Related papers: The generality of transient compartmentalization a…
Spatio-temporal extensions of familiar compartment models for disease transmission incorporating diffusive behavior, or interactions between individuals at separate locations, are explored. The models considered have the character of…
In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…
In Bayesian nonparametric inference, random discrete probability measures are commonly used as priors within hierarchical mixture models for density estimation and for inference on the clustering of the data. Recently, it has been shown…
Bursting cells lead to ambient RNA that contaminates sequencing data. This process is especially problematic in perturbation experiments where transcription factors are implanted into cells to determine their effects. The presence of…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
We consider a reaction-diffusion process with retardation. The particles, immersed in traps initially, remain inactive until another particle is annihilated spontaneously with a rate $\lambda$ at a certain point $\vec x$. In that case the…
In this paper, we introduce a one-dimensional model of particles performing independent random walks, where only pairs of particles can produce offspring ("cooperative branching"), and particles that land on an occupied site merge with the…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
We propose a model to characterize how a diffusing population adapts under a time periodic selection, while its environment undergoes shifts and size changes, leading to significant differences with classical results on fixed domains. After…
We investigate the effects of cooperativity between contagion processes that spread and persist in a host population. We propose and analyze a dynamical model in which individuals that are affected by one transmissible agent $A$ exhibit a…
Through in-depth thinking and reasoning about the conditions required for cells to maintain unchanged material distribution, it is concluded that life metabolic reactions require high information content. However, the self-replication of a…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bi-directional traffic occurring in a narrow channel can easily lead to…
Compartmental models are the most widely used framework for modeling infectious diseases. These models have been continuously refined to incorporate all the realistic mechanisms that can shape the course of an epidemic outbreak. Building on…
We present a systematic comparison and analysis of four discrete-time, host--parasitoid models. For each model, we specify that density-dependent effects occur prior to parasitism in the life cycle of the host. We compare density-dependent…
The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…
We consider a class of biologically-motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final…
Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions…
We investigate a three-dimensional kinetically-constrained model that exhibits two types of phase transitions at different densities. At the jamming density $ \rho_J $ there is a mixed-order phase transition in which a finite fraction of…