Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Truthful and Quality Conscious Query Incentive Networks

Query incentive networks capture the role of incentives in extracting information from decentralized information networks such as a social network. Several game theoretic tilt:Kids of query incentive networks have been proposed in the literature to study and characterize the dependence, of the monetary reward required to extract the answer for a query, on various factors such as the structure of the network, the level of difficulty of the query, and the required success probability.None of the existing models, however, captures the practical andimportant factor of quality of answers. In this paper, we develop a complete mechanism design based framework to incorporate the quality of answers, in the monetization of query incentive networks. First, we extend the model of Kleinberg and Raghavan [2] to allow the nodes to modulate the incentive on the basis of the quality of the answer they receive. For this qualify conscious model. we show are existence of a unique Nash equilibrium and study the impact of quality of answers on the growth rate of the initial reward, with respect to the branching factor of the network. Next, we present two mechanisms; the direct comparison mechanism and the peer prediction mechanism, for truthful elicitation of quality from the agents. These mechanisms are based on scoring rules and cover different; scenarios which may arise in query incentive networks. We show that the proposed quality elicitation mechanisms are incentive compatible and ex-ante budget balanced. We also derive conditions under which ex-post budget balance can beachieved by these mechanisms.

A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa–Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

Clustering in Concept Association Networks

We view association of concepts as a complex network and present a heuristic for clustering concepts by taking into account the underlying network structure of their associations. Clusters generated from our approach are qualitatively better than clusters generated from the conventional spectral clustering mechanism used for graph partitioning.

Design of incentive compatible protocols for wireless networks: A game theoretic approach

In this thesis work, we design rigorous and efficient protocols/mechanisms for different types of wireless networks using a mechanism design [1] and game theoretic approach [2]. Our work can broadly be viewed in two parts. In the first part, we concentrate on ad hoc wireless networks [3] and [4]. In particular, we consider broadcast in these networks where each node is owned by independent and selfish users. Being selfish, these nodes do not forward the broadcast packets. All existing protocols for broadcast assume that nodes forward the transit packets. So, there is need for developing new broadcast protocols to overcome node selfishness. In our paper [5], we develop a strategy proof pricing mechanism which we call immediate predecessor node pricing mechanism (IPNPM) and an efficient new broadcast protocol based on IPNPM. We show the efficacy of our proposed broadcast protocol using simulation results.

An efficient pricing based protocol for broadcasting in wireless ad hoc networks

In many applications of wireless ad hoc networks, wireless nodes are owned by rational and intelligent users. In this paper, we call nodes selfish if they are owned by independent users and their only objective is to maximize their individual goals. In such situations, it may not be possible to use the existing protocols for wireless ad hoc networks as these protocols assume that nodes follow the prescribed protocol without deviation. Stimulating cooperation among these nodes is an interesting and challenging problem. Providing incentives and pricing the transactions are well known approaches to stimulate cooperation. In this paper, we present a game theoretic framework for truthful broadcast protocol and strategy proof pricing mechanism called Immediate Predecessor Node Pricing Mechanism (IPNPM). The phrase strategy proof here means that truth revelation of cost is a weakly dominant-strategy (in game theoretic terms) for each node. In order to steer our mechanism-design approach towards practical implementation, we compute the payments to nodes using a distributed algorithm. We also propose a new protocol for broadcast in wireless ad hoc network with selfish nodes based on IPNPM. The features of the proposed broadcast protocol are reliability and a significantly reduced number of packet forwards compared to the number of network nodes, which in turn leads to less system-wide power consumption to broadcast a single packet. Our simulation results show the efficacy of the proposed broadcast protocol.

QoS with selfish nodes in wireless networks

The IEEE 802.1le medium access control (MAC) standard provides distributed service differentiation or Quality-of- Service (QoS) by employing a priority system. In 802.1 le networks, network traffic is classified into different priorities or access categories (ACs). Nodes maintain separate queues for each AC and packets at the head-of-line (HOL) of each queue contend for channel access using AC-specific parameters. Such a mechanism allows the provision of differentiated QoS where high priority, performance sensitive traffic such as voice and video applications will enjoy less delay, greater throughput and smaller loss, compared to low priority traffic (e. g. file transfer). The standard implicitly assumes that nodes are honest and will truthfully classify incoming traffic into its appropriate AC. However, in the absence of any additional mechanism, selfish users can gain enhanced performance by selectively classifying low priority traffic as high priority, potentially destroying the QoS capability of the system.

Neural network approach for fault location in unbalanced distribution networks with limited measurements

This paper presents an Artificial Neural Network (ANN) approach for locating faults in distribution systems. Different from the traditional Fault Section Estimation methods, the proposed approach uses only limited measurements. Faults are located according to the impedances of their path using a Feed Forward Neural Networks (FFNN). Various practical situations in distribution systems, such as protective devices placed only at the substation, limited measurements available, various types of faults viz., three-phase, line (a, b, c) to ground, line to line (a-b, b-c, c-a) and line to line to ground (a-b-g, b-c-g, c-a-g) faults and a wide range of varying short circuit levels at substation, are considered for studies. A typical IEEE 34 bus practical distribution system with unbalanced loads and with three- and single- phase laterals and a 69 node test feeder with different configurations are considered for studies. The results presented show that the proposed approach of fault location gives close to accurate results in terms of the estimated fault location.

