Random walks on weighted networks

Entropy rate of random walks on complex networks under stochastic resetting

Stochastic processes under resetting at random times have attracted a lot of attention in recent years and served as illustrations of nontrivial and interesting static and dynamic features of stochastic dynamics. In this paper, we aim to address how the entropy rate is affected by stochastic resetting in discrete-time Markovian processes, and we explore nontrivial effects of the resetting in the mixing properties of a stochastic process. In particular, we consider resetting random walks (RRWs) with a single resetting node on three different types of networks: degree-regular random networks, a finite-size Cayley tree, and a Barabási-Albert (BA) scale-free network, and we compute the entropy rate as a function of the resetting probability γ. Interestingly, for the first two types of networks, the entropy rate shows a nonmonotonic dependence on γ. There exists an optimal value of γ at which the entropy rate reaches a maximum. Such a maximum is larger than that of maximal-entropy random walks (MREWs) and standard random walks (SRWs) on the same topology, while for the BA network the entropy rate of RRWs either shows a unique maximum or decreases monotonically with γ, depending upon the choice of the resetting node. When the maximum entropy rate of RRWs exists, it can be higher or lower than that of MREWs or SRWs. Our study reveals a nontrivial effect of stochastic resetting on nonequilibrium statistical physics.

Random walks on complex networks under time-dependent stochastic resetting

We study discrete-time random walks on networks subject to a time-dependent stochastic resetting, where the walker either hops randomly between neighboring nodes with a probability 1-ϕ(a) or is reset to a given node with a complementary probability ϕ(a). The resetting probability ϕ(a) depends on the time a since the last reset event (also called a, the age of the walker). Using the renewal approach and spectral decomposition of the transition matrix, we formulate the stationary occupation probability of the walker at each node and the mean first passage time between two arbitrary nodes. Concretely, we consider two different time-dependent resetting protocols that are both exactly solvable. One is that ϕ(a) is a step-shaped function of a and the other one is that ϕ(a) is a rational function of a. We demonstrate the theoretical results on several different networks, also validated by numerical simulations, and find that the time-modulated resetting protocols can be more advantageous than the constant-probability resetting in accelerating the completion of a target search process.

Lexicons of Key Terms in Scholarly Texts and Their Disciplinary Differences: From Quantum Semantics Construction to Relative-Entropy-Based Comparisons

Complex networks are often used to analyze written text and reports by rendering texts in the form of a semantic network, forming a lexicon of words or key terms. Many existing methods to construct lexicons are based on counting word co-occurrences, having the advantage of simplicity and ease of applicability. Here, we use a quantum semantics approach to generalize such methods, allowing us to model the entanglement of terms and words. We show how quantum semantics can be applied to reveal disciplinary differences in the use of key terms by analyzing 12 scholarly texts that represent the different positions of various disciplinary schools (of conceptual change research) on the same topic (conceptual change). In addition, attention is paid to how closely the lexicons corresponding to different positions can be brought into agreement by suitable tuning of the entanglement factors. In comparing the lexicons, we invoke complex network-based analysis based on exponential matrix transformation and use information theoretic relative entropy (Jensen-Shannon divergence) as the operationalization of differences between lexicons. The results suggest that quantum semantics is a viable way to model the disciplinary differences of lexicons and how they can be tuned for a better agreement.

COSNet i : ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes

BACKGROUND

Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex.

RESULTS

[Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites.

CONCLUSIONS

[Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.

Nearly reducible finite Markov chains: Theory and algorithms

Finite Markov chains, memoryless random walks on complex networks, appear commonly as models for stochastic dynamics in condensed matter physics, biophysics, ecology, epidemiology, economics, and elsewhere. Here, we review exact numerical methods for the analysis of arbitrary discrete- and continuous-time Markovian networks. We focus on numerically stable methods that are required to treat nearly reducible Markov chains, which exhibit a separation of characteristic timescales and are therefore ill-conditioned. In this metastable regime, dense linear algebra methods are afflicted by propagation of error in the finite precision arithmetic, and the kinetic Monte Carlo algorithm to simulate paths is unfeasibly inefficient. Furthermore, iterative eigendecomposition methods fail to converge without the use of nontrivial and system-specific preconditioning techniques. An alternative approach is provided by state reduction procedures, which do not require additional a priori knowledge of the Markov chain. Macroscopic dynamical quantities, such as moments of the first passage time distribution for a transition to an absorbing state, and microscopic properties, such as the stationary, committor, and visitation probabilities for nodes, can be computed robustly using state reduction algorithms. The related kinetic path sampling algorithm allows for efficient sampling of trajectories on a nearly reducible Markov chain. Thus, all of the information required to determine the kinetically relevant transition mechanisms, and to identify the states that have a dominant effect on the global dynamics, can be computed reliably even for computationally challenging models. Rare events are a ubiquitous feature of realistic dynamical systems, and so the methods described herein are valuable in many practical applications.

