Related papers: The generality of transient compartmentalization a…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle,…
One of the leading theories for the origin of life includes the hypothesis according to which life would have evolved as cooperative networks of molecules. Explaining cooperation$-$and particularly, its emergence in favoring the evolution…
For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that…
A significant obstacle in the development of robust machine learning models is covariate shift, a form of distribution shift that occurs when the input distributions of the training and test sets differ while the conditional label…
We present a stochastic approach to modeling the dynamics of coexistence of prey and predator populations. It is assumed that the space of coexistence is explicitly subdivided in a grid of cells. Each cell can be occupied by only one…
Growth-fragmentation processes model systems of cells that grow continuously over time and then fragment into smaller pieces. Typically, on average, the number of cells in the system exhibits asynchronous exponential growth and, upon…
We introduce a general class of branching Markov processes for the modelling of a parasite infection in a cell population. Each cell contains a quantity of parasites which evolves as a diffusion with positive jumps. The drift, diffusive…
Many biological processes, from cell division to viral lysis, are triggered when an internal stochastic variable reaches a threshold. Here we introduce Branching under First-Passage Resetting, a general framework in which replication events…
We consider a branching model introduced by Kimmel for cell division with parasite infection. Cells contain proliferating parasites which are shared randomly between the two daughter cells when they divide. We determine the probability that…
Host-parasitoid population dynamics is often probed using a semi-discrete/hybrid modeling framework. Here, the update functions in the discrete-time model connecting year-to-year changes in the population densities are obtained by solving…
Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is…
We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
We study an asymmetric simple exclusion process in a strip in the presence of a solid impenetrable barrier. We focus on the effect of the barrier on the residence time of the particles, namely, the typical time needed by the particles to…
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
It has been pointed out that if an autocatalytic cycle produces primitive membrane chemicals, it can compose a self-maintaining proto cell. Moreover, it is known that a proto cell can divide itself spontaneously as it grows. An unsolved…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…