Multiple scale analysis of complex networks using the empirical mode decomposition method

Empirical mode decomposition (EMD) method can decompose any complicated data into finite ‘intrinsic mode functions’ (IMFs). In this paper, we use EMD method to analyze and discuss the structural properties of complex networks. A random-walk method is used to collect the data series of network systems. Utilizing the EMD method, we decompose the obtained data into finite IMFs under different spatial scales. The analysis results show that EMD method is an effective tool for capturing the topological properties of network systems under different spatial scales, such as the modular structures of network systems and their energy densities.     

Electronic transport in double-strand poly(dG)-poly(dC) DNA segments

We study the electronic properties of a double-strand quasiperiodic DNA molecule modeled by a one-dimensional effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, considering an electronic tight-binding Hamiltonian model to investigate the electronic density of states (DOS) and the electronic transmissivity of sequences of DNA finite segments. To mimic the DNA segments, we consider the finite quasiperiodic sequences of Fibonacci's type, in a poly(dG)-poly(dC) configuration, whose building blocks are the bases guanine G and cytosine C. We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.     

Low-temperature specific heat spectra considering nonextensive long-range correlated quasiperiodic DNA molecules

We consider the low-temperature specific heat spectra of long-range correlated quasiperiodic DNA molecules using a q-gaussian distribution, and compare them with those considering the Boltzmann-Gibbs distribution. The energy spectra are calculated using the one-dimensional Schrödinger equation in a tight-binding approximation with the on-site energy exhibiting long-range disorder and non-random hopping amplitudes. We focus our attention at the low temperature region, where the specific heat spectra presents a logarithmic-periodic oscillations as a function of the temperature T around a mean value given by a characteristic dimension of the energy spectrum.     

Strategies for the separation of polyelectrolytes based on non-linear dynamics and entropic ratchets in a simple microfluidic device

We perform Monte Carlo simulations of an existing electrophoretic microchannel device used for the size separation of large DNA fragments. This device is normally operated with a constant (dc) driving field. In contrast, we consider the case of a varying (ac) driving field, in the zero-frequency limit. We find that a time-asymmetric pulse can yield interesting migration regimes, in particular bidirectional transport for different molecular sizes. We also study a spatially asymmetric version of the device and show that it can rectify unbiased but non-equilibrium molecular motion, in agreement with previous predictions for entropic ratchets. Finally, at finite frequency we uncover a resonance for the molecular velocity in the channel which could lead to improved performance. Received: 16 November 2001 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Evolution of canalizing Boolean networks

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive walk, which allows us to explore the fitness landscape. Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations. We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness. Furthermore, in spite of having such a high degree of robustness, the evolved networks still share many features with “chaotic” networks.     

Evolutionary ultimatum game on complex networks under incomplete information

This paper studies the evolutionary ultimatum game on networks when agents have incomplete information about the strategies of their neighborhood agents. Our model assumes that agents may initially display low fairness behavior, and therefore, may have to learn and develop their own strategies in this unknown environment. The Genetic Algorithm Learning Classifier System (GALCS) is used in the model as the agent strategy learning rule. Aside from the Watts-Strogatz (WS) small-world network and its variations, the present paper also extends the spatial ultimatum game to the Barabási-Albert (BA) scale-free network. Simulation results show that the fairness level achieved is lower than in situations where agents have complete information about other agents’ strategies. The research results display that fairness behavior will always emerge regardless of the distribution of the initial strategies. If the strategies are randomly distributed on the network, then the long-term agent fairness levels achieved are very close given unchanged learning parameters. Neighborhood size also has little effect on the fairness level attained. The simulation results also imply that WS small-world and BA scale-free networks have different effects on the spatial ultimatum game. In ultimatum game on networks with incomplete information, the WS small-world network and its variations favor the emergence of fairness behavior slightly more than the BA network where agents are heterogeneously structured.     

