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This paper proposes an extension of the traditional Central Dogma of molecular biology to a more dynamic model termed the Central Dogma Cycle (CDC) and a broader network called the Central Dogma Cyclic Network (CDCN). While the Central…
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…
Memories in the brain are separated in two categories: short-term and long-term memories. Long-term memories remain for a lifetime, while short-term ones exist from a few milliseconds to a few minutes. Within short-term memory studies,…
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…
The role of T-cells within the immune system is to confirm and assess anomalous situations and then either respond to or tolerate the source of the effect. To illustrate how these mechanisms can be harnessed to solve real-world problems, we…
Currently, there are two major theories for the pathogenesis of sepsis: hyperimmune and hypoimmune. Hyperimmune theory suggests that cytokine storm causes the symptoms of sepsis. On the contrary, hypoimmune theory suggests that…
CD8 T cells are specialized immune cells that play an important role in the regulation of antiviral immune response and the generation of protective immunity. In this paper we investigate the differentiation of memory CD8 T cells in the…
Adaptive response to a varying environment is a common feature of biological organisms. Reproducing such features in electronic systems and circuits is of great importance for a variety of applications. Here, we consider memory models…
Commonly studied cellular automata are memoryless and have fixed topology of connections between cells. However by allowing updates of links and short-term memory in cells we may potentially discover novel complex regimes of spatio-temporal…
Complex behaviors often sit at a critical threshold between order and disorder. But not all disorder is created equal. Disorder can be trivial or constrained, and correlated disorder can even be topological. Crucially, constrained disorder…
Memory has a great impact on the evolution of every process related to human societies. Among them, the evolution of an epidemic is directly related to the individuals' experiences. Indeed, any real epidemic process is clearly sustained by…
Spatial interactions between cancer and immune cells, as well as the recognition of tumour antigens by cells of the immune system, play a key role in the immune response against solid tumours. The existing mathematical models generally…
This paper is a completion of an earlier model proposed by us. In the model different memories are attached at cell surface determinants which are the result of DNA recombination. Our earlier experiments strongly suggest that DNA…
The Guard-Guardee model for plant immunity describes how resistance proteins (guards) in host cells monitor host target proteins (guardees) that are manipulated by pathogen effector proteins. A recently suggested extension of this model…
The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self or non-self substances. It does this with the help of…
The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such…
Mammalian brains operate in a very special surrounding: to survive they have to react quickly and effectively to the pool of stimuli patterns previously recognized as danger. Many learning tasks often encountered by living organisms involve…
We are interested in modeling theoretical immunology within a statistical mechanics flavor: focusing on the antigen-independent maturation process of B-cells, in this paper we try to revise the problem of self vs non-self discrimination by…
The generative process of Diffusion Models (DMs) has recently set state-of-the-art on many AI generation benchmarks. Though the generative process is traditionally understood as an "iterative denoiser", there is no universally accepted…
Sequence memory is an essential attribute of natural and artificial intelligence that enables agents to encode, store, and retrieve complex sequences of stimuli and actions. Computational models of sequence memory have been proposed where…