Related papers: A new model for the immune clonal networks
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
Two-dimensional discrete dislocation models exhibit complex dynamics in relaxation and under external loading. This is manifested both in the time-dependent velocities of individual dislocations and in the ensemble response, the strain…
In this paper we made a review of some papers about probabilistic regulatory networks (PRN), in particular we introduce our concept of homomorphisms of PRN with an example of projection of a regulatory network to a smaller one. We apply the…
Network science is a powerful framework allowing to model complex systems, it is capable to describe and take into account the intricate web of connections existing among the constituting basic element of the system. Recently scholars have…
Complex dynamical systems are prevalent in various domains, but their analysis and prediction are hindered by their high dimensionality and nonlinearity. Dimensionality reduction techniques can simplify the system dynamics by reducing the…
The physical interpretation of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive self-organizing biological system in…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
It is common knowledge that a key dynamical characteristic of a network is its spectrum (the collection of all eigenvalues of the network's weighted adjacency matrix). In \cite{BW10} we demonstrated that it is possible to reduce a network,…
Resonance is a well-known phenomenon that happens in systems with second order dynamics. In this paper we address the fundamental question of making a network robust to signal being periodically pumped into it at or near a resonant…
We propose a new graphical model to describe the comorbidity of allergic diseases. We present our model in two versions. First, we introduce a generative model that correctly reflects the variables' causal relationship. Then we propose an…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
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…
We introduce the concept of network susceptibilities quantifying the response of the collective dy- namics of a network to small parameter changes. We distinguish two types of susceptibilities: vertex susceptibilities and edge…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Random networks are a powerful tool in the analytical modeling of complex networks as they allow us to write approximate mathematical models for diverse properties and behaviors of networks. One notable shortcoming of these models is that…
For networks of coupled dynamical systems we characterize admissible functions, that is, functions whose gradient is an admissible vector field. The schematic representation of a gradient network dynamical system is of an undirected cell…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…