相关论文: A simple physical model for scaling in protein-pro…

Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…

Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…

The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…

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 classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…

A central claim in modern network science is that real-world networks are typically "scale free," meaning that the fraction of nodes with degree $k$ follows a power law, decaying like $k^{-\alpha}$, often with $2 < \alpha < 3$. However,…

Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…

Geometric constraints impact the formation of a broad range of spatial networks, from amino acid chains folding to proteins structures to rearranging particle aggregates. How the network of interactions dynamically self-organizes in such…

In the past few years, several studies have explored the topology of interactions in different complex systems. Areas of investigation span from biology to engineering, physics and the social sciences. Although having different microscopic…

Most of various large-size complex systems in nature and society can be well described as complex networks (graphs) to better understand the evolutional mechanisms and dynamical functions behind themselves. Of some part follow scale-free…

One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…

Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…

The following random graph model was introduced for the evolution of protein-protein interaction networks: Let $\mathcal G = (G_n)_{n=n_0, n_0+1,...}$ be a sequence of random graphs, where $G_n = (V_n, E_n)$ is a graph with $|V_n|=n$…

Scale-free power law structure describes complex networks derived from a wide range of real world processes. The extensive literature focuses almost exclusively on networks with power law exponent strictly larger than 2, which can be…

We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…

We propose a network model with a fixed number of nodes and links with a dynamics which favors links between nodes differing in connectivity. Parameter regimes where the degree distributions follow power-laws, P(k) ~ k^-gamma, high…

Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…

The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world…

Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…