Modular Organization in a Cell: Concepts and Applications

Network biology is conceptualized as an interdisciplinary field, lying at the intersection among graph theory, statistical mechanics and biology. Great efforts have been made to promote the concept of network biology and its various applications in life s

Classical two-site fidelity and quantum phase transitions in the Ising model and the extended Hubbard model

In this Letter, the classical two-site-ground-state fidelity (CTGF) is exploited to identify quantum phase transitions (QPTs) for the transverse field Ising model (TFIM) and the one-dimensional extended Hubbard model (EHM). Our results show that the CTGF exhibits an abrupt change around the regions of criticality and can be used to identify QPTs in spin and fermionic systems. The method is especially convenient when it is connected with the density-matrix renormalization group (DMRG) algorithm. (C) 2008 Elsevier B.V. All rights reserved.

Stochastic resonance for modulated gain in a single-mode laser

Stochastic resonance (SR) induced by the signal modulation is investigated, by introducing the signal-modulated gain into a single-mode laser system. Using the linear approximation method, we detailedly calculate the signal-to-noise ratio (SNR) of a gain-noise model of the single-mode laser, taking the cross-correlation between the quantum noise and pump noise into account. We find that, SR appears in the dependence of the SNR on the intensities of the quantum and the pump noises when the correlation coefficient between both the noises is negative; moreover, when the cross-correlation between the two noises is strongly negative, SR exhibits a resonance and a suppression versus the gain coefficient, meanwhile, the single-peaked SR and multi-peaked SR occur in the behaviors of the SNR as functions of the loss coefficient and the deterministic steady-state intensity. (c) 2005 Elsevier B.V. All rights reserved.

Density matrix Loschmidt echo and quantum phase transitions

We introduce the concept of the Loschmidt echo (LE) to the space of the reduced density matrix of spin and fermionic systems to study the density matrix LEs (DMLEs) of the one-dimensional extended Hubbard model and the transverse field Ising model. Our results show that the DMLEs are remarkably influenced by the criticality of the system, and the method is a convenient way to study quantum phase transitions.

Stochastic resonance in single-mode semiconductor lasers

Owing to the considerable virtues of semiconductor lasers for applications, they have become the main optical source for fiber communication systems recently. The behavior of stochastic resonance (SR) in direct-modulated semiconductor laser systems is investigated in this article. Considering the carrier and photon noises and the cross-correlation between the two noises, the power spectrum of the photon density and the signal-to-noise ratio (SNR) of the modulated laser system were calculated using the linear approximation method. We found that the SR always appears in the dependence of the SNR upon the bias current density, and is strongly affected by the cross-correlation coefficient of the carrier and photon noises, the frequency of modulation signal and the photon lifetime in the laser cavity. Hence, it is promising to use the SR mechanism to enhance the SNR of direct-modulated semiconductor laser systems and improve the quality of optical communication. (c) 2006 Elsevier B.V. All rights reserved.

Complex networks constructed from irrational number sequences

In this paper, we construct (d, r) networks from sequences of different irrational numbers. In detail, segment an irrational number sequence of length M into groups of d digits which represent the nodes while two consecutive groups overlap by r digits (r = 0,1,...,d-1), and the undirected edges indicate the adjacency between two consecutive groups. (3, r) and (4, r) networks are respectively constructed from 14 different irrational numbers and their topological properties are examined. By observation, we find that network topologies change with different values of d, r and even sequence length M instead of the types of irrational numbers, although they share some similar features with traditional random graphs. We make a further investigation to explain these interesting phenomena and propose the identical-degree random graph model. The results presented in this paper provide some insight into distributions of irrational number digits that may help better understanding of the nature of irrational numbers.

Generalized Viscoplastic Modeling of Debris Flow

Various concepts have been proposed or used in the development of rheological models for debris flow. The earliest model developed by Bagnold was based on the concept of the “dispersive” pressure generated by grain collisions. Bagnold’s concept appears to be theoretically sound, but his empirical model has been found to be inconsistent with most theoretical models developed from non-Newtonian fluid mechanics. Although the generality of Bagnold’s model is still at issue, debris-flow modelers in Japan have generally accepted Takahashi’s formulas derived from Bagnold’s model. Some efforts have recently been made by theoreticians in non-Newtonian fluid mechanics to modify or improve Bagnold’s concept or model. A viable rheological model should consist both of a rate-independent part and a rate-dependent part. A generalized viscoplastic fluid (GVF) model that has both parts as well as two major rheological properties (i.e., the normal stress effect and soil yield criterion) is shown to be sufficiently accurate, yet practical, for general use in debris-flow modeling. In fact, Bagnold’s model is found to be only a particular case of the GVF model. Analytical solutions for (steady) uniform debris flows in wide channels are obtained from the GVF model based on Bagnold’s simplified assumption of constant grain concentration.

