Thermodynamic and kinetic analysis of carbohydrate binding to the basic lectin from winged bean (Psophocarpus tetragonolobus)

A basic lectin (pI approximately 10.0) was purified to homogeneity from the seeds of winged bean (Psophocarpus tetragonolobus) by affinity chromatography on Sepharose 6-aminocaproyl-D-galactosamine. The lectin agglutinated trypsinized rabbit erythrocytes and had a relative molecular mass of 58,000 consisting of two subunits of Mr 29,000. The lectin binds to N-dansylgalactosamine, leading to a 15-fold increase in dansyl fluorescence with a concomitant 25-nm blue shift in the emission maximum. The lectin has two binding sites/dimer for this sugar and an association constant of 4.17 X 10(5) M-1 at 25 degrees C. The strong binding to N-dansylgalactosamine is due to a relatively positive entropic contribution as revealed by the thermodynamic parameters: delta H = -33.62 kJ mol-1 and delta S0 = -5.24 J mol-1 K-1. Binding of this sugar to the lectin shows that it can accommodate a large hydrophobic substituent on the C-2 carbon of D-galactose. Studies with other sugars indicate that a hydrophobic substituent in alpha- conformation at the anomeric position increases the affinity of binding. The C-4 and C-6 hydroxyl groups are critical for sugar binding to this lectin. Lectin difference absorption spectra in the presence of N-acetylgalactosamine indicate perturbation of tryptophan residues on sugar binding. The results of stopped flow kinetics with N- dansylgalactosamine and the lectin are consistent with a simple one- step mechanism for which k+1 = 1.33 X 10(4) M-1 s-1 and k-1 = 3.2 X 10(- 2) s-1 at 25 degrees C. This k-1 is slower than any reported for a lectin-monosaccharide complex so far. The activation parameters indicate an enthalpically controlled association process.

Short-window spectral analysis using AMVAR and multitaper methods: a comparison

We compare two popular methods for estimating the power spectrum from short data windows, namely the adaptive multivariate autoregressive (AMVAR) method and the multitaper method. By analyzing a simulated signal (embedded in a background Ornstein-Uhlenbeck noise process) we demonstrate that the AMVAR method performs better at detecting short bursts of oscillations compared to the multitaper method. However, both methods are immune to jitter in the temporal location of the signal. We also show that coherence can still be detected in noisy bivariate time series data by the AMVAR method even if the individual power spectra fail to show any peaks. Finally, using data from two monkeys performing a visuomotor pattern discrimination task, we demonstrate that the AMVAR method is better able to determine the termination of the beta oscillations when compared to the multitaper method.

An algebraic algorithm for the design and analysis of linear dynamical systems

In an earlier paper [1], it has been shown that velocity ratio, defined with reference to the analogous circuit, is a basic parameter in the complete analysis of a linear one-dimensional dynamical system. In this paper it is shown that the terms constituting velocity ratio can be readily determined by means of an algebraic algorithm developed from a heuristic study of the process of transfer matrix multiplication. The algorithm permits the set of most significant terms at a particular frequency of interest to be identified from a knowledge of the relative magnitudes of the impedances of the constituent elements of a proposed configuration. This feature makes the algorithm a potential tool in a first approach to a rational design of a complex dynamical filter. This algorithm is particularly suited for the desk analysis of a medium size system with lumped as well as distributed elements.

The UPAL process: a direct method of preparing cast aluminium alloy-graphite particle composites

A direct method of preparing cast aluminium alloy-graphite particle composites using uncoated graphite particles is reported. The method consists of introducing and dispersing uncoated but suitably pretreated graphite particles in aluminium alloy melts, and casting the resulting composite melts in suitable permanent moulds. The optical pretreatment required for the dispersion of the uncoated graphite particles in aluminium alloy melts consists of heating the graphite particles to 400° C in air for 1 h just prior to their dispersion in the melts. The effects of alloying elements such as Si, Cu and Mg on the dispersability of pretreated graphite in molten aluminium have also been reported. It was found that additions of about 0.5% Mg or 5% Si significantly improve the dispersability of graphite particles in aluminium alloy melts as indicated by the high recoveries of graphite in the castings of these composites. It was also possible to disperse upto 3% graphite in LM 13 alloy melts and retain the graphite particles in a well distributed fashion in the castings using the pre-heat-treated graphite particles. The observations in this study have been related to the information presently available on wetting between graphite and molten aluminium in the presence of different elements and our own thermogravimetric analysis studies on graphite particles. Physical and mechanical properties of LM 13-3% graphite composite made using pre-heat-treated graphite powder, were found to be adequate for many applications, including pistons which have been successfully used in internal combustion engines.

