feedb…
[Phys. Rev. E 94, 042212] Published Tue Oct 18, 2016
Diversity of coupled oscillators can enhance their synchronization
2016-10-18T10:00:00-04:00
Author(s): Ghazal Montaseri and Michael Meyer-Hermann
The heterogeneity of coupled oscillators is important for the degree of their synchronization. According to the classical Kuramoto model, larger heterogeneity reduces synchronization. Here, we show that in a model for coupled pancreatic β-cells, higher diversity of the cells induces higher synchrony…
[Phys. Rev. E 94, 042213] Published Tue Oct 18, 2016
Randomness evaluation for an optically injected chaotic semiconductor laser by attractor reconstruction
2016-10-18T10:00:00-04:00
Author(s): Xiao-Zhou Li, Jun-Ping Zhuang, Song-Sui Li, Jian-Bo Gao, and Sze-Chun Chan
State-space reconstruction is investigated for evaluating the randomness generated by an optically injected semiconductor laser in chaos. The reconstruction of the attractor requires only the emission intensity time series, allowing both experimental and numerical evaluations with good qualitative a…
[Phys. Rev. E 94, 042214] Published Tue Oct 18, 2016
Oscillatory motion of a camphor grain in a one-dimensional finite region
2016-10-18T10:00:00-04:00
Author(s): Yuki Koyano, Tatsunari Sakurai, and Hiroyuki Kitahata
The motion of a self-propelled particle is affected by its surroundings, such as boundaries or external fields. In this paper, we investigated the bifurcation of the motion of a camphor grain, as a simple actual self-propelled system, confined in a one-dimensional finite region. A camphor grain exhi…
[Phys. Rev. E 94, 042215] Published Tue Oct 18, 2016
Parametric autoresonant excitation of the nonlinear Schrödinger equation
2016-10-18T10:00:00-04:00
Author(s): L. Friedland and A. G. Shagalov
Parametric excitation of autoresonant solutions of the nonlinear Schrodinger (NLS) equation by a chirped frequency traveling wave is discussed. Fully nonlinear theory of the process is developed based on Whitham's averaged variational principle and its predictions verified in numerical simulations. …
[Phys. Rev. E 94, 042216] Published Tue Oct 18, 2016
Cooperation driven by success-driven group formation
2016-10-18T10:00:00-04:00
Author(s): Attila Szolnoki and Xiaojie Chen
In the traditional setup of the public goods game all players are involved in every available group and the mutual benefit is shared among competing cooperator and defector strategies. However, in real life situations the group formation of players could be more sophisticated because not all players…
[Phys. Rev. E 94, 042311] Published Tue Oct 18, 2016
Uniform asymptotic approximation of diffusion to a small target: Generalized reaction models
2016-10-18T10:00:00-04:00
Author(s): Samuel A. Isaacson, Ava J. Mauro, and Jay Newby
The diffusion of a reactant to a binding target plays a key role in many biological processes. The reaction radius at which the reactant and target may interact is often a small parameter relative to the diameter of the domain in which the reactant diffuses. We develop uniform in time asymptotic exp…
[Phys. Rev. E 94, 042414] Published Tue Oct 18, 2016
Analytical calculation of the lipid bilayer bending modulus
2016-10-18T10:00:00-04:00
Author(s): Boris Kheyfets, Timur Galimzyanov, Anna Drozdova, and Sergei Mukhin
