Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth

H Dourado, W Liebermeister, O Ebenhöh… - PLoS Computational …, 2023 - journals.plos.org
The physiology of biological cells evolved under physical and chemical constraints, such as
mass conservation across the network of biochemical reactions, nonlinear reaction kinetics …

Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate

D Széliová, S Müller, J Zanghellini - Communications Biology, 2024 - nature.com
Ribosomes are key to cellular self-fabrication and limit growth rate. While most enzymes are
proteins, ribosomes consist of 1/3 protein and 2/3 ribonucleic acid (RNA)(in E. coli). Here …

Thermodynamic and stoichiometric laws ruling the fates of growing systems

A Kamimura, Y Sughiyama, TJ Kobayashi - Physical Review Research, 2024 - APS
We delve into growing open chemical reaction systems (CRSs) characterized by
autocatalytic reactions within a variable volume, which changes in response to these …

Effect and Mechanism of Rice-Pasture Rotation Systems on Yield Increase and Runoff Reduction under Different Fertilizer Treatments

Y Xing, C Wang, Z Li, J Chen, Y Li - Agronomy, 2023 - mdpi.com
This study investigated the effects of crop rotations and different ratios of dairy manure
fertilizer on nitrogen loss and rice yield in the Erhai Lake basin. Two kinds of herbages were …

Growth Mechanics: General principles of optimal cellular resource allocation in balanced growth

H Dourado, W Liebermeister, O Ebenhöh, MJ Lercher - BioRxiv, 2022 - biorxiv.org
The physiology of biological cells evolved under physical and chemical constraints such as
mass conservation, nonlinear reaction kinetics, and limits on cell density. For unicellular …

[HTML][HTML] A Markov constraint to uniquely identify elementary flux mode weights in unimolecular metabolic networks

JG Chitpin, TJ Perkins - Journal of Theoretical Biology, 2023 - Elsevier
Elementary flux modes (EFMs) are minimal, steady state pathways characterizing a flux
network. Fundamentally, all steady state fluxes in a network are decomposable into a linear …

Does ribosome composition maximize growth rate? The role of RNA instability

D Széliová, S Müller, J Zanghellini - bioRxiv, 2023 - biorxiv.org
Ribosomes are protein synthesis machines that are central to cellular self-fabrication, and
the synthesis time of a ribosome places an upper bound on growth rate. While most cellular …

Modeling Uncertain Biomass Composition in Genome-Scale Metabolic Models with Flexible Nets

T Joven, J Lázaro, J Júlvez - International Conference on Quantitative …, 2023 - Springer
Abstract Genome-scale Metabolic Models (GEMs) are mathematical representations of an
organism's metabolism that describe mass-balanced relationships between metabolites …

[PDF][PDF] 1Department of Analytical Chemistry, University of Vienna, Austria, EU; 2Faculty of

D Széliová, S Müller, J Zanghellini - Methods - chemnet.univie.ac.at
Ribosomes are protein synthesis machines that are central to cellular self-fabrication, 8 and
the synthesis time of a ribosome places an upper bound on growth rate. While most cellular …

[PDF][PDF] Development of a Self-Replicating Cell Model for Analyzing Optimal Ribosome Composition

MS Bioinformatik, D Jasiczek - pub.fh-campuswien.ac.at
The ribosome is a fundamental component of all self-replicating cells, responsible for protein
biosynthesis through the translation of messenger RNA (mRNA). Previous research has …