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Recently we have used a cellular automata model which describes the dynamics of a multi-connected network to reproduce the refractory behavior and aging effects obtained in immunization experiments performed with mice when subjected to…
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus.…
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…
Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or…
The immune system can be thought as a complex network of different interacting elements. A cellular automaton, defined in shape-space, was recently shown to exhibit self-regulation and complex behavior and is, therefore, a good candidate to…
B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GC) from which mature B cells arise. It is known that B cells…
Models of Stock Recruitment Relationships (SRRs) are often used to predict fish population dynamics. Commonly used SRRs include the Ricker, Beverton-Holt, and Cushing functional forms, which differ primarily by the degree of density…
Malaria is one of the deadliest infectious diseases globally, causing hundreds of thousands of deaths each year. It disproportionately affects young children, with two-thirds of fatalities occurring in under-fives. Individuals acquire…
The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the…
Larval zebrafish hunting provides a tractable setting to study how ecological and energetic constraints shape adaptive behavior in both biological brains and artificial agents. Here we develop a minimal agent-based model, training recurrent…
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic…
Collective motion provides a spectacular example of self-organization in Nature. Visual information plays a crucial role among various types of information in determining interactions. Recently, experiments have revealed that organisms such…
It has been known for some time that human autoimmune diseases can be triggered by viral infections. Several possible mechanisms of interactions between a virus and immune system have been analysed, with a prevailing opinion being that the…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune…
B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same "clonal family")…
A longstanding problem in biology has been the origin of pervasive quarter-power allometric scaling laws that relate many characteristics of organisms to body mass (M) across the entire spectrum of life from molecules and microbes to…
We present models and computational results which indicate that the spatial and temporal regularity seen in Proteus mirabilis swarm-colony development is largely an expression of a sharp age of dedifferentiation in the cell cycle from…
The similarity between neural and immune networks has been known for decades, but so far we did not understand the mechanism that allows the immune system, unlike associative neural networks, to recall and execute a large number of…