COMMON-Sense net:Improved water management for resource-poor farmers via sensor networks

We describe the on-going design and implementation of a sensor network for agricultural management targeted at resource-poor farmers in India. Our focus on semi-arid regions led us to concentrate on water-related issues. Throughout 2004, we carried out a survey on the information needs of the population living in a cluster of villages in our study area. The results highlighted the potential that environment-related information has for the improvement of farming strategies in the face of highly variable conditions, in particular for risk management strategies (choice of crop varieties, sowing and harvest periods, prevention of pests and diseases, efficient use of irrigation water etc.). This leads us to advocate an original use of Information and Communication Technologies (ICT). We believe our demand-driven approach for the design of appropriate ICT tools that are targeted at the resource-poor to be relatively new. In order to go beyond a pure technocratic approach, we adopted an iterative, participatory methodology.

Locant: A nature inspired location service for ad hoc networks

An efficient location service is a prerequisite to any robust, effective and precise location information aided Mobile Ad Hoc Network (MANET) routing protocol. Locant, presented in this paper is a nature inspired location service which derives inspiration from the insect colony framework, and it is designed to work with a host of location information aided MANET routing protocols. Using an extensive set of simulation experiments, we have compared the performance of Locant with RLS, SLS and DLS, and found that it has comparable or better performance compared to the above three location services on most metrics and has the least overhead in terms of number of bytes transmitted per location query answered.

Design and analysis of rate aware ad hoc 802.11 networks

802.11 WLANs are characterized by high bit error rate and frequent changes in network topology. The key feature that distinguishes WLANs from wired networks is the multi-rate transmission capability, which helps to accommodate a wide range of channel conditions. This has a significant impact on higher layers such as routing and transport levels. While many WLAN products provide rate control at the hardware level to adapt to the channel conditions, some chipsets like Atheros do not have support for automatic rate control. We first present a design and implementation of an FER-based automatic rate control state machine, which utilizes the statistics available at the device driver to find the optimal rate. The results show that the proposed rate switching mechanism adapts quite fast to the channel conditions. The hop count metric used by current routing protocols has proven itself for single rate networks. But it fails to take into account other important factors in a multi-rate network environment. We propose transmission time as a better path quality metric to guide routing decisions. It incorporates the effects of contention for the channel, the air time to send the data and the asymmetry of links. In this paper, we present a new design for a multi-rate mechanism as well as a new routing metric that is responsive to the rate. We address the issues involved in using transmission time as a metric and presents a comparison of the performance of different metrics for dynamic routing.

A new scheme for establishing pairwise keys for wireless sensor networks

This paper addresses the problem of secure path key establishment in wireless sensor networks that uses the random key predistribution technique. Inspired by the recent proxy-based scheme in [1] and [2], we introduce a fiiend-based scheme for establishing pairwise keys securely. We show that the chances of finding friends in a neighbourhood are considerably more than that of finding proxies, leading to lower communication overhead. Further, we prove that the friendbased scheme performs better than the proxy-based scheme in terms of resilience against node capture.

Robust/optimal temperature profile control using neural networks

An approximate dynamic programming (ADP) based neurocontroller is developed for a heat transfer application. Heat transfer problem for a fin in a car's electronic module is modeled as a nonlinear distributed parameter (infinite-dimensional) system by taking into account heat loss and generation due to conduction, convection and radiation. A low-order, finite-dimensional lumped parameter model for this problem is obtained by using Galerkin projection and basis functions designed through the 'Proper Orthogonal Decomposition' technique (POD) and the 'snap-shot' solutions. A suboptimal neurocontroller is obtained with a single-network-adaptive-critic (SNAC). Further contribution of this paper is to develop an online robust controller to account for unmodeled dynamics and parametric uncertainties. A weight update rule is presented that guarantees boundedness of the weights and eliminates the need for persistence of excitation (PE) condition to be satisfied. Since, the ADP and neural network based controllers are of fairly general structure, they appear to have the potential to be controller synthesis tools for nonlinear distributed parameter systems especially where it is difficult to obtain an accurate model.

Design of a FIR filter for image restoration using principal component neural networks

The neural network finds its application in many image denoising applications because of its inherent characteristics such as nonlinear mapping and self-adaptiveness. The design of filters largely depends on the a-priori knowledge about the type of noise. Due to this, standard filters are application and image specific. Widely used filtering algorithms reduce noisy artifacts by smoothing. However, this operation normally results in smoothing of the edges as well. On the other hand, sharpening filters enhance the high frequency details making the image non-smooth. An integrated general approach to design a finite impulse response filter based on principal component neural network (PCNN) is proposed in this study for image filtering, optimized in the sense of visual inspection and error metric. This algorithm exploits the inter-pixel correlation by iteratively updating the filter coefficients using PCNN. This algorithm performs optimal smoothing of the noisy image by preserving high and low frequency features. Evaluation results show that the proposed filter is robust under various noise distributions. Further, the number of unknown parameters is very few and most of these parameters are adaptively obtained from the processed image.