Related papers: A new model for the immune clonal networks
Complex diseases can be modeled as damage to intracellular networks that results in abnormal cell behaviors. Network-based dynamic models such as Boolean models have been employed to model a variety of biological systems including those…
The long-time dynamics of somatic adaptability in immune system is simulated by a simple physical model. The immune system described by the model exhibits a scale free behavior as is observed in living systems. The balance between the…
Recently, motivated by the pioneer works that reveal the small-world effect and scale-free property of various real-life networks, many scientists devote themselves into studying complex networks. One of the ultimate goals is to understand…
We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model by a low-dimensional system of equations permitting analytical…
We develop a new ensemble of modular random graphs in which degree-degree correlations can be different in each module and the inter-module connections are defined by the joint degree-degree distribution of nodes for each pair of modules.…
Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…
Complex networks are the subject of fundamental interest from the scientific community at large. Several metrics have been introduced to characterize the structure of these networks, such as the degree distribution, degree correlation, path…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
Complex networks of real-world systems are believed to be controlled by common phenomena, producing structures far from regular or random. These include scale-free degree distributions, small-world structure and assortative mixing by…
We model a general, hierarchically organized tissue by a multi compartment approach, allowing any number of mutations within a cell. We derive closed solutions for the deterministic clonal dynamics and the reproductive capacity of single…
Deterministic complex networks that use iterative generation algorithms have been found to more closely mirror properties found in real world networks than the traditional uniform random graph models. In this paper we introduce a new,…
The statistical field theory of information dynamics on complex networks concerns the dynamical evolution of large classes of models of complex systems. Previous work has focused on networks where nodes carry an information field, which…
The immune system is a cognitive system of complexity comparable to the brain and its computational algorithms suggest new solutions to engineering problems or new ways of looking at these problems. Using immunological principles, a two (or…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
We propose a novel model-reduction methodology for large-scale dynamic networks with tightly-connected components. First, the coherent groups are identified by a spectral clustering algorithm on the graph Laplacian matrix that models the…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
The clonal expansion of T cells during an infection is tightly regulated to ensure an appropriate immune response against invading pathogens. Although experiments have mapped the trajectory from expansion to contraction, the interplay…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
It is a fundamental challenge to understand how the function of a network is related to its structural organization. Adaptive dynamical networks represent a broad class of systems that can change their connectivity over time depending on…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…