Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

Simultaneous measurement of multiple parameters using a single fiber Bragg grating

A novel approach for simultaneous measurement of chirp (any parameter that can induce strain gradient on FBG) and temperature using a single FBG is proposed. Change in reflectivity at central wavelength of FBG reflection & Bragg wavelength shifts induced due to temperature were used for chirp & temperature measurements respectively. Theoretical resolution limit for chirp and temperature using an Optical Spectrum Analyzer (OSA) with 1pm wavelength resolution and >58dB dynamic range are 12.8fm and 1/13 degrees C respectively.

A non-cooperative game-theoretic approach to channel assignment in multi-channel multi-radio wireless networks

Channel assignment in multi-channel multi-radio wireless networks poses a significant challenge due to scarcity of number of channels available in the wireless spectrum. Further, additional care has to be taken to consider the interference characteristics of the nodes in the network especially when nodes are in different collision domains. This work views the problem of channel assignment in multi-channel multi-radio networks with multiple collision domains as a non-cooperative game where the objective of the players is to maximize their individual utility by minimizing its interference. Necessary and sufficient conditions are derived for the channel assignment to be a Nash Equilibrium (NE) and efficiency of the NE is analyzed by deriving the lower bound of the price of anarchy of this game. A new fairness measure in multiple collision domain context is proposed and necessary and sufficient conditions for NE outcomes to be fair are derived. The equilibrium conditions are then applied to solve the channel assignment problem by proposing three algorithms, based on perfect/imperfect information, which rely on explicit communication between the players for arriving at an NE. A no-regret learning algorithm known as Freund and Schapire Informed algorithm, which has an additional advantage of low overhead in terms of information exchange, is proposed and its convergence to the stabilizing outcomes is studied. New performance metrics are proposed and extensive simulations are done using Matlab to obtain a thorough understanding of the performance of these algorithms on various topologies with respect to these metrics. It was observed that the algorithms proposed were able to achieve good convergence to NE resulting in efficient channel assignment strategies.

Guessing Revisited: A Large Deviations Approach

The problem of guessing a random string is revisited. A close relation between guessing and compression is first established. Then it is shown that if the sequence of distributions of the information spectrum satisfies the large deviation property with a certain rate function, then the limiting guessing exponent exists and is a scalar multiple of the Legendre-Fenchel dual of the rate function. Other sufficient conditions related to certain continuity properties of the information spectrum are briefly discussed. This approach highlights the importance of the information spectrum in determining the limiting guessing exponent. All known prior results are then re-derived as example applications of our unifying approach.

Particle filters for structural system identification using multiple test and sensor data: A combined computational and experimental study

The problem of structural system identification when measurements originate from multiple tests and multiple sensors is considered. An offline solution to this problem using bootstrap particle filtering is proposed. The central idea of the proposed method is the introduction of a dummy independent variable that allows for simultaneous assimilation of multiple measurements in a sequential manner. The method can treat linear/nonlinear structural models and allows for measurements on strains and displacements under static/dynamic loads. Illustrative examples consider measurement data from numerical models and also from laboratory experiments. The results from the proposed method are compared with those from a Kalman filter-based approach and the superior performance of the proposed method is demonstrated. Copyright (C) 2009 John Wiley & Sons, Ltd.

Bounds on the Lifetime of Wireless Sensor Networks Employing Multiple Data Sinks

Employing multiple base stations is an attractive approach to enhance the lifetime of wireless sensor networks. In this paper, we address the fundamental question concerning the limits on the network lifetime in sensor networks when multiple base stations are deployed as data sinks. Specifically, we derive upper bounds on the network lifetime when multiple base stations are employed, and obtain optimum locations of the base stations (BSs) that maximize these lifetime bounds. For the case of two BSs, we jointly optimize the BS locations by maximizing the lifetime bound using a genetic algorithm based optimization. Joint optimization for more number of BSs is complex. Hence, for the case of three BSs, we optimize the third BS location using the previously obtained optimum locations of the first two BSs. We also provide simulation results that validate the lifetime bounds and the optimum locations of the BSs.

