The restriction mapping problem revisited

In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction. In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n(2) log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n(4)) worst-case algorithm that can provably tolerate an absolute error of O(Delta/n) (where Delta is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule. Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest-the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al. (C) 2002 Elsevier Science (USA). All rights reserved.

A waveguide problem involving a thick iris in the theory of electromagnetism

The problem of electromagnetic wave propagation in a rectangular waveguide containing a thick iris is considered for its complete solution by reducing it to two suitable integral equations, one of which is of the first kind and the other is of the second kind. These integral equations are solved approximately, by using truncated Fourier series for the unknown functions. The reflection coefficient is computed numerically from the two integral equation approaches, and almost the same numerical results are obtained. This is also depicted graphically against the wave number and compared with thin iris results, which are computed by using complementary formulations coupled with Galerkin approximations. While the reflection coefficient for a thin iris steadily increases with the wave number, for a thick iris it fluctuates and zero reflection occurs. The number of zeros of the reflection coefficient for a thick iris increases with the thickness. Thus a thick iris becomes completely transparent for some discrete wave numbers. This phenomenon may be significant in the modelling of rectangular waveguides.

Spherical piston problem in water

In this paper, we study the propagation of a shock wave in water, produced by the expansion of a spherical piston with a finite initial radius. The piston path in the x, t plane is a hyperbola. We have considered the following two cases: (i) the piston accelerates from a zero initial velocity and attains a finite velocity asymptotically as t tends to infinity, and (ii) the piston decelerates, starting from a finite initial velocity. Since an analytic approach to this problem is extremely difficult, we have employed the artificial viscosity method of von Neumann & Richtmyer after examining its applicability in water. For the accelerating piston case, we have studied the effect of different initial radii of the piston, different initial curvatures of the piston path in the x, t plane and the different asymptotic speeds of the piston. The decelerating case exhibits the interesting phenomenon of the formation of a cavity in water when the deceleration of the piston is sufficiently high. We have also studied the motion of the cavity boundary up to 550 cycles.

On the solution of the problem of scattering of surface water waves by a sharp discontinuity in the surface boundary conditions

Closed-form analytical expressions are derived for the reflection and transmission coefficients for the problem of scattering of surface water waves by a sharp discontinuity in the surface-boundary-conditions, for the case of deep water. The method involves the use of the Havelock-type expansion of the velocity potential along with an analysis to solve a Carleman-type singular integral equation over a semi-infinite range. This method of solution is an alternative to the Wiener-Hopf technique used previously.

Solving a part classification problem using simulated annealing-like hybrid

Part classification and coding is still considered as laborious and time-consuming exercise. Keeping in view, the crucial role, which it plays, in developing automated CAPP systems, the attempts have been made in this article to automate a few elements of this exercise using a shape analysis model. In this study, a 24-vector directional template is contemplated to represent the feature elements of the parts (candidate and prototype). Various transformation processes such as deformation, straightening, bypassing, insertion and deletion are embedded in the proposed simulated annealing (SA)-like hybrid algorithm to match the candidate part with their prototype. For a candidate part, searching its matching prototype from the information data is computationally expensive and requires large search space. However, the proposed SA-like hybrid algorithm for solving the part classification problem considerably minimizes the search space and ensures early convergence of the solution. The application of the proposed approach is illustrated by an example part. The proposed approach is applied for the classification of 100 candidate parts and their prototypes to demonstrate the effectiveness of the algorithm. (C) 2003 Elsevier Science Ltd. All rights reserved.

Benchmark Control Problem for Highway Bridge based on FLC

Fuzzy logic control (FLC) systems have been applied as an effective control system in various fields, including vibration control of structures. The advantage of this approach is its inherent robustness and ability to handle non‐linearities and uncertainties in structural behavior and loading. The study evaluates the three‐dimensional benchmark control problem for a seismically excited highway bridge using an ANFIS driven hydraulic actuators. An ANN based training strategy that considers both velocity and acceleration feedback together with a fuzzy logic rule base is developed. Present study needs only 4 accelerometers and 4 fuzzy rule bases to determine the control force, instead of 8 accelerometers and 4 displacement transducers used in the benchmark study problem. The results obtained are better than that obtained from the benchmark control algorithm.