Random walks on complex networks with multiple resetting nodes: A renewal approach

Due to wide applications in diverse fields, random walks subject to stochastic resetting have attracted considerable attention in the last decade. In this paper, we study discrete-time random walks on complex networks with multiple resetting nodes. Using a renewal approach, we derive exact expressions of the occupation probability of the walker in each node and mean first-passage time between arbitrary two nodes. All the results can be expressed in terms of the spectral properties of the transition matrix in the absence of resetting. We demonstrate our results on circular networks, stochastic block models, and Barabási-Albert scale-free networks and find the advantage of the resetting processes to multiple resetting nodes in a global search on such networks. Finally, the distribution of resetting probabilities is optimized via a simulated annealing algorithm, so as to minimize the mean first-passage time averaged over arbitrary two distinct nodes.

Numerical analysis of first-passage processes in finite Markov chains exhibiting metastability

We describe state-reduction algorithms for the analysis of first-passage processes in discrete- and continuous-time finite Markov chains. We present a formulation of the graph transformation algorithm that allows for the evaluation of exact mean first-passage times, stationary probabilities, and committor probabilities for all nonabsorbing nodes of a Markov chain in a single computation. Calculation of the committor probabilities within the state-reduction formalism is readily generalizable to the first hitting problem for any number of alternative target states. We then show that a state-reduction algorithm can be formulated to compute the expected number of times that each node is visited along a first-passage path. Hence, all properties required to analyze the first-passage path ensemble (FPPE) at both a microscopic and macroscopic level of detail, including the mean and variance of the first-passage time distribution, can be computed using state-reduction methods. In particular, we derive expressions for the probability that a node is visited along a direct transition path, which proceeds without returning to the initial state, considering both the nonequilibrium and equilibrium (steady-state) FPPEs. The reactive visitation probability provides a rigorous metric to quantify the dynamical importance of a node for the productive transition between two endpoint states and thus allows the local states that facilitate the dominant transition mechanisms to be readily identified. The state-reduction procedures remain numerically stable even for Markov chains exhibiting metastability, which can be severely ill-conditioned. The rare event regime is frequently encountered in realistic models of dynamical processes, and our methodology therefore provides valuable tools for the analysis of Markov chains in practical applications. We illustrate our approach with numerical results for a kinetic network representing a structural transition in an atomic cluster.

Random walks on complex networks with first-passage resetting

We study discrete-time random walks on arbitrary networks with first-passage resetting processes. To the end, a set of nodes are chosen as observable nodes, and the walker is reset instantaneously to a given resetting node whenever it hits either of observable nodes. We derive exact expressions of the stationary occupation probability, the average number of resets in the long time, and the mean first-passage time between arbitrary two nonobservable nodes. We show that all the quantities can be expressed in terms of the fundamental matrix Z=(I-Q)^{-1}, where I is the identity matrix and Q is the transition matrix between nonobservable nodes. Finally, we use ring networks, two-dimensional square lattices, barbell networks, and Cayley trees to demonstrate the advantage of first-passage resetting in global search on such networks.

Identifying molecules as biosignatures with assembly theory and mass spectrometry

The search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab.

Mean encounter times for multiple random walkers on networks

We introduce a general approach for the study of the collective dynamics of noninteracting random walkers on connected networks. We analyze the movement of R independent (Markovian) walkers, each defined by its own transition matrix. By using the eigenvalues and eigenvectors of the R independent transition matrices, we deduce analytical expressions for the collective stationary distribution and the average number of steps needed by the random walkers to start in a particular configuration and reach specific nodes the first time (mean first-passage times), as well as global times that characterize the global activity. We apply these results to the study of mean first-encounter times for local and nonlocal random walk strategies on different types of networks, with both synchronous and asynchronous motion.

