Related papers: Topological Catenation-induced Pore Size in 2D Oly…
In this work, an evolving Linked Quantum register has been introduced, which are group vector of binary pair of genes, which in its local proximity represent those nodes that will have high connectivity and keep the energy consumption at…
Cellular renewing active matter - assemblies of proliferating and apoptotic cells - underlies tissue homeostasis, morphogenesis, and clonal competition. Previous work in one-dimensional periodic systems identified a fitness advantage…
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of…
We investigate the chemical dissolution of porous media using a network model in which the system is represented as a series of interconnected pipes with the diameter of each segment increasing in proportion to the local reactant…
The mammalian cell membrane is embedded with biomolecular condensates of protein and lipid clusters, which interact with an underlying viscoelastic cytoskeleton network to organize the cell surface and mechanically interact with the…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
Entangled networks are ubiquitous in tissues, polymers, and fabrics. However, their mechanics remain insufficiently understood due to the complexity of the topological constraints at the network level. Here, we develop a mathematical…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
This study introduces a pore morphology algorithm that emphasizes the central role of topology in multiphase flow through porous media. Analysis of drainage in lattice-based pore networks identifies two key quantities, the percolation…
Topological edge states in systems of two (or more) dimensions offer scattering-free transport, exhibiting robustness to inhomogeneities and disorder. In a different domain, time-modulated systems, such as photonic time crystals (PTCs),…
The investigation of topological properties of ovarian cancer network (OCN) and the roles of hubs involved in it by digging the network at various levels of organization are important to understand how OCN is organized to understand disease…
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…
Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed through the kinetics of particular models, which requires…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Network generators that capture the Internet's large-scale topology are crucial for the development of efficient routing protocols and modeling Internet traffic. Our ability to design realistic generators is limited by the incomplete…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…