An algorithm to find similar internal sequence repeats

In recent years, identification of sequence patterns has been given immense importance to understand better their significance with respect to genomic organization and evolutionary processes. To this end, an algorithm has been derived to identify all similar sequence repeats present in a protein sequence. The proposed algorithm is useful to correlate the three-dimensional structure of various similar sequence repeats available in the Protein Data Bank against the same sequence repeats present in other databases like SWISS-PROT, PIR and Genome databases.

Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

We demonstrate a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures of the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like (circular) for small chains (CnH2n+2; n <= 20) and spherical for very long ones (n = 100), we find the emergence of ordered helical structures at intermediate lengths (n similar to 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier.

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.

Correlation between corona current and radio interference due to high voltage insulator string

The Radio Interference (RI) from electric power transmission line hardware, if not controlled, poses serious electromagnetic interference to system in the vicinity. The present work mainly concerns with the RI from the insulator string along with the associated line hardware. The laboratory testing for the RI levels are carried out through the measurement of the conducted radio interference levels. However such measurements do not really locate the coronating point, as well as, the mode of corona. At the same time experience shows that it is rather difficult to locate the coronating points by mere inspection. After a thorough look into the intricacies of the problem, it is ascertained that the measurement of associated ground end currents could give a better picture of the prevailing corona modes and their intensities. A study on the same is attempted in the present work. Various intricacies of the problem,features of ground end current pulses and its correlation with RI are dealt with. Owing to the complexity of such experimental investigations, the study made is not fully complete nevertheless it seems to be first of its kind.

Modeling Time-Varying Aggregate Interference in Cognitive Radio Systems, and Application to Primary Exclusive Zone Design

Accurately characterizing the time-varying interference caused to the primary users is essential in ensuring a successful deployment of cognitive radios (CR). We show that the aggregate interference at the primary receiver (PU-Rx) from multiple, randomly located cognitive users (CUs) is well modeled as a shifted lognormal random process, which is more accurate than the lognormal and the Gaussian process models considered in the literature, even for a relatively dense deployment of CUs. It also compares favorably with the asymptotically exact stable and symmetric truncated stable distribution models, except at high CU densities. Our model accounts for the effect of imperfect spectrum sensing, which depends on path-loss, shadowing, and small-scale fading of the link from the primary transmitter to the CU; the interweave and underlay modes or CR operation, which determine the transmit powers of the CUs; and time-correlated shadowing and fading of the links from the CUs to the PU-Rx. It leads to expressions for the probability distribution function, level crossing rate, and average exceedance duration. The impact of cooperative spectrum sensing is also characterized. We validate the model by applying it to redesign the primary exclusive zone to account for the time-varying nature of interference.