Other-regarding preference and the evolutionary prisoner’s dilemma on complex networks

Prevailing models of the evolutionary prisoner’s game on networks always assume that agents are pursuing their own profit maximization. But the results from experimental games show that many agents have other-regarding preference. In this paper, we study the emergence of cooperation from the prisoner’s dilemma game on complex networks while some agents exhibit other-regarding preference such as inequality aversion, envious and guilty emotions. Contrary to common ideas, the simulation results show that the existence of inequality aversion agents does not promote cooperation emergence on a BA (Barabási and Albert) scale-free network in most situations. If the defection attraction is big and agents exhibit strong preference for inequality aversion, the frequency of cooperators will be lower than in situations where no inequality aversion agents exist. In some cases, the existence of the inequality agents will even induce the frequency of cooperators to zero, a feature which is not observed in previous research on the prisoner’s dilemma game when the underlying interaction topology is a BA scale-free network. This means that if an agent cares about equality too much, it will be difficult for cooperation to emerge and the frequency of cooperators will be low on BA networks. The research on the effect of envy or guilty emotions on the emergence of cooperation in the prisoner’s dilemma game on BA networks obtains similar results, though some differences exist. However, simulation results on a WS (Watts and Strogatz) small-world network display another scenario. If agents care about the inequality of agents very much, the WS network favors cooperation emergence in the prisoners’ dilemma game when other-regarding agents exist. If the agent weight on other-regarding is lowered, the cooperation frequencies emerging on a WS network are not much different from those in situations without other-regarding agents, although the frequency of cooperators is lower than those of the situation without other-regarding preference agents sometimes. All the simulation results imply that inequality aversion and its variations can have important effects on cooperation emergence in the prisoner’s dilemma game, and different network topologies have different effects on cooperation emergence in the prisoner’s dilemma game played on complex networks.     

Dynamics-driven evolution to structural heterogeneity in complex networks

The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local mutations have higher chances of getting integrated into its structure, the system can evolve into a highly heterogeneous small-world with a global hub (whose connectivity is proportional to the network size), strong local connection correlations and power-law-like degree distribution. Networks with better dynamical performance are achieved if structural evolution occurs much slower than the network dynamics. Structural heterogeneity of many biological and social dynamical systems may also be driven by various dynamics-structure coupling mechanisms.     

Conduction transition of nano-scaled molecular wires driven by environment coupling

We propose a hybridization model to simulate a molecular wire coupling with the environmental molecules. Results reveal that the conduction transition from conducting to semiconducting depends on the coupling strength. In our simulations, the non-equilibrium Green's function method is employed to calculate the current-voltage relationship for the molecular wire through metallic contacts. Our calculations show that the band gap can be manipulated from the outside molecules coupling. Temperature dependence of the conductivity is represented in our results with strong dependence in high temperature range, which is qualitatively comparable with the experimental results of DNA. In our results, with small coupling, the current is enhanced by the exchange. On the contrary, too large a coupling results in localization of the transport carriers, leading to a semiconducting like property. We try to associate this study with the conducting property of DNA, which can be manipulated by environmental modulation.     

Dimensionality-induced effects on transport properties of poly(G)-poly(C)

We consider a ladder model of DNA for addressing the relation between the transport properties and electronic structure and the interbase coupling in poly(G)-poly(C). Based on the negative eigenvalue theorem and transfer matrix method, the density of states and current-voltage characteristics are evaluated, and an expression for the dependence of the band gap on intra- and inter-strand nucleobase couplings is proposed. There exists a semiconducting-metallic transition in poly(G)-poly(C) by modulating the interbase coupling, and the physical nature is traced back to dimensionality-induced effects. Our results provide possibility for interpreting a variety of transport behaviors observed in DNA molecules.     

Networking effects on evolutionary snowdrift game in networks with fixed degrees

We study the effects of spatial structures other than the degree distribution on the extent of the emergence of cooperation in an evolutionary snowdrift game. By swapping the links in three different types of regular lattices with a fixed degree k, we study how the frequency of cooperator f_C changes as the clustering coefficient (CC), which signifies how the nearest neighbors of a vertex are connected, and the sharing coefficient (SC), which signifies how the next-nearest neighbors of a vertex are shared by the nearest neighbors, are varied. For small k, a non-vanishing CC tends to suppress f_C. A non-vanishing SC also leads to a suppressed f_C for the networks studied. As the degree increases, the sensitivity of f_C to the network properties is found to become increasingly weak. The result is discussed within the context of the ranking patterns of average payoffs as k changes. An approximation for f_C, which is based on the idea of a finite fully connected network and gives results in good agreement with numerical results, is derived in the limit of large k.     

