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The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
Many systems in nature, society and technology can be described as networks, where the vertices are the system's elements and edges between vertices indicate the interactions between the corresponding elements. Edges may be weighted if the…
Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great…
The rate equations are used to study the scale-free behavior of the weight distribution in evolving networks whose topology is determined only by degrees of preexisting vertices. An analysis of these equations shows that the degree…
In this work, we study the topological transition on the associated networks in a model proposed by Saeedian et al. (Scientific Reports 2019 9:9726), which considers a coupled dynamics of node and link states. Our goal was to better…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Real-world networks process structured connections since they have non-trivial vertex degree correlation and clustering. Here we propose a toy model of structure formation in real-world weighted network. In our model, a network evolves by…
We study diffusion of information packets on several classes of structured networks. Packets diffuse from a randomly chosen node to a specified destination in the network. As local transport rules we consider random diffusion and an…
Few of food web theory hypotheses/predictions can be readily tested using empirical data. An exception is represented by simple probabilistic models for food web structure, for which the likelihood has been derived. Here I test the…
We represent transport between different regions of a fluid domain by flow networks, constructed from the discrete representation of the Perron-Frobenius or transfer operator associated to the fluid advection dynamics. The procedure is…
The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth…
Allometric scaling laws, such as Kleiber's law for metabolic rate, highlight how efficiency emerges with size across living systems. The brain, with its characteristic sublinear scaling of activity, has long posed a puzzle: why do larger…
This paper aims to measure the efficiency of urban street networks (a kind of complex networks) from the perspective of the multidimensional chain of connectivity (or flow). More specifically, we define two quantities: flow dimension and…
It is shown that the excellent scaling of the elliptic flow found for all centralities, species and energies from RHIC to the LHC for $p_{T}$ less than the saturation momentum is a consequence of the energy lost by a parton interacting with…
Network alignment is a problem of finding the node mapping between similar networks. It links the data from separate sources and is widely studied in bioinformation and social network fields. The critical difference between network…
We minimize the dissipation rate of an electrical network under a global constraint on the sum of powers of the conductances. We construct the explicit scaling relation between currents and conductances, and show equivalence to a a previous…
In order to take the weight of connection into consideration and to find a natural measurement of weight, we have collected papers in Econophysics and constructed a network of scientific communication to integrate idea transportation among…
We study a problem of data packet transport in scale-free networks whose degree distribution follows a power-law with the exponent $\gamma$. We define load at each vertex as the accumulated total number of data packets passing through that…