Algorithms for 13C metabolic flux analysis

The metabolism of an organism consists of a network of biochemical reactions that transform small molecules, or metabolites, into others in order to produce energy and building blocks for essential macromolecules. The goal of metabolic flux analysis is to uncover the rates, or the fluxes, of those biochemical reactions. In a steady state, the sum of the fluxes that produce an internal metabolite is equal to the sum of the fluxes that consume the same molecule. Thus the steady state imposes linear balance constraints to the fluxes. In general, the balance constraints imposed by the steady state are not sufficient to uncover all the fluxes of a metabolic network. The fluxes through cycles and alternative pathways between the same source and target metabolites remain unknown. More information about the fluxes can be obtained from isotopic labelling experiments, where a cell population is fed with labelled nutrients, such as glucose that contains 13C atoms. Labels are then transferred by biochemical reactions to other metabolites. The relative abundances of different labelling patterns in internal metabolites depend on the fluxes of pathways producing them. Thus, the relative abundances of different labelling patterns contain information about the fluxes that cannot be uncovered from the balance constraints derived from the steady state. The field of research that estimates the fluxes utilizing the measured constraints to the relative abundances of different labelling patterns induced by 13C labelled nutrients is called 13C metabolic flux analysis. There exist two approaches of 13C metabolic flux analysis. In the optimization approach, a non-linear optimization task, where candidate fluxes are iteratively generated until they fit to the measured abundances of different labelling patterns, is constructed. In the direct approach, linear balance constraints given by the steady state are augmented with linear constraints derived from the abundances of different labelling patterns of metabolites. Thus, mathematically involved non-linear optimization methods that can get stuck to the local optima can be avoided. On the other hand, the direct approach may require more measurement data than the optimization approach to obtain the same flux information. Furthermore, the optimization framework can easily be applied regardless of the labelling measurement technology and with all network topologies. In this thesis we present a formal computational framework for direct 13C metabolic flux analysis. The aim of our study is to construct as many linear constraints to the fluxes from the 13C labelling measurements using only computational methods that avoid non-linear techniques and are independent from the type of measurement data, the labelling of external nutrients and the topology of the metabolic network. The presented framework is the first representative of the direct approach for 13C metabolic flux analysis that is free from restricting assumptions made about these parameters.In our framework, measurement data is first propagated from the measured metabolites to other metabolites. The propagation is facilitated by the flow analysis of metabolite fragments in the network. Then new linear constraints to the fluxes are derived from the propagated data by applying the techniques of linear algebra.Based on the results of the fragment flow analysis, we also present an experiment planning method that selects sets of metabolites whose relative abundances of different labelling patterns are most useful for 13C metabolic flux analysis. Furthermore, we give computational tools to process raw 13C labelling data produced by tandem mass spectrometry to a form suitable for 13C metabolic flux analysis.

Propagation of ion-acoustic waves in a multi-component plasma

The authors derive the Korteweg-de Vries equation in a multicomponent plasma that includes any number of positive and negative ions. The solitary wave solutions are also found explicitly for the case of isothermal and non-isothermal electrons.

Electron paramagnetic resonance study of vanadyl ion in K2Zn(SO4)2·6H2O and K2Mg(SO4)2·6H2O

EPR study of the vanadyl ion has been carried out in its paramagnetically dilute form in K2Zn(SO4)2·6H2O and K2Mg(SO4)2·6H2O at room temperature at X-band. The vanadyl ion enters the divalent metal site and preferentially orients itself in the direction of the water molecules forming the octahedron and forms the vanadyl sulfate pentahydrate complex. The g and A tensorscorresponding to the two populous V-O orientations have been analyzed to obtain the principal values and their direction cosines with respect to the crystallographics axes. It is found that the g and A tensor have the same principal frames of reference within the limits of eperimental error. A correlation between the metal-water distance and the populations of the different V-O orientations is observed.