Hydrate dissociation conditions for gas mixtures containing carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons using SAFT

A new method, a molecular thermodynamic model based on statistical mechanics, is employed to predict the hydrate dissociation conditions for binary gas mixtures with carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons in the presence of aqueous solutions. The statistical associating fluid theory (SAFT) equation of state is employed to characterize the vapor and liquid phases and the statistical model of van der Waals and Platteeuw for the hydrate phase. The predictions of the proposed model were found to be in satisfactory to excellent agreement with the experimental data.

Magnetic frustration induced quantum phase transitions in the S=1/2 vertically asymmetric diamond chain

This work was supported by the National Basic Research Program of China (973 Program) grant No. G2009CB929300 and the National Natural Science Foundation of China under Grant Nos. 60521001 and 60776061.

Numerical simulation of a bubble rising in shear-thinning fluids

The motion of a single bubble rising freely in quiescent non-Newtonian viscous fluids was investigated experimentally and computationally. The non-Newtonian effects in the flow of viscous inelastic fluids are modeled by the Carreau theological model. An improved level set approach for computing the incompressible two-phase flow with deformable free interface is used. The control volume formulation with the SIMPLEC algorithm incorporated is used to solve the governing equations on a staggered Eulerian grid. The simulation results demonstrate that the algorithm is robust for shear-thinning liquids with large density (rho(1)/rho(g) up to 10(3)) and high viscosity (eta(1)/eta(g) up to 10(4)). The comparison of the experimental measurements of terminal bubble shape and velocity with the computational results is satisfactory. It is shown that the local change in viscosity around a bubble greatly depends on the bubble shape and the zero-shear viscosity of non-Newtonian shear-thinning liquids. The shear-rate distribution and velocity fields are used to elucidate the formation of a region of large viscosity at the rear of a bubble as a result of the rather stagnant flow behind the bubble. The numerical results provide the basis for further investigations, such as the numerical simulation of viscoelastic fluids. (C) 2010 Elsevier B.V. All rights reserved.

Range-based attacks on links in random scale-free networks

Range and load play key roles in the problem of attacks on links in random scale-free (RSF) networks. In this paper we obtain the approximate relation between range and load in RSF networks by the generating function theory, and then give an estimation about the impact of attacks on the efficiency of the network. The results show that short-range attacks are more destructive for RSF networks, and are confirmed numerically.

Knotlike chi disclinations in the cholesteric liquid crystals

We investigate the topological properties of N(N >= 1) disclination lines in cholesteric liquid crystals. The topological structure of N disclination lines is obtained with the Hopf index and Brouwer degree. Furthermore, the knotted x disclination loops is proposed with the Hopf invariant. And we consider the stability of such configuration based on the higher order interaction. At last, the evolution of the disclinations is discussed.

Efficiency Dynamics on Two Coupled Small-World Networks

We investigate the effect of clusters in complex networks on efficiency dynamics by studying a simple efficiency model in two coupled small-world networks. It is shown that the critical network randomness corresponding to transition from a stagnant phase to a growing one decreases to zero as the connection strength of clusters increases. It is also shown for fixed randomness that the state of clusters transits from a stagnant phase to a growing one as the connection strength of clusters increases. This work can be useful for understanding the critical transition appearing in many dynamic processes on the cluster networks.

EFFICIENCY DYNAMICS ON SCALE-FREE NETWORKS WITH COMMUNITIES

The simple efficiency model is developed on scale-free networks with communities to study the effect of the communities in complex networks on efficiency dynamics. For some parameters, we found that the state of system will transit from a stagnant phase to a growing phase as the strength of community decreases.

Promotion of cooperation in the form C0C1D classified by 'degree grads' in a scale-free network

In this paper, we revisit the issue of the public goods game (PGG) on a heterogeneous graph. By introducing a new effective topology parameter, 'degree grads' phi, we clearly classify the agents into three kinds, namely, C-0, C-1, and D. The mechanism for the heterogeneous topology promoting cooperation is discussed in detail from the perspective of C0C1D, which reflects the fact that the unreasoning imitation behaviour of C-1 agents, who are 'cheated' by the well-paid C-0 agents inhabiting special positions, stabilizes the formation of the cooperation community. The analytical and simulation results for certain parameters are found to coincide well with each other. The C0C1D case provides a picture of the actual behaviours in real society and thus is potentially of interest.