Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

Diversity and degrees of freedom of cooperative wireless networks

Two key parameters in the outage characterization of a wireless fading network are the diversity and the degrees of freedom (DOF). These two quantities represent the two endpoints of the diversity multiplexing gain tradeoff, In this paper, we present max-flow min-cut type theorems for computing both the diversity and the DOF of arbitrary single-source single-sink networks with nodes possessing multiple antennas. We also show that an amplify-and-forward protocol is sufficient to achieve the same. The DOF characterization is obtained using a conversion to a deterministic wireless network for which the capacity was recently found. This conversion is operational in the sense that a capacity-achieving scheme for the deterministic network can be converted into a DOF-achieving scheme for the fading network. We also show that the diversity result easily extends to multisource multi-sink networks whereas the DOF result extends to a single-source multi-cast network. Along the way, we prove that the zero error capacity of the deterministic network is the same as its c-error capacity.

DMT of Multi-hop Cooperative Networks-Part II: Layered and Multi-Antenna Networks

We consider single-source, single-sink (ss-ss) multi-hop relay networks, with slow-fading Rayleigh links. This two part paper aims at giving explicit protocols and codes to achieve the optimal diversity-multiplexing tradeoff (DMT) of two classes of multi-hop networks: K-parallel-path (KPP) networks and Layered networks. While single-antenna KPP networks were the focus of the first part, we consider layered and multi-antenna networks in this second part. We prove that a linear DMT between the maximum diversity d(max). and the maximum multiplexing gain of 1 is achievable for single-antenna fully-connected layered networks under the half-duplex constraint. This is shown to be equal to the optimal DMT if the number of relaying layers is less than 4. For the multiple-antenna case, we provide an achievable DMT, which is significantly better than known lower bounds for half duplex networks. Along the way, we compute the DMT of parallel MIMO channels in terms of the DMT of the component channel. For arbitrary ss-ss single-antenna directed acyclic networks with full-duplex relays, we prove that a linear tradeoff between maximum diversity and maximum multiplexing gain is achievable using an amplify-and-forward (AF) protocol. Explicit short-block-length codes are provided for all the proposed protocols. Two key implications of the results in the two-part paper are that the half-duplex constraint does not necessarily entail rate loss by a factor of two as previously believed and that simple AN protocols are often sufficient to attain the best possible DMT.

DMT of Multi-hop Cooperative Networks-Part I: K-Parallel-Path Networks

We consider single-source, single-sink multi-hop relay networks, with slow-fading Rayleigh fading links and single-antenna relay nodes operating under the half-duplex constraint. While two hop relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this two-part paper, we identify two families of networks that are multi-hop generalizations of the two hop network: K-Parallel-Path (KPP) networks and Layered networks. In the first part, we initially consider KPP networks, which can be viewed as the union of K node-disjoint parallel paths, each of length > 1. The results are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the optimal DMT of KPP(D) networks with K >= 4, and KPP(I) networks with K >= 3. Along the way, we derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. As a special case, the DMT of two-hop relay network without direct link is obtained. Two key implications of the results in the two-part paper are that the half-duplex constraint does not necessarily entail rate loss by a factor of two, as previously believed and that, simple AF protocols are often sufficient to attain the best possible DMT.

Distributed space-time codes for cooperative networks with partial CSI

Design criteria and full-diversity Distributed Space Time Codes (DSTCs) for the two phase transmission based cooperative diversity protocol of Jing-Hassibi and the Generalized Nonorthogonal Amplify and Forward (GNAF) protocol are reported, when the relay nodes are assumed to have knowledge of the phase component of the source to relay channel gains. It is shown that this under this partial channel state information (CSI), several well known space time codes for the colocated MIMO (Multiple Input Multiple Output) channel become amenable for use as DSTCs. In particular, the well known complex orthogonal designs, generalized coordinate interleaved orthogonal designs (GCIODs) and unitary weight single symbol decodable (UW-SSD) codes are shown to satisfy the required design constraints for DSTCs. Exploiting the relaxed code design constraints, we propose DSTCs obtained from Clifford Algebras which have low ML decoding complexity.

