Related papers: A graph model for the evolution of specificity in …
Biomimetics has played a key role in the evolution of artificial neural networks. Thus far, in silico metaphors have been dominated by concepts from neuroscience and cognitive psychology. In this paper we introduce a different type of…
Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating…
When a fraction of a population becomes immune to an infectious disease, the population-wide infection risk decreases nonlinearly due to collective protection, known as herd immunity. Some studies based on mean-field models suggest that…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
Models of the consensus of the individual state in social systems have been the subject of recent researches in the physics literature. We investigate how network structures coevolve with the individual state under the framework of social…
Patterns of nestedness and specialization asymmetry, where specialist species interact mainly with generalists while generalists interact with both generalists and specialists, are often observed in mutualistic and antagonistic bi-partite…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with…
We show existence of a non-trivial phase transition for the contact process, a simple model for infection without immunity, on a network which reacts dynamically to the infection trying to prevent an epidemic. This network initially has the…
Evolutionary dynamics have been traditionally studied in the context of homogeneous populations, mainly described my the Moran process. Recently, this approach has been generalized in \cite{LHN} by arranging individuals on the nodes of a…
Our main purpose is to compare classical nonself-centered, two-signal theoretical models of the adaptive immune system with a novel, self-centered, one-signal model developed by our research group. Our model hypothesizes that the immune…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM…
A model has been proposed to simulate the evolution of interpersonal relationships in a social group. The small social community is simply assumed as an undirected and weighted graph, where individuals are denoted by vertices, and the…