Related papers: Affinity maturation for an optimal balance between…
The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of…
We analyse a minimal model for the primary response in the adaptive immune system comprising three different players: antigens, T and B cells. We assume B-T interactions to be diluted and sampled locally from heterogeneous degree…
A model of strategy formulation is used to study how an adaptive attacker learns to overcome a moving target cyber defense. The attacker-defender interaction is modeled as a game in which a defender deploys a temporal platform migration…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
We live within an increasingly technological, information-laden environment for the first time in human evolution.This subjects us, and will continue to subject us in an accelerating fashion, to an unremitting exposure to meaningful…
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between…
Starting from common assumptions, we build a rate equation model for multi-strain disease dynamics in terms of immune repertoire classes. We then move to a strain-level description where a low-order closure reminiscent of a pair…
Despite being optimized, the information processing of biological organisms exhibits significant variability in its complexity and capability. One potential source of this diversity is the limitation of resources required for information…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
The immune system protects the body against health-threatening entities, known as antigens, through very complex interactions involving the antigens and the system's own entities. One remarkable feature resulting from such interactions is…
Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates.…
Antibody therapies have been employed to address some of today's most challenging diseases, but must meet many criteria during drug development before reaching a patient. Humanization is a sequence optimization strategy that addresses one…
B cells receptor (BCR) signaling in response to membrane-bound antigen increases with antigen affinity, a process known as affinity discrimination. We use computational modeling to show that B cell affinity discrimination requires that…
When facing many options, we narrow down our focus to very few of them. Although behaviors like this can be a sign of heuristics, they can actually be optimal under limited cognitive resources. Here we study the problem of how to optimally…
We consider a simple deterministic model which describes an asymmetric competition between an immune system with a specific and powerful response, and a virus with a broad toxicity and fast mutations. Interest in this model relies on the…
Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically…
A plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where…
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
This paper addresses the question of optimal phenotypic plasticity as a response to environmental fluctuations while optimizing the cost/benefit ratio, where the cost is energetic expense of plasticity, and benefit is fitness. The…
Recent works have shown that the input domain of any machine learning classifier is bound to contain adversarial examples. Thus we can no longer hope to immune classifiers against adversarial examples and instead can only aim to achieve the…