Inverse models to analyze the spatiotemporal variations of chemical weathering fluxes in a granito-gneissic watershed: Mule Hole, South India

Water-rock reactions are driven by the influx of water, which are out of equilibrium with the mineral assemblage in the rock. Here a mass balance approach is adopted to quantify these reactions. Based on field experiments carried out in a granito-gneissic small experimental watershed (SEW), Mule Hole SEW (similar to 4.5 km(2)), quartz, oligoclase, sericite, epidote and chlorite are identified as the basic primary minerals while kaolinite, goethite and smectite are identified as the secondary minerals. Observed groundwater chemistry is used to determine the weathering rates, in terms of `Mass Transfer Coefficients' (MTCs), of both primary and secondary minerals. Weathering rates for primary and secondary minerals are quantified in two steps. In the first step, top red soil is analyzed considering precipitation chemistry as initial phase and water chemistry of seepage flow as final phase. In the second step, minerals present in the saprolite layer are analyzed considering groundwater chemistry as the output phase. Weathering rates thus obtained are converted into weathering fluxes (Q(weathering)) using the recharge quantity. Spatial variability in the mineralogy observed among the thirteen wells of Mule Hole SEW is observed to be reflected in the MTC results and thus in the weathering fluxes. Weathering rates of the minerals in this silicate system varied from few 10 mu mol/L (in case of biotite) to 1000 s of micromoles per liter (calcite). Similarly, fluxes of biotite are observed to be least (7 +/- 5 mol/ha/yr) while those of calcite are highest (1265 791 mol/ha/yr). Further, the fluxes determined annually for all the minerals are observed to be within the bandwidth of the standard deviation of these fluxes. Variations in these annual fluxes are indicating the variations in the precipitation. Hence, the standard deviation indicated the temporal variations in the fluxes, which might be due to the variations in the annual rainfall. Thus, the methodology adopted defines an inverse way of determining weathering fluxes, which mainly contribute to the groundwater concentration. (C) 2011 Elsevier B.V. All rights reserved.

Pickup and delivery problem using metaheuristics techniques

Dial-a-ride problem (DARP) is an optimization problem which deals with the minimization of the cost of the provided service where the customers are provided a door-to-door service based on their requests. This optimization model presented in earlier studies, is considered in this study. Due to the non-linear nature of the objective function the traditional optimization methods are plagued with the problem of converging to a local minima. To overcome this pitfall we use metaheuristics namely Simulated Annealing (SA), Particle Swarm Optimization (PSO), Genetic Algorithm (GA) and Artificial Immune System (AIS). From the results obtained, we conclude that Artificial Immune System method effectively tackles this optimization problem by providing us with optimal solutions. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.

The pursuit-evasion problem of two aircraft in a horizontal plane

The pursuit-evasion problem of two aircraft in a horizontal plane is modelled as a zerosum differential game with capture time as payoff. The aircraft are modelled as point masses with thrust and bank angle controls. The games of kind and degree for this differential game are solved.

Zero-phase inverse filtering for extraction of source characteristics

The instants at which significant excitation of vocal tract take place during voicing are referred to as epochs. Epochs and strengths of excitation pulses at epochs are useful in characterizing voice source. Epoch filtering technique proposed by the authors determine epochs from speech waveform. In this paper we propose zero-phase inverse filtering to obtain strengths of excitation pulses at epochs. Zero-phase inverse filter compensates the gross spectral envelope of short-time spectrum of speech without affecting phase characteristics. Linear prediction analysis is used to realize the zero-phase inverse filter. Source characteristics that can be derived from speech using this technique are illustrated with examples.