Estimation of Execution Times of Process Control Algorithms on Microcomputers

An important question which has to be answered in evaluting the suitability of a microcomputer for a control application is the time it would take to execute the specified control algorithm. In this paper, we present a method of obtaining closed-form formulas to estimate this time. These formulas are applicable to control algorithms in which arithmetic operations and matrix manipulations dominate. The method does not require writing detailed programs for implementing the control algorithm. Using this method, the execution times of a variety of control algorithms on a range of 16-bit mini- and recently announced microcomputers are calculated. The formulas have been verified independently by an analysis program, which computes the execution time bounds of control algorithms coded in Pascal when they are run on a specified micro- or minicomputer.

Sustainable bioenergy for India: Technical, economic and policy analysis

India's energy challenges are multi-pronged. They are manifested through growing demand for modern energy carriers, a fossil fuel dominated energy system facing a severe resource crunch, the need for creating access to quality energy for the large section of deprived population, vulnerable energy security, local and global pollution regimes and the need for sustaining economic development. Renewable energy is considered as one of the most promising alternatives. Recognizing this potential, India has been implementing one of the largest renewable energy programmes in the world. Among the renewable energy technologies. bioenergy has a large diverse portfolio including efficient biomass stoves, biogas, biomass combustion and gasification and process heat and liquid fuels. India has also formulated and implemented a number of innovative policies and programmes to promote bioenergy technologies. However, according to some preliminary studies, the success rate is marginal compared to the potential available. This limited success is a clear indicator of the need for a serious reassessment of the bioenergy programme. Further, a realization of the need for adopting a sustainable energy path to address the above challenges will be the guiding force in this reassessment. In this paper an attempt is made to consider the potential of bioenergy to meet the rural energy needs: (I) biomass combustion and gasification for electricity; (2) biomethanation for cooking energy (gas) and electricity; and (3) efficient wood-burning devices for cooking. The paper focuses on analysing the effectiveness of bioenergy in creating this rural energy access and its sustainability in the long run through assessing: the demand for bioenergy and potential that could be created; technologies, status of commercialization and technology transfer and dissemination in India; economic and environmental performance and impacts: bioenergy policies, regulatory measures and barrier analysis. The whole assessment aims at presenting bioenergy as an integral part of a sustainable energy strategy for India. The results show that bioenergy technology (BET) alternatives compare favourably with the conventional ones. The cost comparisons show that the unit costs of BET alternatives are in the range of 15-187% of the conventional alternatives. The climate change benefits in terms of carbon emission reductions are to the tune of 110 T C per year provided the available potential of BETs are utilized.

Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage Delta D-III T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an xcellent substrate for Ni(II) ions, while the SPR Studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/- 12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/- 3.6) kcal mol(-1), The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/- 2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established.

Analysis of the MAP/G(a,b)/1/N queue with multiple vacations

This paper deals with a batch service queue and multiple vacations. The system consists of a single server and a waiting room of finite capacity. Arrival of customers follows a Markovian arrival process (MAP). The server is unavailable for occasional intervals of time called vacations, and when it is available, customers are served in batches of maximum size ‘b’ with a minimum threshold value ‘a’. We obtain the queue length distributions at various epochs along with some key performance measures. Finally, some numerical results have been presented.

