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Physical Review. E

Debabrata Biswas, Tanmoy Banerjee, Jürgen Kurths
Birhythmicity arises in several physical, biological, and chemical systems. Although many control schemes have been proposed for various forms of multistability, only a few exist for controlling birhythmicity. In this paper we investigate the control of birhythmic oscillation by introducing a self-feedback mechanism that incorporates the variable to be controlled and its canonical conjugate. Using a detailed analytical treatment, bifurcation analysis, and experimental demonstrations, we establish that the proposed technique is capable of eliminating birhythmicity and generates monorhythmic oscillation...
October 2016: Physical Review. E
Jinglong Zhu, Rupert Klein, Luigi Delle Site
Adaptive molecular resolution approaches in molecular dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in the way the change of molecular resolution is made in a buffer (transition) region. In particular a central question concerns the possibility of the existence of a global Hamiltonian which, by describing the change of resolution, is at the same time physically consistent, mathematically well defined, and numerically accurate...
October 2016: Physical Review. E
František Slanina
We investigate analytically a microfluidic device consisting of a tube with a nonuniform but spatially periodic diameter, where a fluid driven back and forth by a pump carries colloidal particles. Although the net flow of the fluid is zero, the particles move preferentially in one direction due to the ratchet mechanism, which occurs due to the simultaneous effect of inertial hydrodynamics and Brownian motion. We show that the average current is strongly sensitive to particle size, thus facilitating colloidal particle sorting...
October 2016: Physical Review. E
Marcel Wellner
This two-dimensional study is motivated by cardiac electrophysiology, and focuses on rotating spiral waves in reaction-diffusion (RD) models. Here we deal with a spiral's translational drift under a constant externally imposed gradient G. A long-standing problem may be stated as follows: Given the dimensionless drift velocity V/G, find its nontrivial direction angle Γ relative to G. A deductive algebraic treatment yields a solution, cosΓ=-V/G. Three features are worth noting: the combination of algebraic and RD contexts; a somewhat extensive derivation contrasting with a compact result; and the generality due to the absence of reaction details in the formula...
October 2016: Physical Review. E
David B Saakian, Chin-Kun Hu
The discrete time mathematical models of evolution (the discrete time Eigen model, the Moran model, and the Wright-Fisher model) have many applications in complex biological systems. The discrete time Eigen model rather realistically describes the serial passage experiments in biology. Nevertheless, the dynamics of the discrete time Eigen model is solved in this paper. The 90% of results in population genetics are connected with the diffusion approximation of the Wright-Fisher and Moran models. We considered the discrete time Eigen model of asexual virus evolution and the Wright-Fisher model from population genetics...
October 2016: Physical Review. E
Howard W Levinson, Vadim A Markel
We propose a conceptually different method for solving nonlinear inverse scattering problems (ISPs) such as are commonly encountered in tomographic ultrasound imaging, seismology, and other applications. The method is inspired by the theory of nonlocality of physical interactions and utilizes the relevant formalism. We formulate the ISP as a problem whose goal is to determine an unknown interaction potential V from external scattering data. Although we seek a local (diagonally dominated) V as the solution to the posed problem, we allow V to be nonlocal at the intermediate stages of iterations...
October 2016: Physical Review. E
Peter Grassberger, Deepak Dhar, P K Mohanty
We present simulations of the one-dimensional Oslo rice pile model in which the critical height at each site is randomly reset after each toppling. We use the fact that the stationary state of this sand-pile model is hyperuniform to reach system of sizes >10^{7}. Most previous simulations were seriously flawed by important finite-size corrections. We find that all critical exponents have values consistent with simple rationals: ν=4/3 for the correlation length exponent, D=9/4 for the fractal dimension of avalanche clusters, and z=10/7 for the dynamical exponent...
October 2016: Physical Review. E
Chong Liu, Zhan-Ying Yang, Li-Chen Zhao, Liang Duan, Guangye Yang, Wen-Li Yang
We study symmetric and asymmetric optical multipeak solitons on a continuous wave background in the femtosecond regime of a single-mode fiber. Key characteristics of such multipeak solitons, such as the formation mechanism, propagation stability, and shape-changing collisions, are revealed in detail. Our results show that this multipeak (symmetric or asymmetric) mode could be regarded as a single pulse formed by a nonlinear superposition of a periodic wave and a single-peak (W-shaped or antidark) soliton. In particular, a phase diagram for different types of nonlinear excitations on a continuous wave background, including the unusual multipeak soliton, the W-shaped soliton, the antidark soliton, the periodic wave, and the known breather rogue wave, is established based on the explicit link between exact solution and modulation instability analysis...
October 2016: Physical Review. E
Jun Wang, Yi Xiao
The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA...
October 2016: Physical Review. E
María Isabel García de Soria, Carlos E Álvarez, Emmanuel Trizac
In an attempt to quantify the role of polydispersity in colloidal suspensions, we present an efficient implementation of the renormalized jellium model for a mixture of spherical charged colloids. The different species may have different size, charge, and density. Advantage is taken from the fact that the electric potential pertaining to a given species obeys a Poisson's equation that is species independent; only boundary conditions do change from one species to the next. All species are coupled through the renormalized background (jellium) density, that is determined self-consistently...