Nonlinear saturation of ion-acoustic instability

It is proposed that the wave mediated indirect wave-particle interaction may be responsible for nonlinear saturation of current driven low frequency ion-acoustic turbulence. This process decreases the growth rate and increases the damping rate of the wave. Comparison has been made with some experiments.

Effect of ionic temperature on propagation of ion-acoustic solitary waves in a collisionless plasma of warm-ion fluid and non-isothermal electrons

Using a perturbation technique, we derive Modified Korteweg—de Vries (MKdV) equations for a mixture of warm-ion fluid (γ i = 3) and hot and non-isothermal electrons (γ e> 1), (i) when deviations from isothermality are finite, and (ii) when deviations from isothermality are small. We obtain stationary solutions for these equations, and compare them with the corresponding solutions for a mixture of warm-ion fluid (γ i = 3) and hot, isothermal electrons (γ i = 1).

Factors influencing kinetic and equilibrium behaviour of sodium ion exchange with strong acid cation resin

This study reports an investigation of the ion exchange treatment of sodium chloride solutions in relation to use of resin technology for applications such as desalination of brackish water. In particular, a strong acid cation (SAC) resin (DOW Marathon C) was studied to determine its capacity for sodium uptake and to evaluate the fundamentals of the ion exchange process involved. Key questions to answer included: impact of resin identity; best models to simulate the kinetics and equilibrium exchange behaviour of sodium ions; difference between using linear least squares (LLS) and non-linear least squares (NLLS) methods for data interpretation; and, effect of changing the type of anion in solution which accompanied the sodium species. Kinetic studies suggested that the exchange process was best described by a pseudo first order rate expression based upon non-linear least squares analysis of the test data. Application of the Langmuir Vageler isotherm model was recommended as it allowed confirmation that experimental conditions were sufficient for maximum loading of sodium ions to occur. The Freundlich expression best fitted the equilibrium data when analysing the information by a NLLS approach. In contrast, LLS methods suggested that the Langmuir model was optimal for describing the equilibrium process. The Competitive Langmuir model which considered the stoichiometric nature of ion exchange process, estimated the maximum loading of sodium ions to be 64.7 g Na/kg resin. This latter value was comparable to sodium ion capacities for SAC resin published previously. Inherent discrepancies involved when using linearized versions of kinetic and isotherm equations were illustrated, and despite their widespread use, the value of this latter approach was questionable. The equilibrium behaviour of sodium ions form sodium fluoride solution revealed that the sodium ions were now more preferred by the resin compared to the situation with sodium chloride. The solution chemistry of hydrofluoric acid was suggested as promoting the affinity of the sodium ions to the resin.

Rapid synthetic routes to prepare LiNi1/3Mn1/3Co1/3O2 as a high voltage, high-capacity Li-ion battery cathode material

LiNi1/3Mn1/3Co1/3O2, a high voltage and high-capacity cathode material for Li-ion batteries, has been synthesized by three different rapid synthetic methods. viz. nitrate-melt decomposition, combustion and sol-gel methods. The first two methods are ultra rapid and a time period as small as 15 min is sufficient to prepare nano-crystalline LiNi1/3Mn1/3Co1/3O2. The processing parameters in obtaining the best performing materials are optimized for each process and their electrochemical performance is evaluated in Li-ion cells. The combustion-derived LiNi1/3Mn1/3Co1/3O2 sample exhibits large extent of cation mixing (10%) while the other two methods yield LiNi1/3Mn1/3Co1/3O2 with cation mixing <5%. LiNi1/3Mn1/3Co1/3O2 prepared by nitrate-melt decomposition method exhibits superior performance as Li-ion battery cathode material.

