Flux balance analysis of biological systems: applications and challenges

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.

Heat balance analysis of single stage Gifford-McMahon cycle cryorefrigerator

A heat balance analysis of single stage Gifford-McMahon cycle cryorefrigerator is presented. Ideal refrigeration, actual refrigeration, net refrigeration and the various losses are tabulated. It is observed that pressure-volume losses account for a major fraction of the total losses.

Measurement of aerodynamic forces for missile shaped body in hypersonic shock tunnel using 6-component accelerometer based balance system

This paper reports the basic design of a new six component force balance system using miniature piezoelectric accelerometers to measure all aerodynamic forces and moments for a test model in hypersonic shock tunnel (HST2). Since the flow duration in a hypersonic shock tunnel is of the order of $1$ ms, the balance system [1] uses fast response accelerometers (PCB Piezotronics; frequency range of 1-10 kHz) for obtaining the aerodynamic data. The alance system has been used to measure the basic aerodynamic forces and moments on a missile shaped body at Mach $8$ in the IISc hypersonic shock tunnel. The experimentally measured values match well with theoretical predictions.

Water balance modelling in a tropical watershed under deciduous forest (Mule Hole, India): Regolith matric storage buffers the groundwater recharge process

Accurate estimations of water balance are needed in semi-arid and sub-humid tropical regions, where water resources are scarce compared to water demand. Evapotranspiration plays a major role in this context, and the difficulty to quantify it precisely leads to major uncertainties in the groundwater recharge assessment, especially in forested catchments. In this paper, we propose to assess the importance of deep unsaturated regolith and water uptake by deep tree roots on the groundwater recharge process by using a lumped conceptual model (COMFORT). The model is calibrated using a 5 year hydrological monitoring of an experimental watershed under dry deciduous forest in South India (Mule Hole watershed). The model was able to simulate the stream discharge as well as the contrasted behaviour of groundwater table along the hillslope. Water balance simulated for a 32 year climatic time series displayed a large year-to-year variability, with alternance of dry and wet phases with a time period of approximately 14 years. On an average, input by the rainfall was 1090 mm year(-1) and the evapotranspiration was about 900 mm year(-1) out of which 100 mm year(-1) was uptake from the deep saprolite horizons. The stream flow was 100 mm year(-1) while the groundwater underflow was 80 mm year(-1). The simulation results suggest that (i) deciduous trees can uptake a significant amount of water from the deep regolith, (ii) this uptake, combined with the spatial variability of regolith depth, can account for the variable lag time between drainage events and groundwater rise observed for the different piezometers and (iii) water table response to recharge is buffered due to the long vertical travel time through the deep vadose zone, which constitutes a major water reservoir. This study stresses the importance of long term observations for the understanding of hydrological processes in tropical forested ecosystems. (C) 2009 Elsevier B.V. All rights reserved.

A new framework for solution of multidimensional population balance equations

A new framework is proposed in this work to solve multidimensional population balance equations (PBEs) using the method of discretization. A continuous PBE is considered as a statement of evolution of one evolving property of particles and conservation of their n internal attributes. Discretization must therefore preserve n + I properties of particles. Continuously distributed population is represented on discrete fixed pivots as in the fixed pivot technique of Kumar and Ramkrishna [1996a. On the solution of population balance equation by discretization-I A fixed pivot technique. Chemical Engineering Science 51(8), 1311-1332] for 1-d PBEs, but instead of the earlier extensions of this technique proposed in the literature which preserve 2(n) properties of non-pivot particles, the new framework requires n + I properties to be preserved. This opens up the use of triangular and tetrahedral elements to solve 2-d and 3-d PBEs, instead of the rectangles and cuboids that are suggested in the literature. Capabilities of computational fluid dynamics and other packages available for generating complex meshes can also be harnessed. The numerical results obtained indeed show the effectiveness of the new framework. It also brings out the hitherto unknown role of directionality of the grid in controlling the accuracy of the numerical solution of multidimensional PBEs. The numerical results obtained show that the quality of the numerical solution can be improved significantly just by altering the directionality of the grid, which does not require any increase in the number of points, or any refinement of the grid, or even redistribution of pivots in space. Directionality of a grid can be altered simply by regrouping of pivots.

A voltage-sensorless control method to balance the input currents of a three-wire boost rectifier under unbalanced input voltages condition

This paper proposes a control method that can balance the input currents of the three-phase three-wire boost rectifier under unbalanced input voltage condition. The control objective is to operate the rectifier in the high-power-factor mode under balanced input voltage condition but to give overriding priority to the current balance function in case of unbalance in the input voltage. The control structure has been divided into two major functional blocks. The inner loop current-mode controller implements resistor emulation to achieve high-power-factor operation on each of the two orthogonal axes of the stationary reference frame. The outer control loop performs magnitude scaling and phase-shifting operations on current of one of the axes to make it balanced with the current on the other axis. The coefficients of scaling and shifting functions are determined by two closed-loop prportional-integral (PI) controllers that impose the conditions of input current balance as PI references. The control algorithm is simple and high performing. It does not require input voltage sensing and transformation of the control variables into a rotating reference frame. The simulation results on a MATLAB-SIMULINK platform validate the proposed control strategy. In implementation Texas Instrument's digital signal processor TMS320F24OF is used as the digital controller. The control algorithm for high-power-factor operation is tested on a prototype boost rectifier under nominal and unbalanced input voltage conditions.

