Related papers: Network analysis of protein dynamics
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
Recent development of network structure analysis shows that it plays an important role in characterizing complex system of many branches of sciences. Different from previous network centrality measures, this paper proposes the notion of…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…
It is notoriously difficult to predict the behaviour of a complex self-organizing system, where the interactions among dynamical units form a heterogeneous topology. Even if the dynamics of each microscopic unit is known, a real…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Network dynamics offers critical insights into the behavior and evolution of complex systems. Here, we focus on the topological dynamics of networks to explore a unique process for reducing the average distance: topological compression. The…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Across all scales of the physical world, dynamical systems can often be usefully represented as abstract networks that encode the system's units and inter-unit interactions. Understanding how physical rules shape the topological structure…
Networks are a fundamental model of complex systems throughout the sciences, and network datasets are typically analyzed through lower-order connectivity patterns described at the level of individual nodes and edges. However, higher-order…
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and…
Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…
One of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
We review the main tools which allow for the statistical characterization of weighted networks. We then present two case studies, the airline connection network and the scientific collaboration network, which are representative of critical…
What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct…
Just as a herd of animals relies on its robust social structure to survive in the wild, similarly robustness is a crucial characteristic for the survival of a complex network under attack. The capacity to measure robustness in complex…
Networks are pervasive in the real world. Nature, society, economy, and technology are supported by ostensibly different networks that in fact share an amazing number of interesting structural properties. Network thinking exploded in the…
A major achievement in the study of complex networks is the observation that diverse systems, from sub-cellular biology to social networks, exhibit universal topological characteristics. Yet this universality does not naturally translate to…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…