Korteweg-De Vries Equation for Non-Linear Ion-Acoustic Waves in a Plasma with Negative Ions

The theoretical analysis, based on the perturbation technique, of ion-acoustic waves in the vicinity of a Korteweg-de Vries (K-dV) equation derived in a plasma with some negative ions has been made. The investigation shows that the negative ions in plasma with isothermal electrons introduced a critical concentration at which the ion-acoustic wave plays an important role of wave-breaking and forming a precursor while the plasma with non-isothermal electrons has no such singular behaviour of the wave. These two distinct features of ion waves lead to an overall different approach of present study of ion-waves. A distinct feature of non-uniform transition from the nonisothermal case to isothermal case has been shown. Few particular plasma models have been chosen to show the characteristics behaviour of the ion-waves existing in different cases

Korteweg-de Vries equation for the propagation of fast ion-acoustic waves in multi-dimensions

Abstract is not available.

Studies of multiple ionization in the RF spark and vacuum vibrator arc ion sources

Relative abundance distributions of multiply-charged ionic species have been measured for the RF spark and vacuum vibrator are ion sources, for a number of elements. An attempt has been made to explain the observed charge state distribution on the basis of models for the arc and spark plasma. The difficulties in the way of explaining the observed charge state distributions, using the LTE model with Saha distribution as well as the corona model, are pointed out. The distribution can be explained by a diffusion-dominated plasma model with known or calculated values for ionization cross-sections, the single impact model being suitable for the RF spark and the multiple impact model for the vibrator arc.

Heat transfer to power-law fluids in thermal entrance region with viscous dissipation for constant heat flux conditions

An analytical solution of the heat transfer problem with viscous dissipation for non-Newtonian fluids with power-law model in the thermal entrance region of a circular pipe and two parallel plates under constant heat flux conditions is obtained using eigenvalue approach by suitably replacing one of the boundary conditions by total energy balance equation. Analytical expressions for the wall and the bulk temperatures and the local Nusselt number are presented. The results are in close agreement with those obtained by implicit finite-difference scheme. It is found that the role of viscous dissipation on heat transfer is completely different for heating and cooling conditions at the wall. The results for the case of cooling at the wall are of interest in the design of the oil pipe line.

A possible explanation of the Maunder minimum from a flux transport dynamo model

We propose that the poloidal field at the end of the last sunspot cycle before the Maunder minimum fell to a very low value due to fluctuations in the Babcock-Leighton process. With this assumption, a flux transport dynamo model is able to explain various aspects of the historical records of the Maunder minimum remarkably well by suitably choosing the parameters of the model to give the correct growth time.

Nonlinear saturation of ion-acoustic instability

It is proposed that the wave mediated indirect wave-particle interaction may be responsible for nonlinear saturation of current driven low frequency ion-acoustic turbulence. This process decreases the growth rate and increases the damping rate of the wave. Comparison has been made with some experiments.

Response of a turbulent boundary layer to a step change in surface heat flux

Measurements of both the velocity and the temperature field have been made in the thermal layer that grows inside a turbulent boundary layer which is subjected to a small step change in surface heat flux. Upstream of the step, the wall heat flux is zero and the velocity boundary layer is nearly self-preserving. The thermal-layer measurements are discussed in the context of a self-preserving analysis for the temperature disturbance which grows underneath a thick external turbulent boundary layer. A logarithmic mean temperature profile is established downstream of the step but the budget for the mean-square temperature fluctuations shows that, in the inner region of the thermal layer, the production and dissipation of temperature fluctuations are not quite equal at the furthest downstream measurement station. The measurements for both the mean and the fluctuating temperature field indicate that the relaxation distance for the thermal layer is quite large, of the order of 1000θ0, where θ0 is the momentum thickness of the boundary layer at the step. Statistics of the thermal-layer interface and conditionally sampled measurements with respect to this interface are presented. Measurements of the temperature intermittency factor indicate that the interface is normally distributed with respect to its mean position. Near the step, the passive heat contaminant acts as an effective marker of the organized turbulence structure that has been observed in the wall region of a boundary layer. Accordingly, conditional averages of Reynolds stresses and heat fluxes measured in the heated part of the flow are considerably larger than the conventional averages when the temperature intermittency factor is small.