Bending and Gaussian moduli of a homogenious single-component lipid bilayer are calculated analytically using microscopic model of the lipid hydrocarbon chains. The approach allows for thermodynamic averaging over different chains conformations. Each chain is modeled as a flexible string with finite…
[Phys. Rev. E 94, 042415] Published Tue Oct 18, 2016
Computer simulation study of a mesogenic lattice model based on long-range dispersion interactions
2016-10-18T10:00:00-04:00
Author(s): Silvano Romano
In contrast to thermotropic biaxial nematic phases, for which some long sought for experimental realizations have been obtained, no experimental realizations are yet known for their tetrahedratic and cubatic counterparts, involving orientational orders of ranks 3 and 4, respectively, also studied th…
[Phys. Rev. E 94, 042702] Published Tue Oct 18, 2016
Superexponential fluctuation relation for dichotomous work reservoir systems
2016-10-17T10:00:00-04:00
Author(s): Sílvio M. Duarte Queirós
This paper introduces an analytical description of the probability density function of the dissipated and injected powers p(j_{dis}) and p(j_{inj}), respectively, in a paradigmatic nonequilibrium damped system in contact with a work reservoir that is analytically represented by telegraph noise and t…
[Phys. Rev. E 94, 042114] Published Mon Oct 17, 2016
Role of the range of the interactions in thermal conduction
2016-10-17T10:00:00-04:00
Author(s): Carlos Olivares and Celia Anteneodo
We investigate thermal transport along a one-dimensional lattice of classical inertial rotators, with attractive couplings that decrease with distance as r^{−α} (α≥0), subject at its ends to Brownian heat reservoirs at different temperatures with average value T. By means of numerical integration of…
[Phys. Rev. E 94, 042117] Published Mon Oct 17, 2016
Resummed mean-field inference for strongly coupled data
2016-10-17T10:00:00-04:00
Author(s): Hugo Jacquin and A. Rançon
We present a resummed mean-field approximation for inferring the parameters of an Ising or a Potts model from empirical, noisy, one- and two-point correlation functions. Based on a resummation of a class of diagrams of the small correlation expansion of the log-likelihood, the method outperforms sta…
[Phys. Rev. E 94, 042118] Published Mon Oct 17, 2016
Analysis of etching at a solid-solid interface
2016-10-17T10:00:00-04:00
Author(s): Washington S. Alves, Evandro A. Rodrigues, Henrique A. Fernandes, Bernardo A. Mello, Fernando A. Oliveira, and Ismael V. L. Costa
We present a method to derive an analytical expression for the roughness of an eroded surface whose dynamics are ruled by cellular automaton. Starting from the automaton, we obtain the time evolution of the height average and height variance (roughness). We apply this method to the etching model in …
[Phys. Rev. E 94, 042119] Published Mon Oct 17, 2016
Pattern formation with repulsive soft-core interactions: Discrete particle dynamics and Dean-Kawasaki equation
2016-10-17T10:00:00-04:00
Author(s): Jean-Baptiste Delfau, Hélène Ollivier, Cristóbal López, Bernd Blasius, and Emilio Hernández-García
Recent theoretical and simulation work has predicted the existence of a so-called cluster crystal, where soft colloidal particles interacting through a repulsive potential are able to aggregate and form periodic crystals of particle clusters. The authors study this phenomenon using Brownian dynamics simulation and analytical theory based on the Dean-Kawasaki equation, and focus on the appearance and structure of patterns in one- and two-dimensional realizations.