Evolutionary public goods games on scale-free networks with unequal payoff allocation mechanism

In this paper, we bring an unequal payoff allocation mechanism into evolutionary public goods game on scale-free networks and focus on the cooperative behavior of the system. The unequal mechanism can be tuned by one parameter α: if α>0, the hub nodes can use its degree advantage to collect more payoff; if α<0, numerous non-hub nodes will obtain more payoff in a single round game. Simulation results show that the cooperation level has a non-trivial dependence on α. For the small enhancement factor r, the cooperator frequency can be promoted by both negative and positive α. For large r, there exists an optimal α that can obtain the highest cooperation level. Our results may sharpen the understanding of the emergence of cooperation induced by the unequal payoff allocation mechanism.     

A very fast algorithm for detecting community structures in complex networks

In this paper, a new algorithm is proposed, which uses only local information to analyze community structures in complex networks. The algorithm is based on a table that describes a network and a virtual cache similar to the cache in the computer structure. When being tested on some typical computer-generated and real-world networks, this algorithm demonstrates excellent detection results and very fast processing performance, much faster than the existing comparable algorithms of the same kind.     

Adaptation to synchronization in phase-oscillator networks

We introduce an adaptation algorithm by which an ensemble of coupled oscillators with attractive and repulsive interactions is induced to adopt a prescribed synchronized state. While the performance of adaptation is controlled by measuring a macroscopic quantity, which characterizes the achieved degree of synchronization, adaptive changes are introduced at the microscopic level of the interaction network, by modifying the configuration of repulsive interactions. This scheme emulates the distinct levels of selection and mutation in biological evolution and learning.     

Effects of small world topology on the critical boundary for Boolean networks

Due to their complexity, real dynamic systems are widely regarded as operating on the boundary between order and chaos. Therefore it is of great interest to determine analytical expressions for this boundary. For random Boolean networks model, a well known critical value of bias is established as , where K is the mean connectivity. Recent research shows, however, that this expression may need to be modified. In this paper, we shall focus on the effects of topology deviation from the random network assumption since the topologies of many real networks are neither pure random nor fully regular Boolean networks. A modification of the critical boundary condition is given with parameters of the degree distribution in the setting of more realistic networks modeled with small world features.     

Networks of interactions in the secondary and tertiary structure of ribosomal RNA

We construct four different structural networks for both the secondary and tertiary structures of the 16S and 23S ribosomal RNAs (rRNAs) in the high-resolution crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits, and investigate topological characteristics of the rRNA structures by determining relevant measures, such as the characteristic path length, the clustering coefficient, and the helix betweenness. This study reveals that the 23S rRNA network is more compact than the 16S rRNA networks, reflecting the more globular overall structure of the 23S rRNA relative to the 16S rRNA. In particular, the large number of tertiary interactions in the 23S rRNA tends to cluster, accounting for its small-world network properties. In addition, although the rRNA networks are not the scale-free network, their helix betweenness has a power-law distribution and is correlated with the phylogenetic conservation of helices. The higher the helix betweenness, the more conserved the helix. These results suggest a potential role of the rRNA network as a new quantitative approach in rRNA research.     

Cooperation in N-person evolutionary snowdrift game in scale-free Barabási-Albert networks

Cooperation in the N-person evolutionary snowdrift game (NESG) is studied in scale-free Barabási-Albert (BA) networks. Due to the inhomogeneity of the network, two versions of NESG are proposed and studied. In a model where the size of the competing group varies from agent to agent, the fraction of cooperators drops as a function of the payoff parameter. The networking effect is studied via the fraction of cooperative agents for nodes with a particular degree. For small payoff parameters, it is found that the small-k agents are dominantly cooperators, while large-k agents are of non-cooperators. Studying the spatial correlation reveals that cooperative agents will avoid to be nearest neighbors and the correlation disappears beyond the next-nearest neighbors. The behavior can be explained in terms of the networking effect and payoffs. In another model with a fixed size of competing groups, the fraction of cooperators could show a non-monotonic behavior in the regime of small payoff parameters. This non-trivial behavior is found to be a combined effect of the many agents with the smallest degree in the BA network and the increasing fraction of cooperators among these agents with the payoff for small payoffs.     

Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.     

Statistical properties of weighted complex networks characterized by metaweights

We propose several characterizations of weighted complex networks by incorporating the concept of metaweight into the clustering coefficient, degree correlation, and module decomposition. These incorporations make it possible to describe weighted networks depending on how strongly we emphasize weights. Using some applications to real-world weighted networks, we demonstrate that the proposed approach provides rich information that was inaccessible by previous analyses such as the degree correlation for a specific magnitude of weights or the community structure under controlling the importance of roles of the topology and weights.     

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system, one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational heat resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process.