DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes

EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site- bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site- bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.

Dielectric anomaly in Li-doped zinc oxide thin films grown by sol-gel route

Sol-gel route was employed to grow polycrystalline thin films of Li-doped ZnO thin films (Zn1-xLixO, x=0.15). Polycrystalline films were obtained at a growth temperature of 400-500 degrees C. Ferroelectricity in Zn0.85Li0.15O was verified by examining the temperature variation of the real and imaginary parts of dielectric constant, and from the C-V measurements. The phase transition temperature was found to be 330 K. The room-temperature dielectric constant and dissipation factor were 15.5 and 0.09 respectively, at a frequency of 100 kHz. The films exhibited well-defined hysteresis loop, and the values of spontaneous polarization (P-s) and coercive field were 0.15 mu C/cm(2) and 20 kV/cm, respectively, confirming the presence of ferroelectricity.

Jointly optimal power control and routing for a single cell, dense, ad hoc wireless network

We consider a dense, ad hoc wireless network confined to a small region, such that direct communication is possible between any pair of nodes. The physical communication model is that a receiver decodes the signal from a single transmitter, while treating all other signals as interference. Data packets are sent between source-destination pairs by multihop relaying. We assume that nodes self-organise into a multihop network such that all hops are of length d meters, where d is a design parameter. There is a contention based multiaccess scheme, and it is assumed that every node always has data to send, either originated from it or a transit packet (saturation assumption). In this scenario, we seek to maximize a measure of the transport capacity of the network (measured in bit-meters per second) over power controls (in a fading environment) and over the hop distance d, subject to an average power constraint. We first argue that for a dense collection of nodes confined to a small region, single cell operation is efficient for single user decoding transceivers. Then, operating the dense ad hoc network (described above) as a single cell, we study the optimal hop length and power control that maximizes the transport capacity for a given network power constraint. More specifically, for a fading channel and for a fixed transmission time strategy (akin to the IEEE 802.11 TXOP), we find that there exists an intrinsic aggregate bit rate (Theta(opt) bits per second, depending on the contention mechanism and the channel fading characteristics) carried by the network, when operating at the optimal hop length and power control. The optimal transport capacity is of the form d(opt)((P) over bar (t)) x Theta(opt) with d(opt) scaling as (P) over bar (1/eta)(t), where (P) over bar (t) is the available time average transmit power and eta is the path loss exponent. Under certain conditions on the fading distribution, we then provide a simple characterisation of the optimal operating point.

Link route pricing for enhanced QoS

Pricing is an effective tool to control congestion and achieve quality of service (QoS) provisioning for multiple differentiated levels of service. In this paper, we consider the problem of pricing for congestion control in the case of a network of nodes under multiple service classes. Our work draws upon [1] and [2] in various ways. We use the Tirupati pricing scheme in conjunction with the stochastic approximation based adaptive pricing methodology for queue control (proposed in [1]) for minimizing network congestion. However, unlike the methodology of [1] where pricing for entire routes is directly considered, we consider prices for individual link-service grade tuples. Further, we adapt the methodology proposed in [21 for a single-node scenario to the case of a network of nodes, for evaluating performance in terms of price, revenue rate and disutility. We obtain considerable performance improvements using our approach over that in [1]. In particular, our approach exhibits a throughput improvement in the range of 54 to 80 percent in all cases studied (over all routes) while exhibiting a lower packet delay in the range of 26 to 38 percent over the scheme in [1].

Average-Delay Optimal Policies for the Point-to-Point Channel

Average-delay optimal scheduflng of messages arriving to the transmitter of a point-to-point channel is considered in this paper. We consider a discrete time batch-arrival batch-service queueing model for the communication scheme, with service time that may be a function of batch size. The question of delay optimality is addressed within the semi-Markov decision-theoretic framework. Approximations to the average-delay optimal policy are obtained.

Design of an optimal auction for sponsored search auctions

In this paper we first describe a framework to model the sponsored search auction on the web as a mechanism design problem. Using this framework, we design a novel auction which we call the OPT (optimal) auction. The OPT mechanism maximizes the search engine's expected revenue while achieving Bayesian incentive compatibility and individual rationality of the advertisers. We show that the OPT mechanism is superior to two of the most commonly used mechanisms for sponsored search namely (1) GSP (Generalized Second Price) and (2) VCG (Vickrey-Clarke-Groves). We then show an important revenue equivalence result that the expected revenue earned by the search engine is the same for all the three mechanisms provided the advertisers are symmetric and the number of sponsored slots is strictly less than the number of advertisers.