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[Phys. Rev. E 94, 042120] Published Mon Oct 17, 2016
Stochastic transport in the presence of spatial disorder: Fluctuation-induced corrections to homogenization
2016-10-17T10:00:00-04:00
Author(s): Matthew J. Russell, Oliver E. Jensen, and Tobias Galla
Motivated by uncertainty quantification in natural transport systems, we investigate an individual-based transport process involving particles undergoing a random walk along a line of point sinks whose strengths are themselves independent random variables. We assume particles are removed from the sy…
[Phys. Rev. E 94, 042121] Published Mon Oct 17, 2016
Waves of DNA: Propagating excitations in extended nanoconfined polymers
2016-10-17T10:00:00-04:00
Author(s): Alexander R. Klotz, Hendrick W. de Haan, and Walter W. Reisner
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain …
[Phys. Rev. E 94, 042603] Published Mon Oct 17, 2016
Imaging grain boundary grooves in hard-sphere colloidal bicrystals
2016-10-17T10:00:00-04:00
Author(s): Eric Maire, Emily Redston, Maria Persson Gulda, David A. Weitz, and Frans Spaepen
Colloidal particles were sedimented onto patterned glass slides to grow three-dimensional bicrystals with a controlled structure. Three types of symmetric tilt grain boundaries between close-packed face-centered-cubic crystals were produced: Σ5(100),Σ17(100), and Σ3(110). The structure of the crysta…
[Phys. Rev. E 94, 042604] Published Mon Oct 17, 2016
Polymorph selection and nucleation pathway in the crystallization of Hertzian spheres
2016-10-17T10:00:00-04:00
Author(s): Wenze Ouyang, Cuiliu Fu, Zhiwei Sun, and Shenghua Xu
The crystallization process of Hertzian spheres is studied by means of molecular dynamics simulations in an NPT ensemble where the total number of particles N, the pressure P, and the temperature T are kept constant. It has been observed that the bond orientational ordering rather than the translati…
[Phys. Rev. E 94, 042805] Published Mon Oct 17, 2016
Analytical results for the wrinkling of graphene on nanoparticles
2016-10-17T10:00:00-04:00
Author(s): M. Guedda, N. Alaa, and M. Benlahsen
A continuum elastic model, describing the wrinkling instability of graphene on substrate-supported silica nanoparticles [M. Yamamoto et al., Phys. Rev. X 2, 041018 (2012)], is analytically studied, and an exact analytical expression of the critical nanoparticle separation or the maximum wrinkle leng…
[Phys. Rev. E 94, 042806] Published Mon Oct 17, 2016
Heat and momentum transfer for magnetoconvection in a vertical external magnetic field
2016-10-17T10:00:00-04:00
Author(s): Till Zürner, Wenjun Liu, Dmitry Krasnov, and Jörg Schumacher
The scaling theory of Grossmann and Lohse [J. Fluid Mech. 407, 27 (2000)] for turbulent heat and momentum transfer is extended to the magnetoconvection case in the presence of a (strong) vertical magnetic field. A comparison with existing laboratory experiments and direct numerical simulations in th…
[Phys. Rev. E 94, 043108] Published Mon Oct 17, 2016
Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study
2016-10-17T10:00:00-04:00
Author(s): Dilina Perera, Thomas Vogel, and David P. Landau
Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with …
[Phys. Rev. E 94, 043308] Published Mon Oct 17, 2016
Numerical simulation of particulate flows using a hybrid of finite difference and boundary integral methods
2016-10-17T10:00:00-04:00
Author(s): Amitabh Bhattacharya and Tejas Kesarkar
A combination of finite difference (FD) and boundary integral (BI) methods is used to formulate an efficient solver for simulating unsteady Stokes flow around particles. The two-dimensional (2D) unsteady Stokes equation is being solved on a Cartesian grid using a second order FD method, while the 2D…
[Phys. Rev. E 94, 043309] Published Mon Oct 17, 2016
Streamwise decay of localized states in channel flow
2016-10-14T10:00:00-04:00
Author(s): Stefan Zammert and Bruno Eckhardt
Channel flow, the pressure driven flow between parallel plates, has exact coherent structures that show various degrees of localization. For states which are localized in streamwise direction but extended in spanwise direction, we show that they are exponentially localized, with decay constants that…
