Scaling theory of transport in complex networks

Transport is an important function in many network systems and understanding its behavior on biological, social, and technological networks is crucial for a wide range of applications. However, it is a property that is not well-understood in these systems and this is probably due to the lack of a general theoretical framework. Here, based on the finding that renormalization can be applied to bio-networks, we develop a scaling theory of transport in self-similar networks. We demonstrate the networks invariance under length scale renormalization and we show that the problem of transport can be characterized in terms of a set of critical exponents. The scaling theory allows us to determine the influence of the modular structure on transport. We also generalize our theory by presenting and verifying scaling arguments for the dependence of transport on microscopic features, such as the degree of the nodes and the distance between them. Using transport concepts such as diffusion and resistance we exploit this invariance and we are able to explain, based on the topology of the network, recent experimental results on the broad flow distribution in metabolic networks.Comment: 8 pages, 6 figure

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by using redundant or alternative pathways. Thus, only a limited number of genes have been identified to be lethal to the cell. In this regard, the reaction-centric gene deletion study has a limitation in understanding the metabolic robustness. Here, we report the use of flux-sum, which is the summation of all incoming or outgoing fluxes around a particular metabolite under pseudo-steady state conditions, as a good conserved property for elucidating such robustness of E. coli from the metabolite point of view. The functional behavior, as well as the structural and evolutionary properties of metabolites essential to the cell survival, was investigated by means of a constraints-based flux analysis under perturbed conditions. The essential metabolites are capable of maintaining a steady flux-sum even against severe perturbation by actively redistributing the relevant fluxes. Disrupting the flux-sum maintenance was found to suppress cell growth. This approach of analyzing metabolite essentiality provides insight into cellular robustness and concomitant fragility, which can be used for several applications, including the development of new drugs for treating pathogens.Comment: Supplements available at http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pd

Dynamics of a Josephson Array in a Resonant Cavity

We derive dynamical equations for a Josephson array coupled to a resonant cavity by applying the Heisenberg equations of motion to a model Hamiltonian described by us earlier [Phys. Rev. B {\bf 63}, 144522 (2001); Phys. Rev. B {\bf 64}, 179902 (E)]. By means of a canonical transformation, we also show that, in the absence of an applied current and dissipation, our model reduces to one described by Shnirman {\it et al} [Phys. Rev. Lett. {\bf 79}, 2371 (1997)] for coupled qubits, and that it corresponds to a capacitive coupling between the array and the cavity mode. From extensive numerical solutions of the model in one dimension, we find that the array locks into a coherent, periodic state above a critical number of active junctions, that the current-voltage characteristics of the array have self-induced resonant steps (SIRS's), that when $N_a$ active junctions are synchronized on a SIRS, the energy emitted into the resonant cavity is quadratic in $N_a$, and that when a fixed number of junctions is biased on a SIRS, the energy is linear in the input power. All these results are in agreement with recent experiments. By choosing the initial conditions carefully, we can drive the array into any of a variety of different integer SIRS's. We tentatively identify terms in the equations of motion which give rise to both the SIRS's and the coherence threshold. We also find higher-order integer SIRS's and fractional SIRS's in some simulations. We conclude that a resonant cavity can produce threshold behavior and SIRS's even in a one-dimensional array with appropriate experimental parameters, and that the experimental data, including the coherent emission, can be understood from classical equations of motion.Comment: 15 pages, 10 eps figures, submitted to Phys. Rev.