Optimal dimensionality reduction of Markov chains using graph transformation

Markov chains can accurately model the state-to-state dynamics of a wide range of complex systems, but the underlying transition matrix is ill-conditioned when the dynamics feature a separation of timescales. Graph transformation (GT) provides a numerically stable method to compute exact mean first passage times (MFPTs) between states, which are the usual dynamical observables in continuous-time Markov chains (CTMCs). Here, we generalize the GT algorithm to discrete-time Markov chains (DTMCs), which are commonly estimated from simulation data, for example, in the Markov state model approach. We then consider the dimensionality reduction of CTMCs and DTMCs, which aids model interpretation and facilitates more expensive computations, including sampling of pathways. We perform a detailed numerical analysis of existing methods to compute the optimal reduced CTMC, given a partitioning of the network into metastable communities (macrostates) of nodes (microstates). We show that approaches based on linear algebra encounter numerical problems that arise from the requisite metastability. We propose an alternative approach using GT to compute the matrix of intermicrostate MFPTs in the original Markov chain, from which a matrix of weighted intermacrostate MFPTs can be obtained. We also propose an approximation to the weighted-MFPT matrix in the strongly metastable limit. Inversion of the weighted-MFPT matrix, which is better conditioned than the matrices that must be inverted in alternative dimensionality reduction schemes, then yields the optimal reduced Markov chain. The superior numerical stability of the GT approach therefore enables us to realize optimal Markovian coarse-graining of systems with rare event dynamics.

Random growth networks with exponential degree distribution

A great variety of complex networks can be well represented as random graphs with some constraints: for instance, a provided degree distribution, a smaller diameter, and a higher clustering coefficient. Among them, the degree distribution has attracted considerable attention from various science communities in the last few decades. In this paper, we focus mainly on a family of random graphs modeling complex networks that have an exponential degree distribution; i.e., P(k)∼ exp(αk), where k is the degree of a vertex, P(k) is a probability for choosing randomly a vertex with degree equal to k, and α is a constant. To do so, we first introduce two types of operations: type-A operation and type-B operation. By both the helpful operations, we propose an available algorithm A for a seminal model to construct exactly solvable random graphs, which are able to be extended to a graph space S(p,p^c,t) with probability parameters p and p^c satisfying p+p^c=1. Based on the graph space S(p,p^c,t), we discuss several topological structure properties of interest on each member N(p,p^c,t) itself and find model N(p,p^c,t) to exhibit the small-world property and assortative mixing. In addition, we also report a fact that in some cases, two arbitrarily chosen members might have completely different other topological properties, such as the total number of spanning trees, although they share a degree distribution in common. Extensive experimental simulations are in strong agreement with our analytical results.

Estimation of global and local complexities of brain networks: A random walks approach

The complexity of brain activity has been observed at many spatial scales and has been proposed to differentiate between mental states and disorders. Here we introduced a new measure of (global) network complexity, constructed as the sum of the complexities of its nodes (i.e., local complexity). The complexity of each node is obtained by comparing the sample entropy of the time series generated by the movement of a random walker on the network resulting from removing the node and its connections, with the sample entropy of the time series obtained from a regular lattice (ordered state) and a random network (disordered state). We studied the complexity of fMRI-based resting-state networks. We found that positively correlated (pos) networks comprising only the positive functional connections have higher complexity than anticorrelation (neg) networks (comprising the negative connections) and the network consisting of the absolute value of all connections (abs). We also observed a significant correlation between complexity and the strength of functional connectivity in the pos network. Our results suggest that the pos network is related to the information processing in the brain and that functional connectivity studies should analyze pos and neg networks separately instead of the abs network, as is commonly done.

Correlation functions, mean first passage times, and the Kemeny constant

Markov processes are widely used models for investigating kinetic networks. Here, we collate and present a variety of results pertaining to kinetic network models in a unified framework. The aim is to lay out explicit links between several important quantities commonly studied in the field, including mean first passage times (MFPTs), correlation functions, and the Kemeny constant. We provide new insights into (i) a simple physical interpretation of the Kemeny constant, (ii) a relationship to infer equilibrium distributions and rate matrices from measurements of MFPTs, and (iii) a protocol to reduce the dimensionality of kinetic networks based on specific requirements that the MFPTs in the coarse-grained system should satisfy. We prove that this protocol coincides with the one proposed by Hummer and Szabo [J. Phys. Chem. B 119, 9029 (2014)], and it leads to a variational principle for the Kemeny constant. Finally, we introduce a modification of this protocol, which preserves the Kemeny constant. Our work underpinning the theoretical aspects of kinetic networks will be useful in applications including milestoning and path sampling algorithms in molecular simulations.

