Related papers: Dynamic resource allocation in eukaryotic Resource…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
We consider a general class of dynamic resource allocation problems within a stochastic optimal control framework. This class of problems arises in a wide variety of applications, each of which intrinsically involves resources of different…
In this article, we focus on a periodic resource allocation problem applied to a dynamical system which comes from a biological system. More precisely, we consider a system with $N$ resources and $N$ activities, each activity use the…
This paper aims to introduce a concept of an equilibrium point of a dynamical system which will call it almost global asymptotically stable. A biological prey-predator model is also analyzed with a modification function growth in prey…
An extensive rewiring of cell metabolism supports enhanced proliferation in cancer cells. We propose a systems level approach to describe this phenomenon based on Flux Balance Analysis (FBA). The approach does not explicit a cell biomass…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
Cells achieve size homeostasis by regulating their division timing based on their size, added size, and cell cycle time. Previous research under steady-state conditions demonstrated the robustness of these mechanisms. However, their dynamic…
Cyanobacteria are an integral part of the Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2 . Growth and metabolism of cyanobacteria are inherently tied to the diurnal…
Despite being optimized, the information processing of biological organisms exhibits significant variability in its complexity and capability. One potential source of this diversity is the limitation of resources required for information…
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principle for metabolism: each enzyme must convert less valuable…
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…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
Dynamic Flux Balance Analysis (dFBA) extends the capabilities of FBA to track changes in metabolite concentrations and fluxes over time in response to environmental conditions and cellular processes. The key idea of the method called…
In this paper, we propose a new approach for stochastic control problems arising from utility maximization. The main idea is to directly start from the dynamical programming equation and compute the conditional expectation using a novel…
In this paper, we conduct a study to optimize resource allocation for adaptive real-time and delay-tolerant applications in cellular systems. To represent the user applications via several devices and equipment, sigmoidal-like and logarithm…
In this work, we study the optimization problem of a renewable resource in finite time. The resource is assumed to evolve according to a logistic stochastic differential equation. The manager may harvest partially the resource at any time…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…