Related papers: Optimal evolutionary decision-making to store immu…
The Prisoner's Dilemma is used to represent many real life phenomena whether from the civilized world of humans or from the wild life of the other living. Researchers working on iterated prisoner's dilemma (IPD) with limited memory…
A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the…
In varying environments it is beneficial for organisms to utilize available cues to infer the conditions they may encounter and express potentially favorable traits. However, external cues can be unreliable or too costly to use. We consider…
Information is a key concept in evolutionary biology. Information is stored in biological organism's genomes, and used to generate the organism as well as to maintain and control it. Information is also "that which evolves". When a…
The mammalian brain is a metabolically expensive device, and evolutionary pressures have presumably driven it to make productive use of its resources. For sensory areas, this concept has been expressed more formally as an optimality…
There are two common approaches for optimizing the performance of a machine: genetic algorithms and machine learning. A genetic algorithm is applied over many generations whereas machine learning works by applying feedback until the system…
The T cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells…
Many events in the vertebrate immune system are influenced by some element of chance. The objective of the present work is to describe affinity maturation of B lymphocytes (in which random events are perhaps the most characteristic), and to…
Prokaryotes have evolved various mechanisms to counter viruses, which in their turn developed numerous strategies to avoid defenses of the hosts. Dozens of such defense and counter-defense mechanisms have recently been discovered, yet the…
Modern consumer devices must execute multimedia applications that exhibit high resource utilization. In order to efficiently execute these applications, the dynamic memory subsystem needs to be optimized. This complex task can be tackled in…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
Many living and artificial systems improve their fitness or performance by adapting to changing environments or diverse training data. However, it remains unclear how such environmental variation influences adaptation, what is learned in…
Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T…
We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their…
Biological systems represent time from microseconds to years. An important gap in our knowledge concerns the mechanisms for encoding time intervals of hundreds of milliseconds to minutes that matter for tasks like navigation, communication,…
In a co-evolutionary context, the survive probability of individual elements of a system depends on their relation with their neighbors. The natural selection process depends on the whole population, which is determined by local events…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
Memory is critical for enabling large language model (LLM) based agents to maintain coherent behavior over long-horizon interactions. However, existing agent memory systems suffer from two key gaps: they rely on a one-size-fits-all memory…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…