Direction of arrival estimation in the presence of distributed noise sources: Cumulant based approach

In the past few years there have been attempts to develop subspace methods for DoA (direction of arrival) estimation using a fourth?order cumulant which is known to de?emphasize Gaussian background noise. To gauge the relative performance of the cumulant MUSIC (MUltiple SIgnal Classification) (c?MUSIC) and the standard MUSIC, based on the covariance function, an extensive numerical study has been carried out, where a narrow?band signal source has been considered and Gaussian noise sources, which produce a spatially correlated background noise, have been distributed. These simulations indicate that, even though the cumulant approach is capable of de?emphasizing the Gaussian noise, both bias and variance of the DoA estimates are higher than those for MUSIC. To achieve comparable results the cumulant approach requires much larger data, three to ten times that for MUSIC, depending upon the number of sources and how close they are. This is attributed to the fact that in the estimation of the cumulant, an average of a product of four random variables is needed to make an evaluation. Therefore, compared to those in the evaluation of the covariance function, there are more cross terms which do not go to zero unless the data length is very large. It is felt that these cross terms contribute to the large bias and variance observed in c?MUSIC. However, the ability to de?emphasize Gaussian noise, white or colored, is of great significance since the standard MUSIC fails when there is colored background noise. Through simulation it is shown that c?MUSIC does yield good results, but only at the cost of more data.

A new approach to the design of electronic exchanges

Electronic Exchanges are double-sided marketplaces that allows multiple buyers to trade with multiple sellers, with aggregation of demand and supply across the bids to maximize the revenue in the market. In this paper, we propose a new design approach for an one-shot exchange that collects bids from buyers and sellers and clears the market at the end of the bidding period. The main principle of the approach is to decouple the allocation from pricing. It is well known that it is impossible for an exchange with voluntary participation to be efficient and budget-balanced. Budget-balance is a mandatory requirement for an exchange to operate in profit. Our approach is to allocate the trade to maximize the reported values of the agents. The pricing is posed as payoff determination problem that distributes the total payoff fairly to all agents with budget-balance imposed as a constraint. We devise an arbitration scheme by axiomatic approach to solve the payoff determination problem using the added-value concept of game theory.

Enhancing lifetime of wireless sensor networks using multiple data sinks

In this paper, we address the fundamental question concerning the limits on the network lifetime in sensor networks when multiple base stations (BSs) are deployed as data sinks. Specifically, we derive upper bounds on the network lifetime when multiple BSs arc employed, and obtain optimum locations of the base stations that maximise these lifetime bounds. For the case of two BSs, we jointly optimise the BS locations by maximising the lifetime bound using genetic algorithm. Joint optimisation for more number of BSs becomes prohibitively complex. Further, we propose a suboptimal approach for higher number of BSs, Individually Optimum method, where we optimise the next BS location using optimum location of previous BSs. Individually Optimum method has advantage of being attractive for solving the problem with more number of BSs at the cost of little compromised accuracy. We show that accuracy degradation is quite small for the case of three BSs.

Optimal scheduling of multiple chlorine sources in water distribution systems

The specified range of free chlorine residual (between minimum and maximum) in water distribution systems needs to be maintained to avoid deterioration of the microbial quality of water, control taste and/or odor problems, and hinder formation of carcino-genic disinfection by-products. Multiple water quality sources for providing chlorine input are needed to maintain the chlorine residuals within a specified range throughout the distribution system. The determination of source dosage (i.e., chlorine concentrations/chlorine mass rates) at water quality sources to satisfy the above objective under dynamic conditions is a complex process. A nonlinear optimization problem is formulated to determine the chlorine dosage at the water quality sources subjected to minimum and maximum constraints on chlorine concentrations at all monitoring nodes. A genetic algorithm (GA) approach in which decision variables (chlorine dosage) are coded as binary strings is used to solve this highly nonlinear optimization problem, with nonlinearities arising due to set-point sources and non-first-order reactions. Application of the model is illustrated using three sample water distribution systems, and it indicates that the GA,is a useful tool for evaluating optimal water quality source chlorine schedules.

