相关论文: A branching process model for flow cytometry and b…
Stochastic dynamic models have been extensively used for the description of processes with uncertainties arising in the operations research, behavioral sciences, and many other application areas. A large class of the problems from these…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
Recent methods have been developed to map single-cell lineage statistics to population growth. Because population growth selects for exponentially rare phenotypes, these methods inherently depend on sampling large deviations from finite…
We consider population models in which the individuals reproduce, die and also migrate in space. The population size scales according to some parameter $N$, which can have different interpretations depending on the context. Each individual…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Markov branching systems form a fundamental class of stochastic models that are extensively applied in biology, physics, finance, and other domains. These systems are distinguished by their continuous-time evolution and inherent branching…
The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the…
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…
A novel approach to moment closure problem is used to derive low dimensional laws for the dynamics of the moments of the membrane potential distribution in a population of spiking neurons. Using spectral expansion of the density equation we…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…
For over two decades, Flux Balance Analysis (FBA) has been successfully used for predicting growth rates and intracellular reaction rates in microbiological metabolism. An aspect that is often omitted from this analysis, is segregation or…
Cytometry enables precise single-cell phenotyping within heterogeneous populations. These cell types are traditionally annotated via manual gating, but this method suffers from a lack of reproducibility and sensitivity to batch-effect.…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
We consider a particle system in continuous time, discrete population, with spatial motion and nonlocal branching. The offspring's weights and their number may depend on the mother's weight. Our setting captures, for instance, the processes…
Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
We study a continuous time Mutually Catalytic Branching model on the $\mathbb{Z}^{d}$. The model describes the behavior of two different populations of particles, performing random walk on the lattice in the presence of branching, that is,…
The goal of this paper is to provide mathematically rigorous tools for modelling the evolution of a community of interacting individuals. We model the population by a measure space where the measure determines the abundance of individual…
This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of…