相关论文: Multistable protocells can aid the evolution of pr…
My goal is to study the dynamics of the Universe from a relational perspective based on the happening of events in temporal relation to each other and their respective points of reference. Accordingly, the flow of time was modeled as the…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…
Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
The time evolution of the adiabatic piston problem and the consequences of its stochastic motion are investigated. The model is a one dimensional piston of mass $M$ separating two ideal fluids made of point particles with mass $m\ll M$. For…
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…
A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole.…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
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…
The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…
An approach to analyse the properties of a particle system is to compare it with different processes to understand when one of them is larger than other ones. The main technique for that is coupling, which may not be easy to construct. We…
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…
Two alternative views of an economy are combined and studied. The first view is that of technological evolution as a process of combinatorial innovation. Recently a simple mathematical model (TAP) was introduced to study such a…
Genetic variation in a population can sometimes arise so fast as to modify ecosystem dynamics. Such phenomena have been observed in natural predator-prey systems, and characterized in the laboratory as showing unusual phase relationships in…
In this paper I describe a cellular automaton model of a multi-species ecosystem, suitable for the study of emergent properties of macroevolution. Unlike majority of ecological models, the number of coexisting species is not fixed. Starting…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in which subpopulations grow…