Process variables in biomimetic synthesis of silver nanoparticles by aqueous extract of Azadirachta indica (Neem) leaves

Owing to widespread applications, synthesis and characterization of silver nanoparticles is recently attracting considerable attention. Increasing environmental concerns over chemical synthesis routes have resulted in attempts to develop biomimetic approaches. One of them is synthesis using plant parts, which eliminates the elaborate process of maintaining the microbial culture and often found to be kinetically favourable than other bioprocesses. The present study deals with investigating the effect of process variables like reductant concentrations, reaction pH, mixing ratio of the reactants and interaction time on the morphology and size of silver nanoparticles synthesized using aqueous extract of Azadirachta indica (Neem) leaves. The formation of crystalline silver nanoparticles was confirmed using X-ray diffraction analysis. By means of UV spectroscopy, Scanning and Transmission Electron Microscopy techniques, it was observed that the morphology and size of the nanoparticles were strongly dependent on the process parameters. Within 4 h interaction period, nanoparticles below 20-nm-size with nearly spherical shape were produced. On increasing interaction time (ageing) to 66 days, both aggregation and shape anisotropy (ellipsoidal, polyhedral and capsular) of the particles increased. In alkaline pH range, the stability of cluster distribution increased with a declined tendency for aggregation of the particles. It can be inferred from the study that fine tuning the bioprocess parameters will enhance possibilities of desired nano-product tailor made for particular applications.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

New insights from a fixed-point analysis of single cell IEEE 802.11 WLANs

We study a fixed-point formalization of the well-known analysis of Bianchi. We provide a significant simplification and generalization of the analysis. In this more general framework, the fixed-point solution and performance measures resulting from it are studied. Uniqueness of the fixed point is established. Simple and general throughput formulas are provided. It is shown that the throughput of any flow will be bounded by the one with the smallest transmission rate. The aggregate throughput is bounded by the reciprocal of the harmonic mean of the transmission rates. In an asymptotic regime with a large number of nodes, explicit formulas for the collision probability, the aggregate attempt rate, and the aggregate throughput are provided. The results from the analysis are compared with ns2 simulations and also with an exact Markov model of the backoff process. It is shown how the saturated network analysis can be used to obtain TCP transfer throughputs in some cases.

Process variability-aware statistical hybrid modeling of dynamic power dissipation in 65 nm CMOS designs

A generalized technique is proposed for modeling the effects of process variations on dynamic power by directly relating the variations in process parameters to variations in dynamic power of a digital circuit. The dynamic power of a 2-input NAND gate is characterized by mixed-mode simulations, to be used as a library element for 65mn gate length technology. The proposed methodology is demonstrated with a multiplier circuit built using the NAND gate library, by characterizing its dynamic power through Monte Carlo analysis. The statistical technique of Response. Surface Methodology (RSM) using Design of Experiments (DOE) and Least Squares Method (LSM), are employed to generate a "hybrid model" for gate power to account for simultaneous variations in multiple process parameters. We demonstrate that our hybrid model based statistical design approach results in considerable savings in the power budget of low power CMOS designs with an error of less than 1%, with significant reductions in uncertainty by atleast 6X on a normalized basis, against worst case design.

Mechanism of lectin-cell interactions: thermodynamic and kinetic analysis of the binding of winged bean acidic lectin (WBA II) to human erythrocytes

In order to identify the forces involved in the binding and to understand the mechanism involved, equilibrium and kinetic studies were performed on the binding of the winged bean acidic lectin to human erythrocytes. The magnitudes of delta S and delta H were positive and negative respectively, an observation differing markedly from the lectin-simple sugar interactions where delta S and delta H are generally negative. Analysis of the sign and magnitudes of these values indicate that ionic and hydrogen bonded interactions prevail over hydrophobic interactions resulting in net -ve delta H (-37.12 kJ.mol-1) and +ve delta S (14.4 J.mole-1 K-1 at 20 degrees C), thereby suggesting that this entropy driven reaction also reflects conformational changes in the lectin and/or the receptor. Presence of two kinds of receptors for WBA II on erythrocytes, as observed by equilibrium studies, is consistent with the biexponential dissociation rate constants (at 20 degrees C K1 = 1.67 x 10(-3) M-1 sec-1 and K2 = 11.1 x 10(-3) M-1 sec-1). These two rate constants differed by an order of magnitude accounting for the difference in the association constants of the two receptors of WBA II. However, the association process remains monoexponential suggesting no observable difference in the association rates of the lectin molecule with both the receptors, under the experimental conditions studied. The thermodynamic parameters calculated from kinetic data correlate well with those observed by equilibrium. A two-step binding mechanism is proposed based on the kinetic parameters for WBA II-receptor interaction

Analysis of dynamics and mechanism of ligand binding to Artocarpus integrifolia agglutinin. A 13C and 19F NMR study