High-rate, Single-Symbol Decodable Distributed STBCs for Partially-Coherent Cooperative Networks

Space-time block codes (STBCs) that are single-symbol decodable (SSD) in a co-located multiple antenna setting need not be SSD in a distributed cooperative communication setting. A relay network with N relays and a single source-destination pair is called a partially-coherent relay channel (PCRC) if the destination has perfect channel state information (CSI) of an the channels and the relays have only the phase information of the source-to-relay channels. In our earlier work, we had derived a set of necessary and sufficient conditions for a distributed STBC (DSTBC) to be SSD for a PCRC. Using these conditions, in this paper we show that the possibility of channel phase compensation operation at the relay nodes using partial CSI at the relays increases the possible rate of SSD DSTBCs from 2/N when the relays do not have CSI to 1/2, which is independent of N. We also show that when a DSTBC is SSD for a PCRC, then arbitrary coordinate interleaving of the in-phase and quadrature-phase components of the variables does not disturb its SSD property. Using this property we are able to construct codes that are SSD and have higher rate than 2/N but giving full diversity only for signal constellations satisfying certain conditions.

OFDM Based Distributed Space Time Coding for Asynchronous Relay Networks

Recently Li and Xia have proposed a transmission scheme for wireless relay networks based on the Alamouti space time code and orthogonal frequency division multiplexing to combat the effect of timing errors at the relay nodes. This transmission scheme is amazingly simple and achieves a diversity order of two for any number of relays. Motivated by its simplicity, this scheme is extended to a more general transmission scheme that can achieve full cooperative diversity for any number of relays. The conditions on the distributed space time block code (DSTBC) structure that admit its application in the proposed transmission scheme are identified and it is pointed out that the recently proposed full diversity four group decodable DST-BCs from precoded co-ordinate interleaved orthogonal designs and extended Clifford algebras satisfy these conditions. It is then shown how differential encoding at the source can be combined with the proposed transmission scheme to arrive at a new transmission scheme that can achieve full cooperative diversity in asynchronous wireless relay networks with no channel information and also no timing error knowledge at the destination node. Finally, four group decodable distributed differential space time block codes applicable in this new transmission scheme for power of two number of relays are also provided.

Noncoherent low-decoding-complexity space-time codes for wireless relay networks

The differential encoding/decoding setup introduced by Kiran et at, Oggier et al and Jing et al for wireless relay networks that use codebooks consisting of unitary matrices is extended to allow codebooks consisting of scaled unitary matrices. For such codebooks to be used in the Jing-Hassibi protocol for cooperative diversity, the conditions that need to be satisfied by the relay matrices and the codebook are identified. A class of previously known rate one, full diversity, four-group encodable and four-group decodable Differential Space-Time Codes (DSTCs) is proposed for use as Distributed DSTCs (DDSTCs) in the proposed set up. To the best of our knowledge, this is the first known low decoding complexity DDSTC scheme for cooperative wireless networks.

Single-Symbol ML Decodable Precoded DSTBCs for Cooperative Networks

Single-symbol maximum likelihood (ML) decodable distributed orthogonal space-time block codes (DOST- BCs) have been introduced recently for cooperative networks and an upper-bound on the maximal rate of such codes along with code constructions has been presented. In this paper, we introduce a new class of distributed space-time block codes (DSTBCs) called semi-orthogonal precoded distributed single-symbol decodable space-time block codes (Semi-SSD-PDSTBCs) wherein, the source performs preceding on the information symbols before transmitting it to all the relays. A set of necessary and sufficient conditions on the relay matrices for the existence of semi-SSD- PDSTBCs is proved. It is shown that the DOSTBCs are a special case of semi-SSD-PDSTBCs. A subset of semi-SSD-PDSTBCs having diagonal covariance matrix at the destination is studied and an upper bound on the maximal rate of such codes is derived. The bounds obtained are approximately twice larger than that of the DOSTBCs. A systematic construction of Semi- SSD-PDSTBCs is presented when the number of relays K ges 4 and the constructed codes are shown to have higher rates than that of DOSTBCs.

Optimal threshold policies for admission control in communication networks via discrete parameter stochastic approximation

The problem of admission control of packets in communication networks is studied in the continuous time queueing framework under different classes of service and delayed information feedback. We develop and use a variant of a simulation based two timescale simultaneous perturbation stochastic approximation (SPSA) algorithm for finding an optimal feedback policy within the class of threshold type policies. Even though SPSA has originally been designed for continuous parameter optimization, its variant for the discrete parameter case is seen to work well. We give a proof of the hypothesis needed to show convergence of the algorithm on our setting along with a sketch of the convergence analysis. Extensive numerical experiments with the algorithm are illustrated for different parameter specifications. In particular, we study the effect of feedback delays on the system performance.

