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The halophilic γ-proteobacterium Halomonas elongata DSM 2581(T) thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to(More)
In the present work we have applied the indirect optimization method (Torres, N. V. et al. Biotechnol. Bioeng. 1996, 49, 247-258) to the maximization of tryptophan biosynthesis in Escherichia coli. The optimization procedure is applied to an updated model of this biochemical system (Xiu, Z-L et al., J. Biotechnol. 1997, 58, 125-140) and thus extended to a(More)
In the near future, computational tools and methods based on the mathematical modeling of biomedically relevant networks and pathways will be necessary for the design of therapeutic strategies that fight complex multifactorial diseases. Beyond the use of pharmacokinetic and pharmacodynamic approaches, we propose here the use of dynamic modeling as a tool(More)
BACKGROUND In the past, tasks of model based yield optimization in metabolic engineering were either approached with stoichiometric models or with structured nonlinear models such as S-systems or linear-logarithmic representations. These models stand out among most others, because they allow the optimization task to be converted into a linear program, for(More)
A new method is proposed for the optimization of biochemical systems. The method, based on the separation of the stoichiometric and kinetic aspects of the system, follows the general approach used in the previously presented indirect optimization method (IOM) developed within biochemical systems theory. It is called GMA-IOM because it makes use of the(More)
Metabolic Engineering aims to improve the performance of biotechnological processes through rational manipulation rather than random mutagenesis of the organisms involved. Such a strategy can only succeed when a mathematical model of the target process is available. Simplifying assumptions are often needed to cope with the complexity of such models in an(More)
BACKGROUND Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need(More)
In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations(More)
Keywords: Biochemical systems Power-law formalism S-systems Generalized mass action Linear programming Multiobjective optimization Geometric programming In this work we present a general (mono and multiobjective) optimization framework for the technological improvement of biochemical systems. The starting point of the method is a mathematical model in(More)
Pathway models in biotechnology are customarily designed with metabolite concentrations as the primary, dependent variables, whereas fluxes are derived quantities that are secondarily computed from the primary variables. In other fields of mathematics, such as graph theory and linear systems analysis, it has proven useful to complement primal network model(More)