October 2016: Physical Review. E
K Gomberoff, H Higaki, C Kaga, K Ito, H Okamoto
The existence of autoresonances for m=2 diocotron oscillations of non-neutral electron plasmas in a uniform magnetic field was predicted by particle-in-cell simulations and it was confirmed in experiments. The obtained results show clear deviations from the standard threshold amplitude dependence on the sweep rate. The threshold amplitude approaches a constant at a lower sweep rate when there is a damping force. It was also found that the aspect ratio for the oval cross section of the confined plasma can be controlled by the frequency of the externally applied driving force...
October 2016: Physical Review. E
Niraj Kumar, Tao Jia, Kourosh Zarringhalam, Rahul V Kulkarni
The sporadic nature of gene expression at the single-cell level-long periods of inactivity punctuated by bursts of mRNA or protein production-plays a critical role in diverse cellular processes. To elucidate the cellular role of bursting in gene expression, synthetic biology approaches have been used to design simple genetic circuits with bursty mRNA or protein production. Understanding how such genetic circuits can be designed with the ability to control burst-related parameters requires the development of quantitative stochastic models of gene expression...
October 2016: Physical Review. E
L T Corson, N J Mottram, B R Duffy, S K Wilson, C Tsakonas, C V Brown
We consider, both theoretically and experimentally, a thin sessile drop of conductive liquid that rests on the lower plate of a parallel-plate capacitor. We derive analytical expressions for both the initial deformation and the relaxation dynamics of the drop as the electric field is either abruptly applied or abruptly removed, as functions of the geometrical, electrical, and material parameters, and investigate the ranges of validity of these expressions by comparison with full numerical simulations. These expressions provide a reasonable description of the experimentally measured dynamic response of a drop of conductive ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate...
October 2016: Physical Review. E
Michael C M Varney, Qiaoxuan Zhang, Bohdan Senyuk, Ivan I Smalyukh
We study elastic interactions between colloidal particles and deformation landscapes of undulations in a cholesteric liquid crystal under an electric field applied normal to cholesteric layers. The onset of undulation instability is influenced by the presence of colloidal inclusions and, in turn, layers' undulations mediate the spatial patterning of particle locations. We find that the bending of cholesteric layers around a colloidal particle surface prompts the local nucleation of an undulations lattice at electric fields below the well-defined threshold known for liquid crystals without inclusions, and that the onset of the resulting lattice is locally influenced, both dimensionally and orientationally, by the initial arrangements of colloids defined using laser tweezers...
October 2016: Physical Review. E
Christopher L Wirth, Sri Harsha Nuthalapati
The electric-field-assisted directed assembly of spherical colloidal particles near an electrode has been studied for nearly three decades. Recently, focus has shifted to the electric-field-assisted assembly and propulsion of nonspherical (i.e., anisotropic) particles. This paper describes calculations and results for a doublet of asymmetric ζ potential and size responding to a dc electric field. The doublet experienced a net vertical force that depended on both the asymmetry in ζ potential and lobe size...
October 2016: Physical Review. E
Muhammad F Afzaal, Jamal Uddin
The disintegration of a compound thread of fluid can be utilized in a wide variety of applications including the production of compound droplets or capsules. In this paper we investigate the linear instability of a compound inviscid liquid jet falling under gravity in a surrounding gas with respect to nonaxisymmetric waves. We derive an analytical expression for the dispersion relation, which takes into account the non-uniform nature of the jet, and which we then solve numerically. Particular attention is paid to investigating the effects of the liquid-to-gas density ratio on the growth and development of different wave modes as well as the influence of gravity...
October 2016: Physical Review. E
J Javier Brey, Pablo Maynar, M I García de Soria
A kinetic equation for a dilute gas of hard spheres confined between two parallel plates separated a distance smaller than two particle diameters is derived. It is a Boltzmann-like equation, which incorporates the effect of the confinement on the particle collisions. A function S(t) is constructed by adding to the Boltzmann expression a confinement contribution. Then it is shown that for the solutions of the kinetic equation, S(t) increases monotonically in time, until the system reaches a stationary inhomogeneous state, when S becomes the equilibrium entropy of the confined system as derived from equilibrium statistical mechanics...
October 2016: Physical Review. E
Joohyun Jeon, 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 sequences display a strong tendency towards homophilic binding and self-assembly, and what are the origins of this behavior? Here, we consider how sequence specificity in oligomerization processes plays out in a simple two-dimensional (2D) lattice statistical-thermodynamic peptide model that permits exhaustive examination of the entire sequence and configurational landscapes...
October 2016: Physical Review. E
Jörg Schumacher, 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 large-scale circulation opens the possibility for a nearly frontal collision of down- and upwelling plumes and the generation of a high-amplitude thermal dissipation layer in the bulk. This collision is locally connected to a subsequent high-amplitude energy dissipation event in the form of a strong shear layer...
October 2016: Physical Review. E
Giovanni Bellesia, Benjamin B Bales
We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes...
October 2016: Physical Review. E
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