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.

Voluntary Energy Harvesting Relays and Selection in Cooperative Wireless Networks

The use of energy harvesting (EH) nodes as cooperative relays is a promising and emerging solution in wireless systems such as wireless sensor networks. It harnesses the spatial diversity of a multi-relay network and addresses the vexing problem of a relay's batteries getting drained in forwarding information to the destination. We consider a cooperative system in which EH nodes volunteer to serve as amplify-and-forward relays whenever they have sufficient energy for transmission. For a general class of stationary and ergodic EH processes, we introduce the notion of energy constrained and energy unconstrained relays and analytically characterize the symbol error rate of the system. Further insight is gained by an asymptotic analysis that considers the cases where the signal-to-noise-ratio or the number of relays is large. Our analysis quantifies how the energy usage at an EH relay and, consequently, its availability for relaying, depends not only on the relay's energy harvesting process, but also on its transmit power setting and the other relays in the system. The optimal static transmit power setting at the EH relays is also determined. Altogether, our results demonstrate how a system that uses EH relays differs in significant ways from one that uses conventional cooperative relays.

Interaction Energy Based Protein Structure Networks

The three dimensional structure of a protein is formed and maintained by the noncovalent interactions among the amino acid residues of the polypeptide chain These interactions can be represented collectively in the form of a network So far such networks have been investigated by considering the connections based on distances between the amino acid residues Here we present a method of constructing the structure network based on interaction energies among the amino acid residues in the protein We have investigated the properties of such protein energy based networks (PENs) and have shown correlations to protein structural features such as the clusters of residues involved in stability formation of secondary and super secondary structural units Further we demonstrate that the analysis of PENs in terms of parameters such as hubs and shortest paths can provide a variety of biologically important information such as the residues crucial for stabilizing the folded units and the paths of communication between distal residues in the protein Finally the energy regimes for different levels of stabilization in the protein structure have clearly emerged from the PEN analysis

A Shapley Value-Based Approach to Discover Influential Nodes in Social Networks

Our study concerns an important current problem, that of diffusion of information in social networks. This problem has received significant attention from the Internet research community in the recent times, driven by many potential applications such as viral marketing and sales promotions. In this paper, we focus on the target set selection problem, which involves discovering a small subset of influential players in a given social network, to perform a certain task of information diffusion. The target set selection problem manifests in two forms: 1) top-k nodes problem and 2) lambda-coverage problem. In the top-k nodes problem, we are required to find a set of k key nodes that would maximize the number of nodes being influenced in the network. The lambda-coverage problem is concerned with finding a set of k key nodes having minimal size that can influence a given percentage lambda of the nodes in the entire network. We propose a new way of solving these problems using the concept of Shapley value which is a well known solution concept in cooperative game theory. Our approach leads to algorithms which we call the ShaPley value-based Influential Nodes (SPINs) algorithms for solving the top-k nodes problem and the lambda-coverage problem. We compare the performance of the proposed SPIN algorithms with well known algorithms in the literature. Through extensive experimentation on four synthetically generated random graphs and six real-world data sets (Celegans, Jazz, NIPS coauthorship data set, Netscience data set, High-Energy Physics data set, and Political Books data set), we show that the proposed SPIN approach is more powerful and computationally efficient. Note to Practitioners-In recent times, social networks have received a high level of attention due to their proven ability in improving the performance of web search, recommendations in collaborative filtering systems, spreading a technology in the market using viral marketing techniques, etc. It is well known that the interpersonal relationships (or ties or links) between individuals cause change or improvement in the social system because the decisions made by individuals are influenced heavily by the behavior of their neighbors. An interesting and key problem in social networks is to discover the most influential nodes in the social network which can influence other nodes in the social network in a strong and deep way. This problem is called the target set selection problem and has two variants: 1) the top-k nodes problem, where we are required to identify a set of k influential nodes that maximize the number of nodes being influenced in the network and 2) the lambda-coverage problem which involves finding a set of influential nodes having minimum size that can influence a given percentage lambda of the nodes in the entire network. There are many existing algorithms in the literature for solving these problems. In this paper, we propose a new algorithm which is based on a novel interpretation of information diffusion in a social network as a cooperative game. Using this analogy, we develop an algorithm based on the Shapley value of the underlying cooperative game. The proposed algorithm outperforms the existing algorithms in terms of generality or computational complexity or both. Our results are validated through extensive experimentation on both synthetically generated and real-world data sets.