A network representation of protein structures: Implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.

Sensor network deployment for agronomical data gathering in semi-arid regions

We share our experience in planning, designing and deploying a wireless sensor network of one square kilometre area. Environmental data such as soil moisture, temperature, barometric pressure, and relative humidity are collected in this area situated in the semi-arid region of Karnataka, India. It is a hope that information derived from this data will benefit the marginal farmer towards improving his farming practices. Soon after establishing the need for such a project, we begin by showing the big picture of such a data gathering network, the software architecture we have used, the range measurements needed for determining the sensor density, and the packaging issues that seem to play a crucial role in field deployments. Our field deployment experiences include designing with intermittent grid power, enhancing software tools to aid quicker and effective deployment, and flash memory corruption. The first results on data gathering look encouraging.

An analytical approach to the study of cooperation in wireless ad hoc networks

In wireless ad hoc networks, nodes communicate with far off destinations using intermediate nodes as relays. Since wireless nodes are energy constrained, it may not be in the best interest of a node to always accept relay requests. On the other hand, if all nodes decide not to expend energy in relaying, then network throughput will drop dramatically. Both these extreme scenarios (complete cooperation and complete noncooperation) are inimical to the interests of a user. In this paper, we address the issue of user cooperation in ad hoc networks. We assume that nodes are rational, i.e., their actions are strictly determined by self interest, and that each node is associated with a minimum lifetime constraint. Given these lifetime constraints and the assumption of rational behavior, we are able to determine the optimal share of service that each node should receive. We define this to be the rational Pareto optimal operating point. We then propose a distributed and scalable acceptance algorithm called Generous TIT-FOR-TAT (GTFT). The acceptance algorithm is used by the nodes to decide whether to accept or reject a relay request. We show that GTFT results in a Nash equilibrium and prove that the system converges to the rational and optimal operating point.

Sequence design for symbol-asynchronous CDMA with power or rate constraints

Sequence design and resource allocation for a symbol-asynchronous chip-synchronous code division multiple access (CDMA) system is considered in this paper. A simple lower bound on the minimum sum-power required for a non-oversized system, based on the best achievable for a non-spread system, and an analogous upper bound on the sum rate are first summarised. Subsequently, an algorithm of Sundaresan and Padakandla is shown to achieve the lower bound on minimum sum power (upper bound on sum rate, respectively). Analogous to the synchronous case, by splitting oversized users in a system with processing gain N, a system with no oversized users is easily obtained, and the lower bound on sum power (upper bound on sum rate, respectively) is shown to be achieved by using N orthogonal sequences. The total number of splits is at most N - 1.

Simulation of wavelength/time multiple-pulses-per-row fiber-optic CDMA network

Passive wavelength/time fiber-optic code division multiple access (WIT FO-CDMA) network is a viable option for highspeed access networks. Constructions of 2-D codes, suitable for incoherent WIT FO-CDMA, have been proposed to reduce the time spread of the 1-D sequences. The 2-D constructions can be broadly classified as 1) hybrid codes and 2) matrix codes. In our earlier work [141, we had proposed a new family of wavelength/time multiple-pulses-per-row (W/T MPR) matrix codes which have good cardinality, spectral efficiency and at the same time have the lowest off-peak autocorrelation and cross-correlation values equal to unity. In this paper we propose an architecture for a WIT MPR FO-CDAM network designed using the presently available devices and technology. A complete FO-CDMA network of ten users is simulated, for various number of simultaneous users and shown that 0 --> 1 errors can occur only when the number of interfering users is at least equal to the threshold value.

Analysis of connectivity map: Control to glutamate injured and phenobarbital treated neuronal network

We study the responses of a cultured neural network when it is exposed to epileptogenesis glutamate injury causing epilepsy and subsequent treatment with phenobarbital by constructing connectivity map of neurons using correlation matrix. This study is particularly useful in understanding the pharmaceutical drug induced changes in the neuronal network properties with insights into changes at the systems biology level. (C) 2010 American Institute of Physics. [doi:10.1063/1.3398025]

Power Optimal Network-on-Chip Interconnect Design

A large part of today's multi-core chips is interconnect. Increasing communication complexity has made essential new strategies for interconnects, such as Network on Chip. Power dissipation in interconnects has become a substantial part of the total power dissipation. Techniques to reduce interconnect power have thus become a necessity. In this paper, we present a design methodology that gives values of bus width for interconnect links, frequency of operation for routers, in Network on Chip scenario that satisfy required throughput and dissipate minimal switching power. We develop closed form analytical expressions for the power dissipation, with bus width and frequency as variables and then use Lagrange multiplier method to arrive at the optimal values. We present a 4 port router in 90 nm technology library as case study. The results obtained from analysis are discussed.

Generic Routing Rules and a Scalable Access Enhancement for the Network-on-Chip RECONNECT

RECONNECT is a Network-on-Chip using a honeycomb topology. In this paper we focus on properties of general rules applicable to a variety of routing algorithms for the NoC which take into account the missing links of the honeycomb topology when compared to a mesh. We also extend the original proposal [5] and show a method to insert and extract data to and from the network. Access Routers at the boundary of the execution fabric establish connections to multiple periphery modules and create a torus to decrease the node distances. Our approach is scalable and ensures homogeneity among the compute elements in the NoC. We synthesized and evaluated the proposed enhancement in terms of power dissipation and area. Our results indicate that the impact of necessary alterations to the fabric is negligible and effects the data transfer between the fabric and the periphery only marginally.

