Related papers: Eigenvector Centrality Distribution for Characteri…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
The problem of connectivity assessment in an asymmetric network represented by a weighted directed graph is investigated in this article. A power iteration algorithm in a centralized implementation is developed first to compute the…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
In this paper, we introduce the concept of self-amplifying structures for hypergraphs, positioning it as a key element for understanding propagation and internal reinforcement in complex systems. To quantify this phenomenon, we define the…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…
Understanding the intertwined contributions of amino acid sequence and spatial structure is essential to explain protein behaviour. Here, we introduce INFUSSE (Integrated Network Framework Unifying Structure and Sequence Embeddings), a deep…
Numerous experimental and theoretical studies have established that intramolecular vibrational energy redistribution (IVR) in isolated molecules has a heirarchical tier structure. The tier structure implies strong correlations between the…
A number of recent works have concentrated on a few statistical properties of complex networks, such as the clustering, the right-skewed degree distribution and the community, which are common to many real world networks. In this paper, we…
Introduction : Mass spectrometry approaches are very attractive to detect protein panels in a sensitive and high speed way. MS can be coupled to many proteomic separation techniques. However, controlling technological variability on these…
We study the inverse eigenvector centrality problem on connected undirected graphs, namely, whether a given positive vector can be realized by assigning suitable edge weights. We provide a complete characterization in terms of stable sets…
Research on the use of information geometry (IG) in modern physics has witnessed significant advances recently. In this review article, we report on the utilization of IG methods to define measures of complexity in both classical and,…
While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein…
In this paper, we use the framework of infinitesimal homeostasis to study general design principles for the occurrence of homeostasis in gene regulatory networks. We assume that the dynamics of the genes explicitly includes both…
Network tomography plays a crucial role in assessing the operational status of internal links within networks through end-to-end path-level measurements, independently of cooperation from the network infrastructure. However, the accuracy of…
A hypergraph is called uniform when every hyperedge contains the same number of vertices, otherwise, it is called non-uniform. In the real world, many systems give rise to non-uniform hypergraphs, such as email networks and co-authorship…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
Mapping a complex network to an atomic cluster, the Anderson localization theory is used to obtain the load distribution on a complex network. Based upon an intelligence-limited model we consider the load distribution and the congestion and…
A central problem in data analysis is the low dimensional representation of high dimensional data, and the concise description of its underlying geometry and density. In the analysis of large scale simulations of complex dynamical systems,…
This paper focuses on obtaining clustering information about a distribution from its i.i.d. samples. We develop theoretical results to understand and use clustering information contained in the eigenvectors of data adjacency matrices based…