Binding of 13C-labeled N-acetylgalactosamine (13C-GalNAc) and N-trifluoroacetylgalactosamine (19F-GalNAc) to Artocarpus integrifolia agglutinin has been studied using 13C and 19F nuclear magnetic resonance spectroscopy, respectively. Binding of these saccharides resulted in broadening of the resonances, and no change in chemical shift was observed, suggesting that the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc experience a magnetically equivalent environment in the lectin combining site. The alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc were found to be in slow exchange between free and protein bound states. Binding of 13C-GalNAc was studied as a function of temperature. From the temperature dependence of the line broadening, the thermodynamic and kinetic parameters were evaluated. The association rate constants obtained for the alpha-anomers of 13C-GalNAc and 19F-GalNAc (k+1 = 1.01 x 10(5) M-1.s-1 and 0.698 x 10(5) M-1.s-1, respectively) are in close agreement with those obtained for the corresponding beta-anomers (k+1 = 0.95 x 10(5) M-1.s-1 and 0.65 x 10(5) M-1.s-1, respectively), suggesting that the two anomers bind to the lectin by a similar mechanism. In addition these values are several orders of magnitude slower than those obtained for diffusion controlled processes. The dissociation rate constants obtained are 49.9, 56.9, 42, and 43 s-1, respectively, for the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc. A two-step mechanism has been proposed for the interaction of 13C-GalNAc and 19F-GalNAc with A. integrifolia lectin in view of the slow association rates and high activation entropies. The thermodynamic parameters obtained for the association and dissociation reactions suggest that the binding process is entropically favored and that there is a small enthalpic contribution.

Studies on design, fabrication and reliability assessment of embedded passives on a high-density interconnect (HDI) organic substrate using a sequential build-up process

One of the foremost design considerations in microelectronics miniaturization is the use of embedded passives which provide practical solution. In a typical circuit, over 80 percent of the electronic components are passives such as resistors, inductors, and capacitors that could take up to almost 50 percent of the entire printed circuit board area. By integrating passive components within the substrate instead of being on the surface, embedded passives reduce the system real estate, eliminate the need for discrete and assembly, enhance electrical performance and reliability, and potentially reduce the overall cost. Moreover, it is lead free. Even with these advantages, embedded passive technology is at a relatively immature stage and more characterization and optimization are needed for practical applications leading to its commercialization.This paper presents an entire process from design and fabrication to electrical characterization and reliability test of embedded passives on multilayered microvia organic substrate. Two test vehicles focusing on resistors and capacitors have been designed and fabricated. Embedded capacitors in this study are made with polymer/ceramic nanocomposite (BaTiO3) material to take advantage of low processing temperature of polymers and relatively high dielectric constant of ceramics and the values of these capacitors range from 50 pF to 1.5 nF with capacitance per area of approximately 1.5 nF/cm(2). Limited high frequency measurement of these capacitors was performed. Furthermore, reliability assessments of thermal shock and temperature humidity tests based on JEDEC standards were carried out. Resistors used in this work have been of three types: 1) carbon ink based polymer thick film (PTF), 2) resistor foils with known sheet resistivities which are laminated to printed wiring board (PWB) during a sequential build-up (SBU) process and 3) thin-film resistor plating by electroless method. Realization of embedded resistors on conventional board-level high-loss epoxy (similar to 0.015 at 1 GHz) and proposed low-loss BCB dielectric (similar to 0.0008 at > 40 GHz) has been explored in this study. Ni-P and Ni-W-P alloys were plated using conventional electroless plating, and NiCr and NiCrAlSi foils were used for the foil transfer process. For the first time, Benzocyclobutene (BCB) has been proposed as a board level dielectric for advanced System-on-Package (SOP) module primarily due to its attractive low-loss (for RF application) and thin film (for high density wiring) properties.Although embedded passives are more reliable by eliminating solder joint interconnects, they also introduce other concerns such as cracks, delamination and component instability. More layers may be needed to accommodate the embedded passives, and various materials within the substrate may cause significant thermo -mechanical stress due to coefficient of thermal expansion (CTE) mismatch. In this work, numerical models of embedded capacitors have been developed to qualitatively examine the effects of process conditions and electrical performance due to thermo-mechanical deformations.Also, a prototype working product with the board level design including features of embedded resistors and capacitors are underway. Preliminary results of these are presented.