Related papers: Understanding the Dynamics and Optimizing the Perf…

In this paper, we consider a resource-consumer model taking into account a mutation effect between species (with constant mutation rate). The corresponding mutation operator is a discretization of the Laplacian in such a way that the…

The collective chemotaxis of multicellular clusters is an important phenomenon in various physiological contexts, ranging from embryonic development to cancer metastasis. Such clusters often display interesting shape dynamics and…

Microplastics contamination is one of the most rapidly growing research topics. However, monitoring microplastics contamination in the environment presents both logistical and statistical challenges, particularly when constrained resources…

In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…

Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…

Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…

The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…

Complex processes in science and engineering are often formulated as multistage decision-making problems. In this paper, we consider a type of multistage decision-making process called a cascade process. A cascade process is a multistage…

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…

In biopharmaceutical manufacturing, fermentation processes play a critical role in productivity and profit. A fermentation process uses living cells with complex biological mechanisms, leading to high variability in the process outputs,…

We study a single-species chemostat model with variable nutrient input and variable dilution rate with delayed (fixed) response in growth. The first goal of this article is to prove that persistence implies uniform persistence. Then we…

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…

We investigate a selection-mutation model for the dynamics of technological innovation,a special case of reaction-diffusion equations. Although mutations are assumed to increase the variety of technologies, not their average success…

Many decision problems in science, engineering and economics are affected by uncertain parameters whose distribution is only indirectly observable through samples. The goal of data-driven decision-making is to learn a decision from finitely…

Multistage stochastic programming is a powerful tool allowing decision-makers to revise their decisions at each stage based on the realized uncertainty. However, in practice, organizations are not able to be fully flexible, as decisions…

Single-cell organisms and various cell types use a range of motility modes when following a chemical gradient, but it is unclear which mode is best suited for different gradients. Here, we model directional decision-making in chemotactic…

Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation, and vascular tumors provide a focus on optimization strategies. Experiments can characterize…

The purpose of this paper is to show that it is possible to replace Monod's type model of a chemostat by a constraint based model of bacteria at the genome scale. This new model is an extension of the RBA model of bacteria developed in a…

How should researchers select experimental sites when the deployment population differs from observed data? I formulate the problem of experimental site selection as an optimal transport problem, developing methods to minimize downstream…

Molecular sorting is a fundamental process that allows eukaryotic cells to distill and concentrate specific chemical factors in appropriate cell membrane subregions, thus endowing them with different chemical identities and functional…