Optimal Nonlinear Control and Estimation for a Reusable Launch Vehicle During Reentry Phase

In this paper a nonlinear optimal controller has been designed for aerodynamic control during the reentry phase of the Reusable Launch Vehicle (RLV). The controller has been designed based on a recently developed technique Optimal Dynamic Inversion (ODI). For full state feedback the controller has required full information about the system states. In this work an Extended Kalman filter (EKF) is developed to estimate the states. The vehicle (RLV) has been has been consider as a nonlinear Six-Degree-Of-Freedom (6-DOF) model. The simulation results shows that EKF gives a very good estimation of the states and it is working well with ODI. The resultant trajectories are very similar to those obtained by perfect state feedback using ODI only.

Optimal resource allocation in conflicts with the Lanchester linear law (2,1) model

This paper presents a detailed analysis of a model for military conflicts where the defending forces have to determine an optimal partitioning of available resources to counter attacks from an adversary in two different fronts in an area fire situation. Lanchester linear law attrition model is used to develop the dynamical equations governing the variation in force strength. Here we address a static resource allocation problem namely, Time-Zero-Allocation (TZA) where the resource allocation is done only at the initial time. Numerical examples are given to support the analytical results.

Optimal sleep-wake scheduling for quickest intrusion detection using sensor networks

We consider the problem of quickest detection of an intrusion using a sensor network, keeping only a minimal number of sensors active. By using a minimal number of sensor devices, we ensure that the energy expenditure for sensing, computation and communication is minimized (and the lifetime of the network is maximized). We model the intrusion detection (or change detection) problem as a Markov decision process (MDP). Based on the theory of MDP, we develop the following closed loop sleep/wake scheduling algorithms: (1) optimal control of Mk+1, the number of sensors in the wake state in time slot k + 1, (2) optimal control of qk+1, the probability of a sensor in the wake state in time slot k + 1, and an open loop sleep/wake scheduling algorithm which (3) computes q, the optimal probability of a sensor in the wake state (which does not vary with time), based on the sensor observations obtained until time slot k. Our results show that an optimum closed loop control on Mk+1 significantly decreases the cost compared to keeping any number of sensors active all the time. Also, among the three algorithms described, we observe that the total cost is minimum for the optimum control on Mk+1 and is maximum for the optimum open loop control on q.

Real-coded genetic algorithm for machining condition optimization

In this paper, we consider the machining condition optimization models presented in earlier studies. Finding the optimal combination of machining conditions within the constraints is a difficult task. Hence, in earlier studies standard optimization methods are used. The non-linear nature of the objective function, and the constraints that need to be satisfied makes it difficult to use the standard optimization methods for the solution. In this paper, we present a real coded genetic algorithm (RCGA), to find the optimal combination of machining conditions. We present various issues related to real coded genetic algorithm such as solution representation, crossover operators, and repair algorithm in detail. We also present the results obtained for these models using real coded genetic algorithm and discuss the advantages of using real coded genetic algorithm for these problems. From the results obtained, we conclude that real coded genetic algorithm is reliable and accurate for solving the machining condition optimization models.

Optimal configurations of active fiber composites based on asymptotic torsional analysis - art. no. 641413

Active Fiber Composites (AFC) possess desirable characteristics over a wide range of smart structure applications, such as vibration, shape and flow control as well as structural health monitoring. This type of material, capable of collocated actuation and sensing, call be used in smart structures with self-sensing circuits. This paper proposes four novel applications of AFC structures undergoing torsion: sensors and actuators shaped as strips and tubes; and concludes with a preliminary failure analysis. To enable this, a powerful mathematical technique, the Variational Asymptotic Method (VAM) was used to perform cross-sectional analyses of thin generally anisotropic AFC beams. The resulting closed form expressions have been utilized in the applications presented herein.

