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A great variety of systems in nature, society and technology -- from the web of sexual contacts to the Internet, from the nervous system to power grids -- can be modeled as graphs of vertices coupled by edges. The network structure,…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Endocytosis underlies many cellular functions including signaling and nutrient uptake. The endocytosed cargo gets redistributed across a dynamic network of endosomes undergoing fusion and fission. Here, a theoretical approach is reviewed…
We develop an agent-based model of vasculogenesis, the de novo formation of blood vessels. Endothelial cells in the vessel network are viewed as linearly elastic spheres and are of two types: vessel elements are contained within the…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Memory is an important cognitive function for humans. How a brain with such a small power can complete such a complex memory function, the working mechanism behind this is undoubtedly fascinating. Engram theory views memory as the…
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…
Information diffusion in online social networks is affected by the underlying network topology, but it also has the power to change it. Online users are constantly creating new links when exposed to new information sources, and in turn…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
In this study, we performed comprehensive morphological investigations of the spontaneous formations of effective network structures among elements in coupled logistic maps, specifically with a delayed connection change. Our proposed model…
Many active fluid systems encountered in biology are set in total geometric confinement. Cytoplasmic streaming in plant cells is a prominent and ubiquitous example, in which cargo-carrying molecular motors move along polymer filaments and…
Collective cell migration in epithelia relies on cell intercalation: a local remodelling of the cellular network that allows neighbouring cells to swap their positions. Unlike foams and passive cellular fluid, in epithelial intercalation…
We present an efficient routing approach for delivering packets in complex networks. On delivering a message from a node to a destination, a node forwards the message to a neighbor by estimating the waiting time along the shortest path from…
This paper introduces a new macroscopic perspective for simulating transportation networks. The idea is to look at the network as connected nodes. Each node sends an information package to its neighbors. Basically, the information package…
Deterministic equilibrium flows in transport networks can be investigated by means of Markov's processes defined on the dual graph representations of the network. Sustained movement patterns are generated by a subset of automorphisms of the…
Cells sense the geometry and stiffness of their adhesive environment by active contractility. For strong adhesion to flat substrates, two-dimensional contractile network models can be used to understand how force is distributed throughout…
The packet is the fundamental unit of transportation in modern communication networks such as the Internet. Physical layer scheduling decisions are made at the level of packets, and packet-level models with exogenous arrival processes have…
Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of…
We present a study of transport on complex networks with routing based on local information. Particles hop from one node of the network to another according to a set of routing rules with different degrees of congestion awareness, ranging…
Water molecules, confined in a carbon nanotube, were monitored using molecular dynamics simulation. Spontaneous directional transportation during a long timescale was observed in the symmetrical nanochannel by a ratchet-like mechanism. This…