Performance Analysis of TCP Uploads in WLANs with Multiple Rates

Throughput analysis of bulk TCP downloads in cases where all WLAN stations are associated at the same rate with the AP is available in the literature. In this paper,we extend the analysis to TCP uploads for the case of multirate associations. The approach is based on a two-dimensional semi- Markov model for the number of backlogged stations. Analytical results are in excellent agreement with simulations performed using QUALNET 4.5.

Compiler-Directed Frequency and Voltage Scaling for a Multiple Clock Domain

Multiple Clock Domain processors provide an attractive solution to the increasingly challenging problems of clock distribution and power dissipation. They allow their chips to be partitioned into different clock domains, and each domain’s frequency (voltage) to be independently configured. This flexibility adds new dimensions to the Dynamic Voltage and Frequency Scaling problem, while providing better scope for saving energy and meeting performance demands. In this paper, we propose a compiler directed approach for MCD-DVFS. We build a formal petri net based program performance model, parameterized by settings of microarchitectural components and resource configurations, and integrate it with our compiler passes for frequency selection.Our model estimates the performance impact of a frequency setting, unlike the existing best techniques which rely on weaker indicators of domain performance such as queue occupancies(used by online methods) and slack manifestation for a particular frequency setting (software based methods).We evaluate our method with subsets of SPECFP2000,Mediabench and Mibench benchmarks. Our mean energy savings is 60.39% (versus 33.91% of the best software technique)in a memory constrained system for cache miss dominated benchmarks, and we meet the performance demands.Our ED2 improves by 22.11% (versus 18.34%) for other benchmarks. For a CPU with restricted frequency settings, our energy consumption is within 4.69% of the optimal.

Extending the Supramolecular Synthon Based Fragment Approach (SBFA) for Transferability of Multipole Charge Density Parameters to Monofluorobenzoic Acids and their Cocrystals with Isonicotinamide: Importance of C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F Intermolecular Regions

An extension of the supramolecular synthon-based fragment approach (SBFA) method for transferability of multipole charge density parameters to include weak supramolecular synthons is proposed. In particular, the SBFA method is applied to C-H center dot center dot center dot O, C-H center dot center dot center dot F, and F center dot center dot center dot F containing synthons. A high resolution charge density study has been performed on 4-fluorobenzoic acid to build a synthon library for C-H center dot center dot center dot F infinite chain interactions. Libraries for C-H center dot center dot center dot O and F center dot center dot center dot F synthons were taken from earlier work. The SBFA methodology was applied successfully to 2- and 3-fluorobenzoic acids, data sets for which were collected in a routine manner at 100 K, and the modularity of the synthons was demonstrated. Cocrystals of isonicotinamide with all three fluorobenzoic acids were also studied with the SBFA method. The topological analysis of inter- and intramolecular interaction regions was performed using Bader's AIM approach. This study shows that the SBFA method is generally applicable to generate charge density maps using information from multiple intermolecular regions.

Development of novel multiple quantummethodologies for the analyses of complex protonNMR spectra of scalar coupled spins

One of the significant advancements in Nuclear Magnetic Resonance spectroscopy (NMR) in combating the problem of spectral complexity for deriving the structure and conformational information is the incorporation of additional dimension and to spread the information content in a two dimensional space. This approach together with the manipulation of the dynamics of nuclear spins permitted the designing of appropriate pulse sequences leading to the evolution of diverse multidimensional NMR experiments. The desired spectral information can now be extracted in a simplified and an orchestrated manner. The indirect detection of multiple quantum (MQ) NMR frequencies is a step in this direction. The MQ technique has been extensively used in the study of molecules aligned in liquid crystalline media to reduce spectral complexity and to determine molecular geometries. Unlike in dipolar coupled systems, the size of the network of scalar coupled spins is not big in isotropic solutions and the MQ 1H detection is not routinely employed,although there are specific examples of spin topology filtering. In this brief review, we discuss our recent studies on the development and application of multiple quantum correlation and resolved techniques for the analyses of proton NMR spectra of scalar coupled spins.