MOTIVATION Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating 'omics' data fro...

Metabolic fluxes are governed by physical and economic principles. Stationarity constrains them to a subspace in flux space and thermodynamics makes them lead from higher to lower chemical potentials. At the same time, fluxes in cells represent a compromise between metabolic performance and enzyme cost. To capture this, some flux prediction methods penalise larger fluxes by heuristic cost terms...

Typical bogs in the boreal forest zone can be characterised by hummock and hollow micro-topography and sparsely vegetated surfaces. Their energy balance has been studied much less than for other types of surface, i.e. fields and forests. Micrometeorological measurements were carried out in central Sweden at two bogs in different summer seasons. From the measured profiles of wind speed, air temp...

Measurements of turbulent exchange in the understorey of a forest canopy are necessary to understand and model both the functioning of the lower stratum and its contribution to turbulent exchange at the whole canopy scale. Eddy covariance measurements of eddy fluxes just above the floor of a forest canopy must be thoroughly validated, given the particular conditions prevailing there. Our object...

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising fro...

MOTIVATION The availability of modern sequencing techniques has led to a rapid increase in the amount of reconstructed metabolic networks. Using these models as a platform for the analysis of high throughput transcriptomic, proteomic and metabolomic data can provide valuable insight into conditional changes in the metabolic activity of an organism. While transcriptomics and proteomics provide i...

An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model whic...

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some...

We have developed a corrosion model that can predict metal oxide growth and dissolution rates as a function of time for a range of solution conditions. Our model considers electrochemical reactions at the metal/oxide and oxide/solution interfaces, and the metal cation flux from the metal to the solution phase through a growing oxide layer, and formulates the key processes using classical chemic...