Related papers: Modeling mutations in bacteria and human tissues
The Luria--Delbr\"uck mutation model is a cornerstone of evolution theory and has been mathematically formulated in a number of ways. In this paper we illustrate how this model of mutation rates can be derived by means of classical…
We propose Radiation Exposure Theory (RET), a mathematical framework to estimate biological damage caused by irradiation. This is an extension of LDM model which was proposed in the paper [Y. Manabe et al.: J. Phys. Soc. Jpn. 81,…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
The entanglement of population dynamics, evolution, and adaptive radiation for species competing for resources is studied. For resource harvesting, we modify the model used in Ref. Phys. Rev. Lett. 118 048103 and introduce new resource…
This study builds upon a model proposed by Joanny and collaborators that examines the dynamics of interfaces between two distinct cell populations, particularly during tumor growth in healthy tissues. This framework leads to the…
We updated the agent based Monte Carlo code HERITAGE that simulates human evolution within restrictive environments such as interstellar, sub-light speed spacecraft in order to include the effects of population genetics. We incorporated a…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Motivated by models of cancer formation in which cells need to acquire $k$ mutations to become cancerous, we consider a spatial population model in which the population is represented by the $d$-dimensional torus of side length $L$.…
The paper presents a multidimensional model for nonlinear Markovian random walks that generalizes one we developed previously (Phys. Rev. E v.79, 011110, 2009) in order to describe the Levy type stochastic processes in terms of continuous…
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
We provide a review of recent advancements in nonlocal continuous models for migration, mainly from the perspective of its involvement in embryonal development and cancer invasion. Particular emphasis is placed on spatial nonlocality…
Recent studies of in vitro evolution of DNA via protein binding indicate that the evolution behavior is qualitatively different in different parameter regimes. I here present a general theory that is valid for a wide range of parameters,…
Recent works have stressed the important role that random mutations have in the development of cancer phenotype. We challenge this current view by means of bioinformatic data analysis and computational modelling approaches. Not all the…
The movement of organisms and cells can be governed by occasional long distance runs, according to an approximate L\'evy walk. For T cells migrating through chronically-infected brain tissue, runs are further interrupted by long pauses, and…
We consider a class of non-local reaction-diffusion problems, referred to as replicator-mutator equations in evolutionary genetics. For a confining fitness function, we prove well-posedness and write the solution explicitly, via some…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
First, we revisit the stochastic Luria-Delbr\"uck model: a classic two-type branching process which describes cell proliferation and mutation. We prove limit theorems and exact results for the mutation times, clone sizes, and number of…
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
Partial differential equation (PDE) models for infectious disease have received renewed interest in recent years. Most models of this type extend classical compartmental formulations with additional terms accounting for spatial dynamics,…