[Phys. Rev. E 94, 041101(R)] Published Fri Oct 14, 2016
Lattice model of reduced jamming by a barrier
2016-10-14T10:00:00-04:00
Author(s): Emilio N. M. Cirillo, Oleh Krehel, Adrian Muntean, and Rutger van Santen
We study an asymmetric simple exclusion process in a strip in the presence of a solid impenetrable barrier. We focus on the effect of the barrier on the residence time of the particles, namely, the typical time needed by the particles to cross the whole strip. We explore the conditions for reduced j…
[Phys. Rev. E 94, 042115] Published Fri Oct 14, 2016
Blockage-induced condensation controlled by a local reaction
2016-10-14T10:00:00-04:00
Author(s): Emilio N. M. Cirillo, Matteo Colangeli, and Adrian Muntean
We consider the setup of stationary zero range models and discuss the onset of condensation induced by a local blockage on the lattice. We show that the introduction of a local feedback on the hopping rates allows us to control the particle fraction in the condensed phase. This phenomenon results in…
[Phys. Rev. E 94, 042116] Published Fri Oct 14, 2016
Sampling methods for the quasistationary regime of epidemic processes on regular and complex networks
2016-10-14T10:00:00-04:00
Author(s): Renan S. Sander, Guilherme S. Costa, and Silvio C. Ferreira
A major hurdle in the simulation of the steady state of epidemic processes is that the system will unavoidably visit an absorbing, disease-free state at sufficiently long times due to the finite size of the networks where epidemics evolves. In the present work, we compare different quasistationary (…
[Phys. Rev. E 94, 042308] Published Fri Oct 14, 2016
Network exploration using true self-avoiding walks
2016-10-14T10:00:00-04:00
Author(s): Yup Kim, Seokjong Park, and Soon-Hyung Yook
We study the mean first passage time (MFPT) of true self-avoiding walks (TSAWs) on various networks as a measure of searching efficiency. From the numerical analysis, we find that the MFPT of TSAWs, τ^{TSAW}, approaches the theoretical minimum τ^{th}/N=1/2 on synthetic networks whose degree-degree c…
[Phys. Rev. E 94, 042309] Published Fri Oct 14, 2016
Population dynamics in an intermittent refuge
2016-10-14T10:00:00-04:00
Author(s): E. H. Colombo and C. Anteneodo
Population dynamics is constrained by the environment, which needs to obey certain conditions to support population growth. We consider a standard model for the evolution of a single species population density, which includes reproduction, competition for resources, and spatial spreading, while subj…
[Phys. Rev. E 94, 042413] Published Fri Oct 14, 2016
Binary mixtures of disks and elongated particles: Texture and mechanical properties
2016-10-14T10:00:00-04:00
Author(s): Emilien Azéma, Itthichai Preechawuttipong, and Farhang Radjai
We analyze the shear strength and microstructure of binary granular mixtures consisting of disks and elongated particles by varying systematically both the mixture ratio and degree of homogeneity (from homogeneous to fully segregated). The contact dynamics method is used for numerical simulations wi…
[Phys. Rev. E 94, 042901] Published Fri Oct 14, 2016
Scaling of heat transfer and temperature distribution in granular flows in rotating drums
2016-10-14T10:00:00-04:00
Author(s): B. Yohannes, H. Emady, K. Anderson, I. Paredes, M. Javed, W. Borghard, F. J. Muzzio, B. J. Glasser, and A. M. Cuitiño
Accurate prediction of the time required to heat up granular materials to a target temperature is crucial for several processes. However, we do not have quantitative models to predict the average temperature or the temperature distribution of the particles. Here, we computationally investigate the s…
[Phys. Rev. E 94, 042902] Published Fri Oct 14, 2016
Data assimilation for massive autonomous systems based on a second-order adjoint method
2016-10-14T10:00:00-04:00
Author(s): Shin-ichi Ito, Hiromichi Nagao, Akinori Yamanaka, Yuhki Tsukada, Toshiyuki Koyama, Masayuki Kano, and Junya Inoue
Data assimilation (DA) is a fundamental computational technique that integrates numerical simulation models and observation data on the basis of Bayesian statistics. Originally developed for meteorology, especially weather forecasting, DA is now an accepted technique in various scientific fields. On…