An ensemble of random graphs with identical degree distribution

Degree distribution, or equivalently called degree sequence, has been commonly used to study a large number of complex networks in the past few years. This reveals some intriguing results, for instance, the popularity of power-law distribution in most of these networks under consideration. Along such a research line, in this paper, we generate an ensemble of random graphs with an identical degree distribution P(k)∼k^-γ (γ=3) as proved shortly, denoted as graph space N(p,q,t), where probability parameters p and q hold on p+q=1. Next, we study some topological structure properties of great interest on each member in the graph space N(p,q,t) using both precisely analytical calculations and extensively numerical simulations, as follows. From the theoretical point of view, given an ultrasmall constant p_c, perhaps only the graph model N(1,0,t) is small-world and the others are not in terms of diameter. Then, we obtain exact solutions for a spanning tree number on two deterministic graph models in the graph space N(p,q,t), which gives both upper bound and lower bound for that of other members. Meanwhile, for an arbitrary p(≠1), we prove using the Pearson correlation coefficient that the graph model N(p,q,t) does go through two phase transitions over time, i.e., starting by a nonassortative pattern, then suddenly going into a disassortative region, and gradually converging to an initial position (nonassortative point). Therefore, to some extent, the three topological parameters above can serve as the complementary measures for degree distribution to help us clearly distinguish all members in the graph space N(p,q,t). In addition, one "null" graph model is built.

Aging in transport processes on networks with stochastic cumulative damage

In this paper we explore the evolution of transport capacity on networks with stochastic incidence of damage and accumulation of faults in their connections. For each damaged configuration of the network, we analyze a Markovian random walker that hops over weighted links that quantify the capacity of transport of each connection. The weights of the links in the network evolve due to randomly occurring damage effects that reduce gradually the transport capacity of the structure. We introduce a global measure to determine the functionality of each configuration and how the system ages due to the accumulation of damage that cannot be repaired completely. Then, by assuming a minimum value of the functionality required for the system to be "alive," we explore the statistics of the lifetimes for several realizations of this process in different types of networks. Finally, we analyze the characteristic longevity of such a system and its relation with the "complexity" of the network structure. One finding is that systems with greater complexity live longer. Our approach introduces a model of aging processes relating the reduction of functionality with the accumulation of "misrepairs" and the lifetime of a complex system.

Approach to the inverse problem of superdiffusion on finite systems based on time-dependent long-range navigation

This work addresses the superdiffusive motion of a random walker on a discrete finite-size substrate. It is shown that, with the inclusion of suitably tuned time-dependent probability of large distance jumps over the substrate, the mean square displacement (MSD) of the walker has a power-law dependence on time with a previously chosen exponent γ>1. The developed framework provides an exact solution to the inverse problem, i.e., an adequate jump probability function leading to a preestablished solution is evaluated. Using the Markov Chain (MC) formalism, an exact map for the time dependence of the probability function is derived, which depends on the topology of the substrate and on the chosen value of γ. While the formalism imposes no restriction on the substrate, being applicable from ordered Euclidean lattices to complex networks, results for the cycle graph and two-dimensional torus are highlighted. It is also shown that, based on the previously derived probability function, MSD values resulting from direct numerical simulations agree quite well with those solely obtained within the MC framework.

Emergence of encounter networks due to human mobility

There is a burst of work on human mobility and encounter networks. However, the connection between these two important fields just begun recently. It is clear that both are closely related: Mobility generates encounters, and these encounters might give rise to contagion phenomena or even friendship. We model a set of random walkers that visit locations in space following a strategy akin to Lévy flights. We measure the encounters in space and time and establish a link between walkers after they coincide several times. This generates a temporal network that is characterized by global quantities. We compare this dynamics with real data for two cities: New York City and Tokyo. We use data from the location-based social network Foursquare and obtain the emergent temporal encounter network, for these two cities, that we compare with our model. We found long-range (Lévy-like) distributions for traveled distances and time intervals that characterize the emergent social network due to human mobility. Studying this connection is important for several fields like epidemics, social influence, voting, contagion models, behavioral adoption and diffusion of ideas.

Lévy random walks on multiplex networks

Random walks constitute a fundamental mechanism for many dynamics taking place on complex networks. Besides, as a more realistic description of our society, multiplex networks have been receiving a growing interest, as well as the dynamical processes that occur on top of them. Here, inspired by one specific model of random walks that seems to be ubiquitous across many scientific fields, the Lévy flight, we study a new navigation strategy on top of multiplex networks. Capitalizing on spectral graph and stochastic matrix theories, we derive analytical expressions for the mean first passage time and the average time to reach a node on these networks. Moreover, we also explore the efficiency of Lévy random walks, which we found to be very different as compared to the single layer scenario, accounting for the structure and dynamics inherent to the multiplex network. Finally, by comparing with some other important random walk processes defined on multiplex networks, we find that in some region of the parameters, a Lévy random walk is the most efficient strategy. Our results give us a deeper understanding of Lévy random walks and show the importance of considering the topological structure of multiplex networks when trying to find efficient navigation strategies.

