Unwinding of heterologous DNA by RecA protein during the search for homologous sequences

The search for homologous sequences promoted by RecA protein in vitro involves a presynaptic filament and naked duplex DNA, the multiple contacts of which produce nucleoprotein networks or coaggregates. The single-stranded DNA within the presynaptic filaments, however, is extended to an axial spacing 1.5 times that of B-form DNA. To investigate this paradoxical difference between the spacing of bases in the RecA presynaptic filament versus the target duplex DNA, we explored the effect of heterologous contacts on the conformation of DNA, and vice versa. In the presence of wheat germ topoisomerase I, RecA presynaptic filaments induced a rapid, limited reduction in the linking number of heterologous circular duplex DNA. This limited unwinding of heterologous duplex DNA, termed heterologous unwinding, was detected within 30 seconds and reached a steady state within a few minutes. Presynaptic filaments that were formed in the presence of ATP?S and separated from free RecA protein by gel filtration also generated a ladder of topoisomers upon incubation with relaxed duplex DNA and topoisomerase. The inhibition of heterologous contacts by 60 mImage -NaCl or 5 mImage -ADP resulted in a corresponding decrease in heterologous unwinding. In reciprocal fashion, the stability or number of heterologous contacts with presynaptic filaments was inversely related to the linking number of circular duplex DNA. These observations show that heterologous contacts with the presynaptic filament cause a limited unwinding of the duplex DNA, and conversely that the ability of the DNA to unwind stabilizes transient heterologous contacts.

Search for sub-mm, mm and radio continuum emission from extremely red objects

We present the results of sub-mm, mm (850 mum, 450 mum and 1250 mum) and radio (1.4 and 4.8 GHz) continuum observations of a sample of 27 K-selected Extremely Red Objects, or EROs, (14 of which form a complete sample with K < 20 and I - K > 5) aimed at detecting dusty starbursts, deriving the fraction of UltraLuminous Infrared Galaxies (ULIGs) in ERO samples, and constraining their redshifts using the radio-FIR correlation. One ERO was tentatively detected at 1250 mum and two were detected at 1.4 GHz, one of which has a less secure identification as an ERO counterpart. Limits on their redshifts and their star forming properties are derived and discussed. We stacked the observations of the undetected objects at 850 mum, 1250 mum and 4.8 GHz in order to search for possible statistical emission from the ERO population as a whole, but no significant detections were derived either for the whole sample or as a function of the average NIR colours. These results strongly suggest that the dominant population of EROs with K < 20 is not comprised of ULIGs like HR 10, but is probably made of radio-quiet ellipticals and weaker starburst galaxies with L < 10(12) L . and SFR < few hundred M. yr(-1).

A Nash Bargaining Approach to Retention Enhancing Bid Optimization in Sponsored Search Auctions with Discrete Bids

Bid optimization is now becoming quite popular in sponsored search auctions on the Web. Given a keyword and the maximum willingness to pay of each advertiser interested in the keyword, the bid optimizer generates a profile of bids for the advertisers with the objective of maximizing customer retention without compromising the revenue of the search engine. In this paper, we present a bid optimization algorithm that is based on a Nash bargaining model where the first player is the search engine and the second player is a virtual agent representing all the bidders. We make the realistic assumption that each bidder specifies a maximum willingness to pay values and a discrete, finite set of bid values. We show that the Nash bargaining solution for this problem always lies on a certain edge of the convex hull such that one end point of the edge is the vector of maximum willingness to pay of all the bidders. We show that the other endpoint of this edge can be computed as a solution of a linear programming problem. We also show how the solution can be transformed to a bid profile of the advertisers.

Multi-agent search using?sensors with heterogeneous capabilities

In this thesis we address the problem of multi-agent search. We formulate two deploy and search strategies based on optimal deployment of agents in search space so as to maximize the search effectiveness in a single step. We show that a variation of centroidal Voronoi configuration is the optimal deployment. When the agents have sensors with different capabilities, the problem will be heterogeneous in nature. We introduce a new concept namely, generalized Voronoi partition in order to formulate and solve the heterogeneous multi-agent search problem. We address a few theoretical issues such as optimality of deployment, convergence and spatial distributedness of the control law and the search strategies. Simulation experiments are carried out to compare performances of the proposed strategies with a few simple search strategies.

