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This work introduces NetDiff, an expressive graph denoising diffusion probabilistic architecture that generates wireless ad hoc network link topologies. Such networks, with directional antennas, can achieve unmatched performance when the…

Transport across heterogeneous, patchy environments is a ubiquitous phenomenon spanning fields of study including ecological movement, intracellular transport and regions of specialised function in a cell. These regions or patches may be…

Percolation, the formation of a macroscopic connected component, is a key feature in the description of complex networks. The dynamical properties of a variety of systems can be understood in terms of percolation, including the robustness…

In this paper we investigate networks whose evolution is governed by the interaction of a random assembly process and an optimization process. In the first process, new nodes are added one at a time and form connections to randomly selected…

Multilayer networks describe well many real interconnected communication and transportation systems, ranging from computer networks to multimodal mobility infrastructures. Here, we introduce a model in which the nodes have a limited…

The work presented in this thesis concerns different aspects of dynamical processes on networks. The first subject considered is the theoretical modeling of exploration processes of complex networks, such as the ``traceroute'' process used…

Robustness of routing policies for networks is a central problem which is gaining increased attention with a growing awareness to safeguard critical infrastructure networks against natural and man-induced disruptions. Routing under limited…

Community structures have been identified in various complex real-world networks, for example, communication, information, internet and shareholder networks. The scaling of community size distribution indicates the heterogeneity in the…

Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…

Continuous-time quantum walk describes the propagation of a quantum particle (or an excitation) evolving continuously in time on a graph. As such, it provides a natural framework for modeling transport processes, e.g., in light-harvesting…

Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…

Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…

Cells and tissues exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, which includes an active gel of actin filaments, crosslinks, and myosin molecular motors. Although individual…

The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…

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…

Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization…

Proximity networks are time-varying graphs representing the closeness among humans moving in a physical space. Their properties have been extensively studied in the past decade as they critically affect the behavior of spreading phenomena…

We study the efficiency of the gradient mechanism of message transfer in a $2-d$ communication network of regular nodes and randomly distributed hubs. Each hub on the network is assigned some randomly chosen capacity and hubs with lower…

We propose a mechanism of cell motility which is based on contraction and does not require protrusion. The contraction driven translocation of a cell is due to internal flow of the cytoskeleton generated by molecular motors. Each motor…

Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…