First-passage phenomena in hierarchical networks

In this paper we study Markov processes and related first-passage problems on a class of weighted, modular graphs which generalize the Dyson hierarchical model. In these networks, the coupling strength between two nodes depends on their distance and is modulated by a parameter σ. We find that, in the thermodynamic limit, ergodicity is lost and the "distant" nodes cannot be reached. Moreover, for finite-sized systems, there exists a threshold value for σ such that, when σ is relatively large, the inhomogeneity of the coupling pattern prevails and "distant" nodes are hardly reached. The same analysis is carried on also for generic hierarchical graphs, where interactions are meant to involve p-plets (p>2) of nodes, finding that ergodicity is still broken in the thermodynamic limit, but no threshold value for σ is evidenced, ultimately due to a slow growth of the network diameter with the size.

Spectra of weighted scale-free networks

Much information about the structure and dynamics of a network is encoded in the eigenvalues of its transition matrix. In this paper, we present a first study on the transition matrix of a family of weight driven networks, whose degree, strength, and edge weight obey power-law distributions, as observed in diverse real networks. We analytically obtain all the eigenvalues, as well as their multiplicities. We then apply the obtained eigenvalues to derive a closed-form expression for the random target access time for biased random walks occurring on the studied weighted networks. Moreover, using the connection between the eigenvalues of the transition matrix of a network and its weighted spanning trees, we validate the obtained eigenvalues and their multiplicities. We show that the power-law weight distribution has a strong effect on the behavior of random walks.

Anomalous behavior of trapping in extended dendrimers with a perfect trap

Compact and extended dendrimers are two important classes of dendritic polymers. The impact of the underlying structure of compact dendrimers on dynamical processes has been much studied, yet the relation between the dynamical and structural properties of extended dendrimers remains not well understood. In this paper, we study the trapping problem in extended dendrimers with generation-dependent segment lengths, which is different from that of compact dendrimers where the length of the linear segments is fixed. We first consider a particular case that the deep trap is located at the central node, and derive an exact formula for the average trapping time (ATT) defined as the average of the source-to-trap mean first passage time over all starting points. Then, using the obtained result we deduce a closed-form expression for the ATT to an arbitrary trap node, based on which we further obtain an explicit solution to the ATT corresponding to the trapping issue with the trap uniformly distributed in the polymer systems. We show that the trap location has a substantial influence on the trapping efficiency measured by the ATT, which increases with the shortest distance from the trap to the central node, a phenomenon similar to that for compact dendrimers. In contrast to this resemblance, the leading terms of ATTs for the three trapping problems differ drastically between extended and compact dendrimers, with the trapping processes in the extended dendrimers being less efficient than in compact dendrimers.

Mixed random walks with a trap in scale-free networks including nearest-neighbor and next-nearest-neighbor jumps

Random walks including non-nearest-neighbor jumps appear in many real situations such as the diffusion of adatoms and have found numerous applications including PageRank search algorithm; however, related theoretical results are much less for this dynamical process. In this paper, we present a study of mixed random walks in a family of fractal scale-free networks, where both nearest-neighbor and next-nearest-neighbor jumps are included. We focus on trapping problem in the network family, which is a particular case of random walks with a perfect trap fixed at the central high-degree node. We derive analytical expressions for the average trapping time (ATT), a quantitative indicator measuring the efficiency of the trapping process, by using two different methods, the results of which are consistent with each other. Furthermore, we analytically determine all the eigenvalues and their multiplicities for the fundamental matrix characterizing the dynamical process. Our results show that although next-nearest-neighbor jumps have no effect on the leading scaling of the trapping efficiency, they can strongly affect the prefactor of ATT, providing insight into better understanding of random-walk process in complex systems.

Full eigenvalues of the Markov matrix for scale-free polymer networks

Much important information about the structural and dynamical properties of complex systems can be extracted from the eigenvalues and eigenvectors of a Markov matrix associated with random walks performed on these systems, and spectral methods have become an indispensable tool in the complex system analysis. In this paper, we study the Markov matrix of a class of scale-free polymer networks. We present an exact analytical expression for all the eigenvalues and determine explicitly their multiplicities. We then use the obtained eigenvalues to derive an explicit formula for the random target access time for random walks on the studied networks. Furthermore, based on the link between the eigenvalues of the Markov matrix and the number of spanning trees, we confirm the validity of the obtained eigenvalues and their corresponding degeneracies.

