Related papers: What Omicron Does, and How It Does It
The purpose of this paper is to analyze the mechanism for the interplay of deterministic and stochastic models for contagious diseases. Deterministic models for contagious diseases are prone to predict global stability. Small natural birth…
In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so…
We study the dynamic evolution of COVID-19 cased by the Omicron variant via a fractional susceptible-exposedinfected-removed (SEIR) model. Preliminary data suggest that the symptoms of Omicron infection are not prominent and the…
BACKGROUND: Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve…
Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution, against a formal interpretation proposed…
Epidemic outbreaks of new pathogens, or known pathogens in new populations, cause a great deal of fear because they are hard to predict. For theoretical models of disease spreading, on the other hand, quantities characterizing the outbreak…
Prevalence of cooperation within groups of selfish individuals is puzzling in that it contradicts with the basic premise of natural selection. Favoring players with higher fitness, the latter is key for understanding the challenges faced by…
The nature and source of evolutionary trends in complexity is difficult to assess from the fossil record, and the driven vs. passive nature of such trends has been debated for decades. There are also questions about how effectively…
We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the…
Culture evolves, not just in the trivial sense that cultures change over time, but also in the strong sense that such change is governed by Darwinian principles. Both biological and cultural evolution are essentially cumulative selection…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
We used a spatially explicit agent-based model of SARS-CoV-2 transmission combined with spatially fine-grained COVID-19 observation data from Public Health Scotland to investigate the initial rise of the Omicron (BA.1) variant of concern.…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
The spread of infectious diseases, rumors, fashions, innovations are complex contagion processes, embedded both in networked and spatial contexts. Here we investigate the pattern dynamics of a complex contagion, where two agents, say $A$…
SARS-CoV-2 usually evolves at a relatively constant rate over time. Occasionally, however, lineages arise with higher-than-expected numbers of mutations given the date of sampling. Such lineages can arise for a variety of reasons, including…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
Natural selection favors the more successful individuals. This is the elementary premise that pervades common models of evolution. Under extreme conditions, however, the process may no longer be probabilistic. Those that meet certain…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…