Optimal auctions for multi-unit procurement with volume discount bids

Our attention, is focused on designing an optimal procurement mechanism which a buyer can use for procuring multiple units of a homogeneous item based on bids submitted by autonomous, rational, and intelligent suppliers. We design elegant optimal procurement mechanisms for two different situations. In the first situation, each supplier specifies the maximum quantity that can be supplied together with a per unit price. For this situation, we design an optimal mechanism S-OPT (Optimal with Simple bids). In the more generalized case, each supplier specifies discounts based on the volume of supply. In this case, we design an optimal mechanism VD-OPT (Optimal with Volume Discount, bids). The VD-OPT mechanism uses the S-OPT mechanism as a building block. The proposed mechanisms minimize the cost to the buyer, satisfying at the same time, (a) Bayesian, incentive compatibility and (b) interim individual rationality.

Optimized Policies for the Retransmission Probabilities in Slotted Aloha

In this paper, we study the behaviour of the slotted Aloha multiple access scheme with a finite number of users under different traffic loads and optimize the retransmission probability q(r) for various settings, cost objectives and policies. First, we formulate the problem as a parameter optimization problem and use certain efficient smoothed functional algorithms for finding the optimal retransmission probability parameter. Next, we propose two classes of multi-level closed-loop feedback policies (for finding in each case the retransmission probability qr that now depends on the current system state) and apply the above algorithms for finding an optimal policy within each class of policies. While one of the policy classes depends on the number of backlogged nodes in the system, the other depends on the number of time slots since the last successful transmission. The latter policies are more realistic as it is difficult to keep track of the number of backlogged nodes at each instant. We investigate the effect of increasing the number of levels in the feedback policies. Wen also investigate the effects of using different cost functions (withn and without penalization) in our algorithms and the corresponding change in the throughput and delay using these. Both of our algorithms use two-timescale stochastic approximation. One of the algorithms uses one simulation while the other uses two simulations of the system. The two-simulation algorithm is seen to perform better than the other algorithm. Optimal multi-level closed-loop policies are seen to perform better than optimal open-loop policies. The performance further improves when more levels are used in the feedback policies.

Optimal Reservoir Operation for Flood Control Using Folded Dynamic Programming

Folded Dynamic Programming (FDP) is adopted for developing optimalnreservoir operation policies for flood control. It is applied to a case study of Hirakud Reservoir in Mahanadi basin, India with the objective of deriving optimal policy for flood control. The river flows down to Naraj, the head of delta where a major city is located and finally joins the Bay of Bengal. As Hirakud reservoir is on the upstream side of delta area in the basin, it plays an important role in alleviating the severity of the flood for this area. Data of 68 floods such as peaks of inflow hydrograph, peak of outflow from reservoir during each flood, peak of flow hydrograph at Naraj and d/s catchment contribution are utilized. The combinations of 51, 54, 57 thousand cumecs as peak inflow into reservoir and 25.5, 20, 14 thousand cumecs respectively as,peak d/s catchment contribution form the critical combinations for flood situation. It is observed that the combination of 57 thousand cumecs of inflow into reservoir and 14 thousand cumecs for d/s catchment contribution is the most critical among the critical combinations of flow series. The method proposed can be extended to similar situations for deriving reservoir operating policies for flood control.

Structure and optical properties of Cd-substituted ZnO (Zn1-xCdxO) nanostructures synthesized by the high-pressure solution route

We report the synthesis of Cd-substituted ZnO nanostructures (Zn1-xCdxO with x up to approximate to 0.09) by the high-pressure solution growth method. The synthesized nanostructures comprise nanocrystals that are both particles (similar to 10-15 nm) and rods which grow along the [002] direction as established by transmission electron microscope (TEM) and x-ray diffraction (XRD) analysis. Rietveld analysis of the XRD data shows a monotonic increase of the unit cell volume with the increase of Cd concentration. The optical absorption, as well as the photoluminescence (PL), shows a red shift on Cd substitution. The line width of the PL spectrum is related to the strain inhomogeneity and it peaks in the region where the CdO phase separates from the Zn1-xCdxO nanostructures. The time-resolved photoemission showed a long-lived (similar to 10 ns) component. We propose that the PL behaviour of the Zn1-xCdxO is dominated by strain in the sample with the red shift of the PL linked to the expansion of the unit cell volume on Cd substitution.