[Phys. Rev. E 94, 043307] Published Fri Oct 14, 2016
Piezothermal effect in a spinning gas
2016-10-13T10:00:00-04:00
Author(s): V. I. Geyko and N. J. Fisch
A spinning gas, heated adiabatically through axial compression, is known to exhibit a rotation-dependent heat capacity. However, as equilibrium is approached, an effect is identified here wherein the temperature does not grow homogeneously in the radial direction, but develops a temperature differen…
[Phys. Rev. E 94, 042113] Published Thu Oct 13, 2016
Transport of chaotic trajectories from regions distant from or near to structures of regular motion of the Fermi-Ulam model
2016-10-13T10:00:00-04:00
Author(s): Nilson B. de Faria, Daniel S. Tavares, Wenderson C. S. de Paula, Edson D. Leonel, and Denis G. Ladeira
The chaotic portion of phase space of the simplified Fermi-Ulam model is studied under the context of transport of trajectories in two scenarios: (i) the trajectories are originated from a region distant from the islands of regular motion and are transported to a region located at a high portion of …
[Phys. Rev. E 94, 042208] Published Thu Oct 13, 2016
Stable and unstable periodic orbits in the one-dimensional lattice ϕ^{4} theory
2016-10-13T10:00:00-04:00
Author(s): Kenichiro Aoki
Periodic orbits for the classical ϕ^{4} theory on the one-dimensional lattice are systematically constructed by extending the normal modes of the harmonic theory, for periodic, free and fixed boundary conditions. Through the process, we investigate which normal modes of the linear theory can or cann…
[Phys. Rev. E 94, 042209] Published Thu Oct 13, 2016
Traveling phase waves in asymmetric networks of noisy chaotic attractors
2016-10-13T10:00:00-04:00
Author(s): Thomas K. DM. Peron, Jürgen Kurths, Francisco A. Rodrigues, Lutz Schimansky-Geier, and Bernard Sonnenschein
We explore identical Rössler systems organized into two equally sized groups, among which differing positive and negative in- and out-coupling strengths are allowed. With this asymmetric coupling, we analyze patterns in the phase dynamics that coexist with chaotic amplitudes. We specifically investi…
[Phys. Rev. E 94, 042210] Published Thu Oct 13, 2016
Long-range correlations in rectangular cavities containing pointlike perturbations
2016-10-13T10:00:00-04:00
Author(s): Małgorzata Białous, Vitalii Yunko, Szymon Bauch, Michał Ławniczak, Barbara Dietz, and Leszek Sirko
We investigated experimentally the short- and long-range correlations in the fluctuations of the resonance frequencies of flat, rectangular microwave cavities that contained antennas acting as pointlike perturbations. We demonstrate that their spectral properties exhibit the features typical for sin…
[Phys. Rev. E 94, 042211] Published Thu Oct 13, 2016
Inhibitory loop robustly induces anticipated synchronization in neuronal microcircuits
2016-10-13T10:00:00-04:00
Author(s): Fernanda S. Matias, Leonardo L. Gollo, Pedro V. Carelli, Claudio R. Mirasso, and Mauro Copelli
We investigate the synchronization properties between two excitatory coupled neurons in the presence of an inhibitory loop mediated by an interneuron. Dynamic inhibition together with noise independently applied to each neuron provide phase diversity in the dynamics of the neuronal motif. We show th…
[Phys. Rev. E 94, 042411] Published Thu Oct 13, 2016
Biasing effects of receptor-ligand complexes on protein-unfolding statistics
2016-10-13T10:00:00-04:00
Author(s): Constantin Schoeler, Tobias Verdorfer, Hermann E. Gaub, and Michael A. Nash
Protein receptor-ligand pairs are increasingly used as specific molecular handles in single-molecule protein-unfolding experiments. Further, known marker domains, also referred to as fingerprints, provide unique unfolding signatures to identify specific single-molecule interactions, when receptor-li…
[Phys. Rev. E 94, 042412] Published Thu Oct 13, 2016
Size consistency in smoothed dissipative particle dynamics
2016-10-13T10:00:00-04:00
Author(s): Gérôme Faure, Jean-Bernard Maillet, Julien Roussel, and Gabriel Stoltz