Influence of Oxide Particle Network Morphology on Ion Solvation and Transport in ``Soggy Sand''Electrolytes

The role of oxide surface chemical composition and solvent on ion solvation and ion transport of ``soggy sand'' electrolytes are discussed here. A ``soggy sand'' electrolyte system comprising dispersions of hydrophilic/hydrophobic functionalized aerosil silica in lithium perchlorate methoxy polyethylene glycol solution was employed for the study. Static and dynamic rheology measurements show formation of an attractive particle network in the case of the composite with unmodified aerosil silica (i.e., with surface silanol groups) as well as composites with hydrophobic alkane groups. While particle network in the composite with hydrophilic aerosil silica (unmodified) were due to hydrogen bonding, hydrophobic aerosil silica particles were held together via van der Waals forces. The network strength in the latter case (i.e., for hydrophobic composites) were weaker compared with the composite with unmodified aerosil silica. Both unmodified silica as well as hydrophobic silica composites displayed solid-like mechanical strength. No enhancement in ionic conductivity compared to the liquid electrolyte was observed in the case of the unmodified silica. This was attributed to the existence of a very strong particle network, which led to the ``expulsion'' of all conducting entities from the interfacial region between adjacent particles. The ionic conductivity for composites with hydrophobic aerosil particles displayed ionic conductivity dependent on the size of the hydrophobic chemical moiety. No spanning attractive particle network was observed for aerosil particles with surfaces modified with stronger hydrophilic groups (than silanol). The composite resembled a sol, and no percolation in ionic conductivity was observed.

Stringent constraints on the scalar K pi form factor from analyticity, unitarity and low-energy theorems

We investigate the scalar K pi form factor at low energies by the method of unitarity bounds adapted so as to include information on the phase and modulus along the elastic region of the unitarity cut. Using at input the values of the form factor at t = 0 and the Callan-Treiman point, we obtain stringent constraints on the slope and curvature parameters of the Taylor expansion at the origin. Also, we predict a quite narrow range for the higher-order ChPT corrections at the second Callan-Treiman point.

Two-agent cooperative search using game models with endurance-time constraints

In this article, the problem of two Unmanned Aerial Vehicles (UAVs) cooperatively searching an unknown region is addressed. The search region is discretized into hexagonal cells and each cell is assumed to possess an uncertainty value. The UAVs have to cooperatively search these cells taking limited endurance, sensor and communication range constraints into account. Due to limited endurance, the UAVs need to return to the base station for refuelling and also need to select a base station when multiple base stations are present. This article proposes a route planning algorithm that takes endurance time constraints into account and uses game theoretical strategies to reduce the uncertainty. The route planning algorithm selects only those cells that ensure the agent will return to any one of the available bases. A set of paths are formed using these cells which the game theoretical strategies use to select a path that yields maximum uncertainty reduction. We explore non-cooperative Nash, cooperative and security strategies from game theory to enhance the search effectiveness. Monte-Carlo simulations are carried out which show the superiority of the game theoretical strategies over greedy strategy for different look ahead step length paths. Within the game theoretical strategies, non-cooperative Nash and cooperative strategy perform similarly in an ideal case, but Nash strategy performs better than the cooperative strategy when the perceived information is different. We also propose a heuristic based on partitioning of the search space into sectors to reduce computational overhead without performance degradation.

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.

An auction algorithm for procuring wireless channel in a heterogenous wireless network

In this paper, we develop a novel auction algorithm for procuring wireless channel by a wireless node in a heterogeneous wireless network. We assume that the service providers of the heterogeneous wireless network are selfish and non-cooperative in the sense that they are only interested in maximizing their own utilities. The wireless user needs to procure wireless channels to execute multiple tasks. To solve the problem of the wireless user, we propose a reverse optimal (REVOPT) auction and derive an expression for the expected payment by the wireless user. The proposed auction mechanism REVOPT satisfies important game theoretic properties such as Bayesian incentive compatibility and individual rationality.

Analysis of network architectures for zigbee sensor clusters

We provide a comparative performance analysis of network architectures for beacon enabled Zigbee sensor clusters using the CSMA/CA MAC defined in the IEEE 802.15.4 standard, and organised as (i) a star topology, and (ii) a two-hop topology. We provide analytical models for obtaining performance measures such as mean network delay, and mean node lifetime. We find that the star topology is substantially superior both in delay performance and lifetime performance than the two-hop topology.

Classification of magnetic resonance brain images using wavelets as input to support vector machine and neural network

In this paper. we propose a novel method using wavelets as input to neural network self-organizing maps and support vector machine for classification of magnetic resonance (MR) images of the human brain. The proposed method classifies MR brain images as either normal or abnormal. We have tested the proposed approach using a dataset of 52 MR brain images. Good classification percentage of more than 94% was achieved using the neural network self-organizing maps (SOM) and 98% front support vector machine. We observed that the classification rate is high for a Support vector machine classifier compared to self-organizing map-based approach.