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The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Most classical (non-spiking) neural network models disregard internal neuron dynamics and treat neurons as simple input integrators. However, biological neurons have an internal state governed by complex dynamics that plays a crucial role…
Hierarchical Bayesian models are increasingly used in large, inhomogeneous complex network dynamical systems by modeling parameters as draws from a hyperparameter-governed distribution. However, theoretical guarantees for these estimates as…
Distribution grid is the medium and low voltage part of a large power system. Structurally, the majority of distribution networks operate radially, such that energized lines form a collection of trees, i.e. forest, with a substation being…
The network representation is becoming increasingly popular for the description of cardiovascular interactions based on the analysis of multiple simultaneously collected variables. However, the traditional methods to assess network links…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
One of the advantages of adopting a Model Based Development (MBD) process is that it enables testing and verification at early stages of development. However, it is often desirable to not only verify/falsify certain formal system…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
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…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Complex networks are frequently employed to model physical or virtual complex systems. When certain entities exist across multiple systems simultaneously, unveiling their corresponding relationships across the networks becomes crucial. This…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds.…
Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And…