Related papers: Multiscale metabolic modeling of C4 plants: connec…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo…
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…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
A computational framework integrating optimization algorithms, parallel computing and plant physiology was developed to explore crop ideotype design. The backbone of the framework is a plant physiology model that accurately tracks water use…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
In the last decades, the area under cultivation of maize products has increased because of its essential role in the food cycle for humans, livestock, and poultry. Moreover, the diseases of plants impact food safety and can significantly…
Carbon containing molecules in cold molecular clouds show various levels of isotopic fractionation through multiple observations. To understand such effects, we have developed a new gas-grain chemical model with updated 13C fractionation…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees.…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
The appropriate design, construction, and operation of carbon capture and storage (CCS) and enhanced oil recovery (EOR) processes require a deep understanding of the resulting phases behavior in hydrocarbons-CO_2 multi-component mixtures…
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…