Related papers: A RBA model for the chemostat modeling
The Crump-Young model consists of two fully coupled stochastic processes modeling the substrate and microorganisms dynamics in a chemostat. Substrate evolves following an ordinary differential equation whose coefficients depend of…
The objective of the paper is to evaluate the ability of reactive transport models and their numerical implementations (such as MIN3P) to simulate simple microbial transformations in conditions of chemostat or gradostat models, that are…
Online experiments such as Randomised Controlled Trials (RCTs) or A/B-tests are the bread and butter of modern platforms on the web. They are conducted continuously to allow platforms to estimate the causal effect of replacing system…
We propose a neo-logistic model that can describe bacterial growth data precisely. This model is not derived by modifying the logistic model formally, but by incorporating the synthesis of inducible enzymes into the logistic model…
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…
Computational models that accurately predict the binding affinity of an input protein-chemical pair can accelerate drug discovery studies. These models are trained on available protein-chemical interaction datasets, which may contain…
In this paper we study a nonlinear reaction-diffusion system which models an infectious disease caused by bacteria such as those for cholera. One of the significant features in this model is that a certain portion of the recovered human…
Large-scale self-supervised models have recently revolutionized our ability to perform a variety of tasks within the vision and language domains. However, using such models for autonomous systems is challenging because of safety…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions. One example is the immune system signalling, where infected tissues release chemokines…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action…
The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its pre-stimulus level exactly and this "perfect adaptability" is robust…
In this paper, we propose a regression model where the response variable is beta prime distributed using a new parameterization of this distribution that is indexed by mean and precision parameters. The proposed regression model is useful…
The aim of this study was to build a modelling framework that would allow us to be able to detect mastitis infections before they would normally be found by farmers through the introduction of machine learning techniques. In the making of…
In several clinical areas, traditional clinical trials often use a responder outcome, a composite endpoint that involves dichotomising a continuous measure. An augmented binary method that improves power whilst retaining the original…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare,…
Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In…
Microbial communities play a significant role in bioremediation,plant growth,human and animal digestion,global elemental cycles including the carbon-cycle,and water treatment.They are also posed to be the engines of renewable energy via…