Related papers: Studying viral populations with tools from quantum…
Knowledge of the time at which an HIV-infected individual seroconverts, when the immune system starts responding to HIV infection, plays a vital role in the design and implementation of interventions to reduce the impact of the HIV…
How will the novel coronavirus evolve? I study a simple epidemiological model, in which mutations may change the properties of the virus and its associated disease stochastically and antigenic drifts allow new variants to partially evade…
We introduce a new class of quantum models with time-dependent Hamiltonians of a special scaling form. By using a couple of time-dependent unitary transformations, the time evolution of these models is expressed in terms of related systems…
We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly…
The evolution of RNA viruses such as HIV, Hepatitis C and Influenza virus occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation…
Frequent observation of a quantum system leads to quantum Zeno physics, where the system evolution is constrained to states commensurate with the measurement outcome. We show that, more generally, the system can evolve between such states…
Epidemiological models describe the spread of an infectious disease within a population. They capture microscopic details on how the disease is passed on among individuals in various different ways, while making predictions about the state…
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…
We model the spontaneous assembly of a capsid (a virus's closed outer shell) from many copies of identical units, using entirely irreversible steps and only information local to the growing edge. Our model is formulated in terms of (i) an…
We present numerical simulations of a model of social influence, where the opinion of each agent is represented by a binary vector. Agents adjust their opinions as a result of random encounters, whenever the difference between opinions is…
It is widely known that the spread of the HIV virus was slower than exponential in several populations, even at the very beginning of the epidemic. We show that this implies a significant reduction in the effective reproductive rate of the…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
We discuss a new analytical approach to real-time evolution in quantum many-body systems. Our approach extends the framework of continuous unitary transformations such that it amounts to a novel solution method for the Heisenberg equations…
We study the probabilistic evolution of a birth and death continuous time measure-valued process with mutations and ecological interactions. The individuals are characterized by (phenotypic) traits that take values in a compact metric…
The entanglement distance of evolutionary quantum states of a two-spin system with the XXZ model has been studied. The analysis has been conducted both analytically and using quantum computing. An analytical dependence of the entanglement…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
Most population models assume that individuals within a given population are identical, that is, the fundamental role of variation is ignored. Inhomogeneous models of populations and communities allow for birth and death rates to vary among…
We generalize the Susceptible-Infected-Removed model for epidemics to take into account generic effects of heterogeneity in the degree of susceptibility to infection in the population. We introduce a single new parameter corresponding to a…
In light of the continuing emergence of new SARS-CoV-2 variants and vaccines, we create a simulation framework for exploring possible infection trajectories under various scenarios. The situations of primary interest involve the interaction…
We introduce a mathematical description of the impact of sociality in the spread of infectious diseases by integrating an epidemiological dynamics with a kinetic modeling of population-based contacts. The kinetic description leads to study…