Finite volume formulation of thermal lattice Boltzmann method

Purpose – The main purpose of this paper is to develop a novel thermal lattice Boltzmann method (LBM) based on finite volume (FV) formulation. Validation of the suggested formulation is performed by simulating plane Poiseuille, backward-facing step and flow over circular cylinder. Design/methodology/approach – For this purpose, a cell-centered scheme is used to discretize the convection operator and the double distribution function model is applied to describe the temperature field. To enhance stability, weighting factors are defined as flux correctors on a D2Q9 lattice. Findings – The introduction of pressure-temperature-dependent flux-control coefficients in the streaming operator, in conjunction with suitable boundary conditions, is shown to result in enhanced numerical stability of the scheme. In all cases, excellent agreement with the existing literature is found and shows that the presented method is a promising scheme in simulating thermo-hydrodynamic phenomena. Originality/value – A stable and accurate FV formulation of the thermal DDF-LBM is presented.

Contrasting responses by respiration to elevated CO2 in intact tissue and isolated mitochondria

The question of whether elevated concentrations of CO2 directly inhibit mitochondrial respiration in plants has received considerable attention. Although there is a growing consensus that elevated [CO2] rarely inhibits respiration of intact tissues, past studies have reported that elevated [CO2] does impact on O2 uptake in isolated mitochondria; what remains unclear, however, is the site(s) where elevated [CO2] impacts on mitochondrial electron transport (ETC). Here we investigated direct effects of [CO2] on respiratory activity of ETC enzymes, intact mitochondria and whole tissues using potato tubers (Solanum tuberosum L. cv. Desiree). Plots of O2 uptake against the redox poise of the ubiquinone (UQ) pool in isolated mitochondria were used to determine whether elevated [CO2] inhibits UQ-reducing and UQ-oxidising pathways differentially. Our results show that mitochondrial respiration was more inhibited via [CO2]/[HCO3–] effects on cytochrome c oxidase (COX) than on succinate dehydrogenase, with [HCO3–] rather than [CO2] inhibiting COX. However, the inhibitory effects at the mitochondrial level did not translate into inhibitory effects at the tissue level. Alternative oxidase (AOX) activity is normally absent in young potato tubers, as was the case in the present study. Thus, the lack of CO2-mediated inhibition at the tissue level was not the result of increases in AOX activity masking the effects of CO2 elsewhere in the respiratory system. We discuss whether the direct impact of elevated [CO2] on respiration is dependent on the rate of metabolic activity and flux control coefficients in individual tissues.

Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction affinity. This parameter can often be determined from experiments in vitro. The methodology is applicable only to the analysis of simple two-step pathways, but in many cases larger pathways can be lumped into two overall conversions. In cases where this cannot be done it is necessary to apply an extension of the thermokinetic description of reaction rates to include the influence of effectors. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919–927] can be much more widely applied, although it was originally based on linearized kinetics. The methodology of determining elasticity coefficients directly from pool levels is illustrated with an analysis of the first two steps of the biosynthetic pathway of penicillin. The results compare well with previous findings based on a kinetic analysis.