Search on a Hypercubic Lattice using Quantum Random Walk

We investigate the spatial search problem on the two-dimensional square lattice, using the Dirac evolution operator discretized according to the staggered lattice fermion formalism. d=2 is the critical dimension for the spatial search problem, where infrared divergence of the evolution operator leads to logarithmic factors in the scaling behavior. As a result, the construction used in our accompanying article [ A. Patel and M. A. Rahaman Phys. Rev. A 82 032330 (2010)] provides an O(√NlnN) algorithm, which is not optimal. The scaling behavior can be improved to O(√NlnN) by cleverly controlling the massless Dirac evolution operator by an ancilla qubit, as proposed by Tulsi Phys. Rev. A 78 012310 (2008). We reinterpret the ancilla control as introduction of an effective mass at the marked vertex, and optimize the proportionality constants of the scaling behavior of the algorithm by numerically tuning the parameters.

Bidding Dynamics of Rational Advertisers in Sponsored Search Auctions on the Web

In this paper, we address a key problem faced by advertisers in sponsored search auctions on the web: how much to bid, given the bids of the other advertisers, so as to maximize individual payoffs? Assuming the generalized second price auction as the auction mechanism, we formulate this problem in the framework of an infinite horizon alternative-move game of advertiser bidding behavior. For a sponsored search auction involving two advertisers, we characterize all the pure strategy and mixed strategy Nash equilibria. We also prove that the bid prices will lead to a Nash equilibrium, if the advertisers follow a myopic best response bidding strategy. Following this, we investigate the bidding behavior of the advertisers if they use Q-learning. We discover empirically an interesting trend that the Q-values converge even if both the advertisers learn simultaneously.

Multi-agent Search using Voronoi partitions

This paper addresses the problem of multiagent search in an unknown environment. The agents are autonomous in nature and are equipped with necessary sensors to carry out the search operation. The uncertainty, or lack of information about the search area is known a priori as a probability density function. The agents are deployed in an optimal way so as to maximize the one step uncertainty reduction. The agents continue to deploy themselves and reduce uncertainty till the uncertainty density is reduced over the search space below a minimum acceptable level. It has been shown, using LaSalle’s invariance principle, that a distributed control law which moves each of the agents towards the centroid of its Voronoi partition, modified by the sensor range leads to single step optimal deployment. This principle is now used to devise search trajectories for the agents. The simulations were carried out in 2D space with saturation on speeds of the agents. The results show that the control strategy per step indeed moves the agents to the respective centroid and the algorithm reduces the uncertainty distribution to the required level within a few steps.

Self Assessment-Based Decision Making for Multiagent Cooperative Search

This paper addresses a search problem with multiple limited capability search agents in a partially connected dynamical networked environment under different information structures. A self assessment-based decision-making scheme for multiple agents is proposed that uses a modified negotiation scheme with low communication overheads. The scheme has attractive features of fast decision-making and scalability to large number of agents without increasing the complexity of the algorithm. Two models of the self assessment schemes are developed to study the effect of increase in information exchange during decision-making. Some analytical results on the maximum number of self assessment cycles, effect of increasing communication range, completeness of the algorithm, lower bound and upper bound on the search time are also obtained. The performance of the various self assessment schemes in terms of total uncertainty reduction in the search region, using different information structures is studied. It is shown that the communication requirement for self assessment scheme is almost half of the negotiation schemes and its performance is close to the optimal solution. Comparisons with different sequential search schemes are also carried out. Note to Practitioners-In the futuristic military and civilian applications such as search and rescue, surveillance, patrol, oil spill, etc., a swarm of UAVs can be deployed to carry out the mission for information collection. These UAVs have limited sensor and communication ranges. In order to enhance the performance of the mission and to complete the mission quickly, cooperation between UAVs is important. Designing cooperative search strategies for multiple UAVs with these constraints is a difficult task. Apart from this, another requirement in the hostile territory is to minimize communication while making decisions. This adds further complexity to the decision-making algorithms. In this paper, a self-assessment-based decision-making scheme, for multiple UAVs performing a search mission, is proposed. The agents make their decisions based on the information acquired through their sensors and by cooperation with neighbors. The complexity of the decision-making scheme is very low. It can arrive at decisions fast with low communication overheads, while accommodating various information structures used for increasing the fidelity of the uncertainty maps. Theoretical results proving completeness of the algorithm and the lower and upper bounds on the search time are also provided.

