Related papers: Maximum entropy and population heterogeneity in co…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
We propose a new scheme to infer the metabolic fluxes of cell cultures in a chemostat. Our approach is based on the Maximum Entropy Principle and exploits the understanding of the chemostat dynamics and its connection with the actual…
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are…
We introduce two stochastic chemostat models consisting in a coupled population-nutrient process reflecting the interaction between the nutrient and the bacterias in the chemostat with finite volume. The nutrient concentration evolves…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
In many real life applications, a continuous culture bioreactor may cease to function properly due to bioclogging which is typically caused by the microbial overgrowth. This is a problem that has been largely overlooked in the chemostat…
Populations of mammalian stem cells commonly exhibit considerable cell-cell variability. However, the functional role of this diversity is unclear. Here, we analyze expression fluctuations of the stem cell surface marker Sca1 in mouse…
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
We quantify the amount of regulation required to control growth in living cells by a Maximum Entropy approach to the space of underlying metabolic states described by genome-scale models. Results obtained for E. coli and human cells are…
The dynamics of gene regulatory networks are often modeled with the assumption of cellular homogeneity. However, this assumption contradicts the plethora of experimental results in a variety of systems, which designates that cell…
Movement behavior of biological entities plays a crucial role in their destiny through regulating their intraspecific and interspecific interactions as well as their interaction with surrounding environment. In spite of various models for…
This paper is concerned with the evolution of haploid organisms that reproduce asexually. In a seminal piece of work, Eigen and coauthors proposed the quasispecies model in an attempt to understand such an evolutionary process. Their work…
Human bone marrow stromal cells (BMSC) include skeletal stem cells with ground-breaking therapeutic potential. However, BMSC colonies have very heterogeneous in vivo behaviour, due to their different potency; this unpredictability is the…
New experimental methods make it possible to measure the expression levels of many genes, simultaneously, in snapshots from thousands or even millions of individual cells. Current approaches to analyze these experiments involve clustering…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
When confronted with an undesired cell population, such as bacterial infections or tumors, we seek the most effective treatment, designed to eliminate the population as rapidly as possible. A common practice is to monitor the cells…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
The metaphor of a potential epigenetic differentiation landscape broadly suggests that during differentiation a stem cell follows the steepest descending gradient toward a stable equilibrium state which represents the final cell type. It…