Stochastic chemical kinetics at the single-cell level give rise to heterogeneous populations of cells even when all individuals are genetically identical. This heterogeneity can lead to nonuniform behaviour within populations, including different growth characteristics, cell-fate dynamics, and response to stimuli. Ultimately, these diverse behaviours lead to intricate population dynamics that are inherently multiscale: the population composition evolves based on population-level processes that interact with stochastically distributed single-cell states. Therefore, descriptions that account for this heterogeneity are essential to accurately model and control chemical processes. However, for real-world systems such models are computationally expensive to simulate, which can make optimisation problems, such as optimal control or parameter inference, prohibitively challenging. Here, we consider a class of multiscale population models that incorporate population-level mechanisms while remaining faithful to the underlying stochasticity at the single-cell level and the interplay between these two scales. To address the complexity, we study an order-reduction approximations based on the distribution moments. Since previous moment-closure work has focused on the single-cell kinetics, extending these techniques to populations models prompts us to revisit old observations as well as tackle new challenges. In this extended multiscale context, we encounter the previously established observation that the simplest closure techniques can lead to non-physical system trajectories. Despite their poor performance in some systems, we provide an example where these simple closures outperform more sophisticated closure methods in accurately, efficiently, and robustly solving the problem of optimal control of bioproduction in a microbial consortium model.
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http://dx.doi.org/10.1016/j.mbs.2022.108866 | DOI Listing |
Biomolecules
November 2024
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
Regarding Alzheimer's disease (AD), specific neuronal populations and brain regions exhibit selective vulnerability. Understanding the basis of this selective neuronal and regional vulnerability is essential to elucidate the molecular mechanisms underlying AD pathology. However, progress in this area is currently hindered by the incomplete understanding of the intricate functional and spatial diversity of neuronal subtypes in the human brain.
View Article and Find Full Text PDFSci Rep
January 2025
Strathclyde Institute of Education, University of Strathclyde, Lord Hope Building, Glasgow, G4 0LT, UK.
Computational analysis of infant movement has significant potential to reveal markers of developmental health. We report two studies employing dynamic analyses of motor kinematics and motor behaviours, which characterise movement at two levels, in 9-month-old infants. We investigate the effect of preterm birth (< 33 weeks of gestation) and the effect of changing emotional and social-interactive contexts in the still-face paradigm.
View Article and Find Full Text PDFJ Chem Phys
January 2025
School of Physics and Astronomy, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China.
Two-dimensional electronic spectroscopy (2DES) has high spectral resolution and is a useful tool for studying atomic dynamics. In this paper, we show a smallest unit of electromagnetically induced transparency (EIT) for 2DES, i.e.
View Article and Find Full Text PDFFront Comput Neurosci
December 2024
School of Electrical and Electronic Engineering, Chongqing University of Technology, Chongqing, China.
mLife
December 2024
Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering, East China Normal University Shanghai China.
In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance, including molecular docking, molecular dynamics, quantum mechanics, and multiscale QM/MM approaches. However, the manual operation associated with these methods poses challenges for simulating enzymes and enzyme variants in a high-throughput manner. We developed the NAC4ED, a high-throughput enzyme mutagenesis computational platform based on the "near-attack conformation" design strategy for enzyme catalysis substrates.
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