Smoothed dissipative particle dynamics (SDPD) is a mesoscopic method that allows one to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a function of the size of the mesoparticles, both at equilibrium a…
[Phys. Rev. E 94, 043305] Published Thu Oct 13, 2016
Lattice Boltzmann model for incompressible axisymmetric thermal flows through porous media
2016-10-13T10:00:00-04:00
Author(s): Kods Grissa, Raoudha Chaabane, Zied Lataoui, Adel Benselama, Yves Bertin, and Abdelmajid Jemni
The present work proposes a simple lattice Boltzmann model for incompressible axisymmetric thermal flows through porous media. By incorporating forces and source terms into the lattice Boltzmann equation, the incompressible Navier-Stokes equations are recovered through the Chapman-Enskog expansion. …
[Phys. Rev. E 94, 043306] Published Thu Oct 13, 2016
Cross-section fluctuations in chaotic scattering systems
2016-10-12T10:00:00-04:00
Author(s): Torleif E. O. Ericson, Barbara Dietz, and Achim Richter
Exact analytical expressions for the cross-section correlation functions of chaotic scattering systems have hitherto been derived only under special conditions. The objective of the present article is to provide expressions that are applicable beyond these restrictions. The derivation is based on a …
[Phys. Rev. E 94, 042207] Published Wed Oct 12, 2016
Multifractal cross-correlation effects in two-variable time series of complex network vertex observables
2016-10-12T10:00:00-04:00
Author(s): Paweł Oświȩcimka, Lorenzo Livi, and Stanisław Drożdż
We investigate the scaling of the cross-correlations calculated for two-variable time series containing vertex properties in the context of complex networks. Time series of such observables are obtained by means of stationary, unbiased random walks. We consider three vertex properties that provide, …
[Phys. Rev. E 94, 042307] Published Wed Oct 12, 2016
Targeting functional motifs of a protein family
2016-10-12T10:00:00-04:00
Author(s): Pradeep Bhadola and Nivedita Deo
The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties…
[Phys. Rev. E 94, 042409] Published Wed Oct 12, 2016
Classification and predictions of RNA pseudoknots based on topological invariants
2016-10-12T10:00:00-04:00
Author(s): Graziano Vernizzi, Henri Orland, and A. Zee
Merging concepts of statistical mechanics, renormalization, topology, and graph theory, this paper aims to shed light on the problem of the three dimensional structure of RNA. The authors propose to include an additional term in the partition function, associated with a renormalized crossing number, that accounts for the observation that RNA unevenly populates the repertoire of pseudoknots with the same genus.
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[Phys. Rev. E 94, 042410] Published Wed Oct 12, 2016
Correlation-induced DNA adsorption on like-charged membranes
2016-10-12T10:00:00-04:00
Author(s): Sahin Buyukdagli and Ralf Blossey
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulli…
[Phys. Rev. E 94, 042502] Published Wed Oct 12, 2016
Electrical conductivity of a monolayer produced by random sequential adsorption of linear k-mers onto a square lattice
2016-10-11T10:00:00-04:00
Author(s): Yuri Yu. Tarasevich, Valeria A. Goltseva, Valeri V. Laptev, and Nikolai I. Lebovka
The electrical conductivity of a monolayer produced by the random sequential adsorption (RSA) of linear k-mers (particles occupying k adjacent adsorption sites) onto a square lattice was studied by means of computer simulation. Overlapping with predeposited k-mers and detachment from the surface wer…
[Phys. Rev. E 94, 042112] Published Tue Oct 11, 2016
Nonlinear dynamics and intermittency in a turbulent reacting wake with density ratio as bifurcation parameter
2016-10-11T10:00:00-04:00
Author(s): Suhas Suresha, R. I. Sujith, Benjamin Emerson, and Tim Lieuwen
The flame or flow behavior of a turbulent reacting wake is known to be fundamentally different at high and low values of flame density ratio (ρ_{u}/ρ_{b}), as the flow transitions from globally stable to unstable. This paper analyzes the nonlinear dynamics present in a bluff-body stabilized flame, a…
[Phys. Rev. E 94, 042206] Published Tue Oct 11, 2016