Quantum Algorithms with Fixed Points: The Case of Database Search

The standard quantum search algorithm lacks a feature, enjoyed by many classical algorithms, of having a fixed-point, i.e. a monotonic convergence towards the solution. Here we present two variations of the quantum search algorithm, which get around this limitation. The first replaces selective inversions in the algorithm by selective phase shifts of $\frac{\pi}{3}$. The second controls the selective inversion operations using two ancilla qubits, and irreversible measurement operations on the ancilla qubits drive the starting state towards the target state. Using $q$ oracle queries, these variations reduce the probability of finding a non-target state from $\epsilon$ to $\epsilon^{2q+1}$, which is asymptotically optimal. Similar ideas can lead to robust quantum algorithms, and provide conceptually new schemes for error correction.

Federated Search Service for OAI-compliant, Open-Access Repositories in India

Many of the research institutions and universities across the world are facilitating open-access (OA) to their intellectual outputs through their respective OA institutional repositories (IRs) or through the centralized subject-based repositories. The registry of open access repositories (ROAR) lists more than 2850 such repositories across the world. The awareness about the benefits of OA to scholarly literature and OA publishing is picking up in India, too. As per the ROAR statistics, to date, there are more than 90 OA repositories in the country. India is doing particularly well in publishing open-access journals (OAJ). As per the directory of open-access journals (DOAJ), to date, India with 390 OAJs, is ranked 5th in the world in terms of numbers of OAJs being published. Much of the research done in India is reported in the journals published from India. These journals have limited readership and many of them are not being indexed by Web of Science, Scopus or other leading international abstracting and indexing databases. Consequently, research done in the country gets hidden not only from the fellow countrymen, but also from the international community. This situation can be easily overcome if all the researchers facilitate OA to their publications. One of the easiest ways to facilitate OA to scientific literature is through the institutional repositories. If every research institution and university in India set up an open-access IR and ensure that copies of the final accepted versions of all the research publications are uploaded in the IRs, then the research done in India will get far better visibility. The federation of metadata from all the distributed, interoperable OA repositories in the country will serve as a window to the research done across the country. Federation of metadata from the distributed OAI-compliant repositories can be easily achieved by setting up harvesting software like the PKP Harvester. In this paper, we share our experience in setting up a prototype metadata harvesting service using the PKP harvesting software for the OAI-compliant repositories in India.

Search on a fractal lattice using a quantum random walk

The spatial search problem on regular lattice structures in integer number of dimensions d >= 2 has been studied extensively, using both coined and coinless quantum walks. The relativistic Dirac operator has been a crucial ingredient in these studies. Here, we investigate the spatial search problem on fractals of noninteger dimensions. Although the Dirac operator cannot be defined on a fractal, we construct the quantum walk on a fractal using the flip-flop operator that incorporates a Klein-Gordon mode. We find that the scaling behavior of the spatial search is determined by the spectral (and not the fractal) dimension. Our numerical results have been obtained on the well-known Sierpinski gaskets in two and three dimensions.

Pulsed radio emission from the Fermi-LAT pulsar J1732-3131: Search and a possible detection at 34.5 MHz

We report our search for and a possible detection of periodic radio pulses at 34.5 MHz from the Fermi Large Area Telescope pulsar J1732-3131. The candidate detection has been possible in only one of the many sessions of observations made with the low-frequency array at Gauribidanur, India, when the otherwise radio weak pulsar may have apparently brightened many folds. The candidate dispersion measure along the sight line, based on the broad periodic profiles from �20min of data, is estimated to be 15.44 ± 0.32 pccc -1. We present the details of our periodic and single-pulse search, and discuss the results and their implications relevant to both, the pulsar and the intervening medium. © 2012 RAS.

As(3)p: A Fast Algorithm to Search Structurally Similar Protiens

Protein structure comparison is essential for understanding various aspects of protein structure, function and evolution. It can be used to explore the structural diversity and evolutionary patterns of protein families. In view of the above, a new algorithm is proposed which performs faster protein structure comparison using the peptide backbone torsional angles. It is fast, robust, computationally less expensive and efficient in finding structural similarities between two different protein structures and is also capable of identifying structural repeats within the same protein molecule.