Abstract Efficiently identifying drug targets with minimal side effects is a major challenge in new drug development. In this paper, we develop a method based on flux balance analysis (FBA) to identify drug targets in metabolic networks. The method, which is formulated into two linear programming models, first finds the steady flux of reactions and mass flow of metabolites in the pathologic sta...

Modeling sophisticated biological systems in a way that makes them more apprehensible, without losing comprehension or robustness, is a challenging task. The flux balance analysis (FBA) model describes metabolic networks of single-celled organisms with the goal of simulating their steady-state behavior. FBA simulations yield reliable and biologically relevant growth rate values, but do not simu...

MOTIVATION Flux variability analysis (FVA) is an important tool to further analyse the results obtained by flux balance analysis (FBA) on genome-scale metabolic networks. For many constraint-based models, FVA identifies unboundedness of the optimal flux space. This reveals that optimal flux solutions with net flux through internal biochemical loops are feasible, which violates the second law of...

UNLABELLED FBA-SimVis is a VANTED plug-in for the constraint-based analysis of metabolic models with special focus on the visual exploration of metabolic flux data resulting from model analysis. The program provides a user-friendly environment for model reconstruction, constraint-based model analysis, and interactive visualization of the simulation results. With the ability to quantitatively an...

Genome-scale metabolic networks are highly robust to the elimination of enzyme-coding genes. Their structure can evolve rapidly through mutations that eliminate such genes and through horizontal gene transfer that adds new enzyme-coding genes. Using flux balance analysis we study a vast space of metabolic network genotypes and their relationship to metabolic phenotypes, the ability to sustain l...

Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of constrainbased modelling methods published throughout the years, only few have focused on thermodynamic issues, in particular the elimination of non-physical and ...

In this research, the thermodynamics and mass transfer of CO2 absorption has been studied in a mixture of MDEA-MEA amines. A relation is presented for mass transfer flux in the reactive-absorption process. For this purpose, the effective parameters on the mass transfer flux were investigated in both liquid and gas phases. Then, using dimensional analysis with the Pi-Buckingham theorem, the effe...