Strain-driven criticality underlies nonlinear mechanics of fibrous networks
2016-10-11T10:00:00-04:00
Author(s): A. Sharma, A. J. Licup, R. Rens, M. Vahabi, K. A. Jansen, G. H. Koenderink, and F. C. MacKintosh
Networks with only central force interactions are floppy when their average connectivity is below an isostatic threshold. Although such networks are mechanically unstable, they can become rigid when strained. It was recently shown that the transition from floppy to rigid states as a function of simp…
[Phys. Rev. E 94, 042407] Published Tue Oct 11, 2016
Dielectrophoretic label-free immunoassay for rare-analyte quantification in biological samples
2016-10-11T10:00:00-04:00
Author(s): Logeeshan Velmanickam, Darrin Laudenbach, and Dharmakeerthi Nawarathna
The current gold standard for detecting or quantifying target analytes from blood samples is the ELISA (enzyme-linked immunosorbent assay). The detection limit of ELISA is about 250 pg/ml. However, to quantify analytes that are related to various stages of tumors including early detection requires d…
[Phys. Rev. E 94, 042408] Published Tue Oct 11, 2016
Active microrheology in a colloidal glass
2016-10-11T10:00:00-04:00
Author(s): M. Gruber, G. C. Abade, A. M. Puertas, and M. Fuchs
This paper uses a modified version of mode-coupling theory to investigate the microrheology of a colloidal glass. By probing and following the dynamics of an individual test particle, two force regimes are identified, one that gives rise to a localized probe and one where the probe has a steady velocity. The authors then compare theory and simulations in the localized regime.
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[Phys. Rev. E 94, 042602] Published Tue Oct 11, 2016
Fingering instability and mixing of a blob in porous media
2016-10-11T10:00:00-04:00
Author(s): Satyajit Pramanik and Manoranjan Mishra
The curvature of the unstable part of the miscible interface between a circular blob and the ambient fluid in two-dimensional homogeneous porous media depends on the viscosity of the fluids. The influence of the interface curvature on the fingering instability and mixing of a miscible blob within a …
[Phys. Rev. E 94, 043106] Published Tue Oct 11, 2016
Anisotropy of a cubic ferromagnet at criticality
2016-10-10T10:00:00-04:00
Author(s): A. Kudlis and A. I. Sokolov
Critical fluctuations change the effective anisotropy of cubic ferromagnet near the Curie point. If the crystal undergoes phase transition into orthorhombic phase and the initial anisotropy is not too strong, reduced anisotropy of nonlinear susceptibility acquires at T_{c} the universal value δ_{4}^…
[Phys. Rev. E 94, 042107] Published Mon Oct 10, 2016
Thermally induced passage and current of particles in a highly unstable optical potential
2016-10-10T10:00:00-04:00
Author(s): Artem Ryabov, Pavel Zemánek, and Radim Filip
We discuss the statistics of first-passage times of a Brownian particle moving in a highly unstable nonlinear potential proportional to an odd power of position. We observe temperature-induced shortening of the mean first-passage time and its dependence on the power of nonlinearity. We propose a pas…
[Phys. Rev. E 94, 042108] Published Mon Oct 10, 2016
Universality class of site and bond percolation on multifractal scale-free planar stochastic lattice
2016-10-10T10:00:00-04:00
Author(s): M. K. Hassan and M. M. Rahman
In this article, we investigate both site and bond percolation on a weighted planar stochastic lattice (WPSL), which is a multifractal and whose dual is a scale-free network. The characteristic property of percolation is that it exhibits threshold phenomena as we find sudden or abrupt jump in spanni…
[Phys. Rev. E 94, 042109] Published Mon Oct 10, 2016
Peptide binding landscapes: Specificity and homophilicity across sequence space in a lattice model
2016-10-10T10:00:00-04:00
Author(s): Joohyun Jeon and M. Scott Shell
Peptide aggregation frequently involves sequences with strong homophilic binding character, i.e., sequences that self-assemble with like species in a crowded cellular environment, in the face of a multitude of other peptides or proteins as potential heterophilic binding partners. What kinds of seque…
