Related papers: A RBA model for the chemostat modeling
Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general…
This paper addresses the problem of model reduction for dynamical system models that describe biochemical reaction networks. Inherent in such models are properties such as stability, positivity and network structure. Ideally these…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
We study the chemostat model for one species competing for one nutrient using a Lyapunov-type analysis. We design the dilution rate function so that all solutions of the chemostat converge to a prescribed periodic solution. In terms of…
Continuous cultures of mammalian cells are complex systems displaying hallmark phenomena of nonlinear dynamics, such as multi-stability, hysteresis, as well as sharp transitions between different metabolic states. In this context…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
Herein an alternative model to reptation to describe concentrated polymer dynamics is developed. The model assumes that the chains act as blobs that are able to diffuse past each other in a compressed state. Allowing that the local…
Stochastic ordering among distributions has been considered in a variety of scenarios. Economic studies often involve research about the ordering of investment strategies or social welfare. However, as noted in the literature, stochastic…
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…
Precise physical descriptions of molecules can be obtained by solving the Schrodinger equation; however, these calculations are intractable and even approximations can be cumbersome. Force fields, which estimate interatomic potentials based…
Microbial ecology serves as a foundation for a wide range of scientific and biomedical studies. Rapidly-evolving high-throughput sequencing technology enables the comprehensive search for microbial biomarkers using longitudinal experiments.…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance.…
Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is instead substituted by an optimization…
We consider the classical chemostat model with an additional compartment connected by pure diffusion, and analyze its asymptotic properties. We investigate conditions under which this spatial structure is beneficial for species survival and…
Growth in bacterial populations generally depends on the environment (availability and quality of nutrients, presence of a toxic inhibitor, product inhibition..). Here, we build a model to describe the action of a bacteriostatic antibiotic,…
The aim of this work is to provide a rigorous mathematical analysis of a stochastic concatenation model presented by Sobottka and Hart (2011) which allows approximation of the first-order stochastic structure in bacterial DNA by means of a…