Related papers: Rediscovering the power of pairwise interactions

In physics we often use very simple models to describe systems with many degrees of freedom, but it is not clear why or how this success can be transferred to the more complex biological context. We consider models for the joint…

In many domains, there is significant interest in capturing novel relationships between time series that represent activities recorded at different nodes of a highly complex system. In this paper, we introduce multipoles, a novel class of…

We present atomistic molecular dynamics simulations of two Polyethylene systems where all entanglements are trapped: a perfect network, and a melt with grafted chain ends. We examine microscopically at what level topological constraints can…

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…

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…

Systems composed of distinct complex networks are present in many real-world environments, from society to ecological systems. In the present paper, we propose a network model obtained as a consequence of interactions between two species…

Multiplex networks describe a large number of systems ranging from social networks to the brain. These multilayer structure encode information in their structure. This information can be extracted by measuring the correlations present in…

With the recent explosion of publicly available biological data, the analysis of networks has gained significant interest. In particular, recent promising results in Neuroscience show that the way neurons and areas of the brain are…

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…

The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to…

We present the complete phase diagram for one-dimensional binary mixtures of bosonic ultracold atomic gases in a harmonic trap. We obtain exact results with direct numerical diagonalization for small number of atoms, which permits us to…

Human populations exhibit complex behaviors---characterized by long-range correlations and surges in activity---across a range of social, political, and technological contexts. Yet it remains unclear where these collective behaviors come…

Complex systems, such as economic, social, biological, and ecological systems, usually feature interactions not only between pairwise entities but also among three or more entities. These multi-entity interactions are known as higher-order…

In two-dimensional random waves, phase singularities are point-like dislocations with a behavior reminiscent of interacting particles. This -- qualitative -- consideration, stems from the spatial arrangement of these entities, which finds…

The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3-cycles). However, many phenomena from division of labor to protein-protein…

We model a social network by a random graph whose nodes represent agents and links between two of them stand for a reciprocal interaction; each agent is also associated to a binary variable which represents a dichotomic opinion or…

A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…