Related papers: Complexity in the Immune System
Most communication networks are complex. In this paper, we address one of the fundamental problems we are facing nowadays, namely, how we can efficiently protect these networks. To this end, we study an immunization strategy and found that…
Affinity Maturation (AM) is the process through which the immune system is able to develop potent antibodies against new pathogens it encounters, and is at the base of the efficacy of vaccines. At its core AM is analogous to a Darwinian…
This chapter introduces evolutionary antifragility as the time-scale interaction characteristics of a natural dynamic system. It describes the benefit derived from input distribution unevenness, based on the emergent system dynamics and its…
Cells are known to exert forces to sense their physical surroundings for guidance of motion and fate decisions. Here, we propose that cells might do mechanical work to drive their own evolution, taking inspiration from the adaptive immune…
The rising complexity of our terrestrial surrounding is an empirical fact. Details of this process evaded description in terms of physics for long time attracting attention and creating myriad of ideas including non-scientific ones. In this…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
We study the interaction between epidemic spreading and a vaccination process. We assume that, similar to the disease spreading, also the vaccination process occurs through direct contact, i.e., it follows the standard…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
A central feature of vertebrate immune response is affinity maturation, wherein antibody-producing B cells undergo evolutionary selection in microanatomical structures called germinal centers, which form in secondary lymphoid organs upon…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
All physical process are subject to some laws which determine with math accurately its time-space evolution. These laws are described, in the last analysis for the principle of causality. The physical space can be homogeneous or…
Danger requires a strong rapid response. Speedy triggers are prone to false signals. False alarms can be costly, requiring strong negative regulators to oppose the initial triggers. Strongly opposed forces can easily be perturbed, leading…
We study some simple mathematical models designed to test the following hypothesis: can a pathogen escape the immune system only because of its high probability of mutation? We propose both spatial and non-spatial models. In all of our…
Molecular biology features numerous complexes of proteins that coordinate in an interlocking fashion to fulfill different functions. Adaptive evolution explains some of this complexity, but needn't be the default when neutral explanations…
Influenza is a contagious respiratory illness that causes significant human morbidity and mortality, affecting 5-15% of the population in a typical epidemic season. Human influenza epidemics are caused by types A and B, with roughly 25% of…
In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in…