[Phys. Rev. E 94, 042405] Published Mon Oct 10, 2016
Emergence of flagellar beating from the collective behavior of individual ATP-powered dyneins
2016-10-10T10:00:00-04:00
Author(s): S. Namdeo and P. R. Onck
Flagella are hair-like projections from the surface of eukaryotic cells, and they play an important role in many cellular functions, such as cell-motility. The beating of flagella is enabled by their internal architecture, the axoneme, and is powered by a dense distribution of motor proteins, dynein…
[Phys. Rev. E 94, 042406] Published Mon Oct 10, 2016
Micromechanical model for isolated polymer-colloid clusters under tension
2016-10-10T10:00:00-04:00
Author(s): Roozbeh Dargazany, Jiaqi Lin, Leila Khalili, Mikhail Itskov, Hsieh Chen, and Alfredo Alexander-Katz
Binary polymer-colloid (PC) composites form the majority of biological load-bearing materials. Due to the abundance of the polymer and particles, and their simple aggregation process, PC clusters are used broadly by nature to create biomaterials with a variety of functions. However, our understandin…
[Phys. Rev. E 94, 042501] Published Mon Oct 10, 2016
Dynamics of ellipsoidal tracers in swimming algal suspensions
2016-10-10T10:00:00-04:00
Author(s): Ou Yang, Yi Peng, Zhengyang Liu, Chao Tang, Xinliang Xu, and Xiang Cheng
Enhanced diffusion of passive tracers immersed in active fluids is a universal feature of active fluids and has been extensively studied in recent years. Similar to microrheology for equilibrium complex fluids, the unusual enhanced particle dynamics reveal intrinsic properties of active fluids. Neve…
[Phys. Rev. E 94, 042601] Published Mon Oct 10, 2016
Extreme dissipation event due to plume collision in a turbulent convection cell
2016-10-10T10:00:00-04:00
Author(s): Jörg Schumacher and Janet D. Scheel
An extreme dissipation event in the bulk of a closed three-dimensional turbulent convection cell is found to be correlated with a strong reduction of the large-scale circulation flow in the system that happens at the same time as a plume emission event from the bottom plate. The reduction in the lar…
[Phys. Rev. E 94, 043104] Published Mon Oct 10, 2016
Geometric effects on electrocapillarity in nanochannels with an overlapped electric double layer
2016-10-10T10:00:00-04:00
Author(s): Jung A. Lee and In Seok Kang
Unsteady filling of electrolyte solution inside a nanochannel by the electrocapillarity effect is studied. The filling rate is predicted as a function of the bulk concentration of the electrolyte, the surface potential (or surface charge density), and the cross sectional shape of the channel. For a …
[Phys. Rev. E 94, 043105] Published Mon Oct 10, 2016
Explicit symplectic approximation of nonseparable Hamiltonians: Algorithm and long time performance
2016-10-10T10:00:00-04:00
Author(s): Molei Tao
Explicit symplectic integrators have been important tools for accurate and efficient approximations of mechanical systems with separable Hamiltonians. This article proposes for arbitrary Hamiltonians similar integrators, which are explicit, of any even order, symplectic in an extended phase space, a…
[Phys. Rev. E 94, 043303] Published Mon Oct 10, 2016
Thermodynamics of slow solutions to the gas-piston equations
2016-10-07T10:00:00-04:00
Author(s): G. Gubbiotti and D. Chiuchiù
Despite its historical importance, a perfect gas enclosed by a pistons and in contact with a thermal reservoirs is a system still largely under study. Its thermodynamic properties are not yet well understood when driven under nonequilibrium conditions, and analytic formulas that describe the heat ex…
[Phys. Rev. E 94, 042106] Published Fri Oct 07, 2016
Universality of market superstatistics
2016-10-07T10:00:00-04:00
Author(s): Mateusz Denys, Tomasz Gubiec, Ryszard Kutner, Maciej Jagielski, and H. Eugene Stanley
We use a key concept of the continuous-time random walk formalism, i.e., continuous and fluctuating interevent times in which mutual dependence is taken into account, to model market fluctuation data when traders experience excessive (or superthreshold) losses or excessive (or superthreshold) profit…
[Phys. Rev. E 94, 042305] Published Fri Oct 07, 2016