Walks on Apollonian networks

We carry out comparative studies of random walks on deterministic Apollonian networks (DANs) and random Apollonian networks (RANs). We perform computer simulations for the mean first passage time, the average return time, the mean-square displacement, and the network coverage for unrestricted random walk. The diffusions both on DANs and RANs are proved to be sublinear. The search efficiency for walks with various strategies and the influence of the topology of underlying networks on the dynamics of walks are discussed. Contrary to one's intuition, it is shown that the self-avoiding random walk, which has been verified as an optimal strategy for searching on scale-free and small-world networks, is not the best strategy for the DAN in the thermodynamic limit.Comment: 5 pages, 4 figure

Two-Component Genetic Switch as a Synthetic Module with Tunable Stability

Despite stochastic fluctuations, some genetic switches are able to retain their expression states through multiple cell divisions, providing epigenetic memory. We propose a novel rationale for tuning the functional stability of a simple synthetic gene switch through protein dimerization. Introducing an approximation scheme to access long-time stochastic dynamics of multiple-component gene circuits, we find that the spontaneous switching rate may exhibit greater than 8orders of magnitude variation. The manipulation of the circuit's biochemical properties offers a practical strategy for designing robust epigenetic memory with synthetic circuits.open101

Recursive graphs with small-world scale-free properties

We discuss a category of graphs, recursive clique trees, which have small-world and scale-free properties and allow a fine tuning of the clustering and the power-law exponent of their discrete degree distribution. We determine relevant characteristics of those graphs: the diameter, degree distribution, and clustering parameter. The graphs have also an interesting recursive property, and generalize recent constructions with fixed degree distributions.Comment: 4 pages, 2 figure

Simple models of small world networks with directed links

We investigate the effect of directed short and long range connections in a simple model of small world network. Our model is such that we can determine many quantities of interest by an exact analytical method. We calculate the function $V(T)$, defined as the number of sites affected up to time $T$ when a naive spreading process starts in the network. As opposed to shortcuts, the presence of un-favorable bonds has a negative effect on this quantity. Hence the spreading process may not be able to affect all the network. We define and calculate a quantity named the average size of accessible world in our model. The interplay of shortcuts, and un-favorable bonds on the small world properties is studied.Comment: 15 pages, 9 figures, published versio

Eigenstates of a Small Josephson Junction Coupled to a Resonant Cavity

We carry out a quantum-mechanical analysis of a small Josephson junction coupled to a single-mode resonant cavity. We find that the eigenstates of the combined junction-cavity system are strongly entangled only when the gate voltage applied at one of the superconducting islands is tuned to certain special values. One such value corresponds to the resonant absorption of a single photon by Cooper pairs in the junction. Another special value corresponds to a {\em two-photon} absorption process. Near the single-photon resonant absorption, the system is accurately described by a simplified model in which only the lowest two levels of the Josephson junction are retained in the Hamiltonian matrix. We noticed that this approximation does not work very well as the number of photons in the resonator increases. Our system shows also the phenomenon of ``collapse and revival'' under suitable initial conditions, and our full numerical solution agrees with the two level approximation result.Comment: 7 pages, and 6 figures. To be published in Phys. Rev.

Potts Model On Random Trees

We study the Potts model on locally tree-like random graphs of arbitrary degree distribution. Using a population dynamics algorithm we numerically solve the problem exactly. We confirm our results with simulations. Comparisons with a previous approach are made, showing where its assumption of uniform local fields breaks down for networks with nodes of low degree.Comment: 10 pages, 3 figure

Constrained spin dynamics description of random walks on hierarchical scale-free networks

We study a random walk problem on the hierarchical network which is a scale-free network grown deterministically. The random walk problem is mapped onto a dynamical Ising spin chain system in one dimension with a nonlocal spin update rule, which allows an analytic approach. We show analytically that the characteristic relaxation time scale grows algebraically with the total number of nodes $N$ as $T \sim N^z$. From a scaling argument, we also show the power-law decay of the autocorrelation function C_{\bfsigma}(t)\sim t^{-\alpha}, which is the probability to find the Ising spins in the initial state {\bfsigma} after $t$ time steps, with the state-dependent non-universal exponent $\alpha$. It turns out that the power-law scaling behavior has its origin in an quasi-ultrametric structure of the configuration space.Comment: 9 pages, 6 figure