Mean first-passage time for maximal-entropy random walks in complex networks

We perform an in-depth study for mean first-passage time (MFPT)--a primary quantity for random walks with numerous applications--of maximal-entropy random walks (MERW) performed in complex networks. For MERW in a general network, we derive an explicit expression of MFPT in terms of the eigenvalues and eigenvectors of the adjacency matrix associated with the network. For MERW in uncorrelated networks, we also provide a theoretical formula of MFPT at the mean-field level, based on which we further evaluate the dominant scalings of MFPT to different targets for MERW in uncorrelated scale-free networks, and compare the results with those corresponding to traditional unbiased random walks (TURW). We show that the MFPT to a hub node is much lower for MERW than for TURW. However, when the destination is a node with the least degree or a uniformly chosen node, the MFPT is higher for MERW than for TURW. Since MFPT to a uniformly chosen node measures real efficiency of search in networks, our work provides insight into general searching process in complex networks.

Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins

Experiments and atomistic simulations of polypeptides have revealed structural intermediates that promote or inhibit conformational transitions to the native state during folding. We invoke a concept of “kinetic frustration” to quantify the prevalence and impact of these behaviors on folding rates within a large set of atomistic simulation data for 10 fast-folding proteins, where each protein’s conformational space is represented as a Markov state model of conformational transitions. Our graph theoretic approach addresses what conformational features correlate with folding inhibition and therefore permits comparison among features within a single protein network and also more generally between proteins. Nonnative contacts and nonnative secondary structure formation can thus be quantitatively implicated in inhibiting folding for several of the tested peptides.

Characteristic times of biased random walks on complex networks

We consider degree-biased random walkers whose probability to move from a node to one of its neighbors of degree k is proportional to k(α), where α is a tuning parameter. We study both numerically and analytically three types of characteristic times, namely (i) the time the walker needs to come back to the starting node, (ii) the time it takes to visit a given node for the first time, and (iii) the time it takes to visit all the nodes of the network. We consider a large data set of real-world networks and we show that the value of α which minimizes the three characteristic times differs from the value α(min)=-1 analytically found for uncorrelated networks in the mean-field approximation. In addition to this, we found that assortative networks have preferentially a value of α(min) in the range [-1,-0.5], while disassortative networks have α(min) in the range [-0.5,0]. We derive an analytical relation between the degree correlation exponent ν and the optimal bias value α(min), which works well for real-world assortative networks. When only local information is available, degree-biased random walks can guarantee smaller characteristic times than the classical unbiased random walks by means of an appropriate tuning of the motion bias.

Random walks in weighted networks with a perfect trap: an application of Laplacian spectra

Trapping processes constitute a primary problem of random walks, which characterize various other dynamical processes taking place on networks. Most previous works focused on the case of binary networks, while there is much less related research about weighted networks. In this paper, we propose a general framework for the trapping problem on a weighted network with a perfect trap fixed at an arbitrary node. By utilizing the spectral graph theory, we provide an exact formula for mean first-passage time (MFPT) from one node to another, based on which we deduce an explicit expression for average trapping time (ATT) in terms of the eigenvalues and eigenvectors of the Laplacian matrix associated with the weighted graph, where ATT is the average of MFPTs to the trap over all source nodes. We then further derive a sharp lower bound for the ATT in terms of only the local information of the trap node, which can be obtained in some graphs. Moreover, we deduce the ATT when the trap is distributed uniformly in the whole network. Our results show that network weights play a significant role in the trapping process. To apply our framework, we use the obtained formulas to study random walks on two specific networks: trapping in weighted uncorrelated networks with a deep trap, the weights of which are characterized by a parameter, and Lévy random walks in a connected binary network with a trap distributed uniformly, which can be looked on as random walks on a weighted network. For weighted uncorrelated networks we show that the ATT to any target node depends on the weight parameter, that is, the ATT to any node can change drastically by modifying the parameter, a phenomenon that is in contrast to that for trapping in binary networks. For Lévy random walks in any connected network, by using their equivalence to random walks on a weighted complete network, we obtain the optimal exponent characterizing Lévy random walks, which have the minimal average of ATTs taken over all target nodes.