Determination of mixture composition by the float balance

Herein is described a method by which component gases can be weighed as they are added one by one to a gas mixture. The float balance, designed for the purpose, is capable of determining a maximum mass of about 3 kg of a gas mixture contained in a cylinder of mass about 5 kg with a sensitivity of ±0·1 g mm-1 of the stem height.

On the momentum balance in linear-combination models for the transition zone

The momentum balance of the linear-combination integral model for the transition zone is investigated for constant pressure flows. The imbalance is found to be small enough to be negligible for all practical purposes. [S0889-504X(00)00703-0].

The fate of the initiator tRNAs is sensitive to the critical balance between interacting proteins

Formylation of the initiator tRNA is essential for normal growth of Escherichia coil, The initiator tRNA containing the U35A36 mutation (CUA anticodon) initiates from UAG codon, However, an additional mutation at position 72 (72A --> G) renders the tRNA (G72/U35A36) inactive in initiation because it is defective in formylation, In this study, we isolated U1G72/U35A36 tRNA containing a wobble base pair at 1-72 positions as an intragenic suppressor of the G72 mutation. The U1G72/U35A36 tRNA is formylated and participates in initiation. More importantly, we show that the mismatch at 1-72 positions of the initiator tRNA, which was thus far thought to be the hallmark of the resistance of this tRNA against peptidyl-tRNA hydrolase (PTH), is not sufficient, The amino acid attached to the initiator tRNA is also important in conferring protection against PTH. Further, we show that the relative levels of PTH and IF2 influence the path adopted by the initiator tRNAs in protein synthesis. These findings provide an important clue to understand the dual function of the single tRNA(Met) in initiation and elongation, in the mitochondria of various organisms.

Accelerometer-Based Force Balance for High Enthalpy Facilities

A single component accelerometer-based force balance is developed, calibrated, and used for high enthalpy applications. Functionality of this force balance, for such applications, is demonstrated for the first time during high enthalpy tests in a newly established free piston-driven shock tunnel, HST3, using a 60 degrees apex angle blunt cone model at 0 degrees angle of incidence. Usefulness of this force balance is also confirmed, for much complicated high enthalpy flow situations, during the drag reduction studies with counterflow supersonic jet from the stagnation point.

Triply-periodic balance surfaces

The list of possible G-H symmetries for triply-periodic balance surfaces, given by Koch and Fischer, is studied with a view to finding new types. It is found that balance surfaces exist for all the cases that were labelled as undecided in the work of Koch and Fischer. For some of these, new minimal surfaces have been found, with the aid of Brakke's 'Surface Evolver'. (C) 1997 Elsevier Science B.V.

Lubricity of an oil in water emulsion in metal cutting: The effect of hydrophilic/lypophilic balance of emulsifiers

A steel disc is cut using a single point tool. The coefficient of friction of the nascent cut surface is measured by a spherical steel pin situated in close proximity of the point of cutting. The tool, disc and the friction pin are immersed in an oil in water emulsion bath during the experiment. The purpose of the experiments conducted here is to record the effect of hydrophilic/lypophilic balance (HLB) of the emulsifier on the lubricity experienced in the cutting operation. The more lypophilic emulsifiers were found to give greater lubricity than what is recorded when the emulsifier is more hydrophilic. XPS and FTIR spectroscopy are used to explore the tribofilm generated on the nascent cut surface to indicate a possible rationale for the effect. (C) 2011 Elsevier B.V. All rights reserved.

Aerodynamic Load Measurements at Hypersonic Speeds Using Internally Mounted Fiber-Optic Balance System

This paper describes the measurement of aerodynamic loads using fiber-optic strain gauge sensors and associated signal processors at hypersonic speeds in the 300mm hypersonic wind tunnel. at the Department of Aerospace Engineering, Indian Institute of Science. Fiber-optic sensors have been developed in USA since 1990, for variety of applications in experimental stress analysis, skin friction measurement in fluid flows, smart structures, smart materials, sensing of acoustic emission and more recently in the development of compact devices for measurement of displacement, stress/strain, pressure, temperature, acceleration etc. Our group at llSc has been playing a lead role in the use of these fiber - optic sensors for successful measurement of aerodynamic loads in wind tunnels and the first ever six-component wind tunnel strain gauge balance in the world based on fiber optic sensors was built at the Indian Institute of Science in the year 1999. We report here the results of our efforts in the development of an internal strain gauge balance for high-speed wind tunnel applications.