A self-consistent formulation for analysis and generation of non-uniform DNA structure

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

End-bearing capacity of driven piles in sand using the stress characteristics method: analysis and implementation

The method of stress characteristics has been employed to compute the end-bearing capacity of driven piles. The dependency of the soil internal friction angle on the stress level has been incorporated to achieve more realistic predictions for the end-bearing capacity of piles. The validity of the assumption of the superposition principle while using the bearing capacity equation based on soil plasticity concepts, when applied to deep foundations, has been examined. Fourteen pile case histories were compiled with cone penetration tests (CPT) performed in the vicinity of different pile locations. The end-bearing capacity of the piles was computed using different methods, namely, static analysis, effective stress approach, direct CPT, and the proposed approach. The comparison between predictions made by different methods and measured records shows that the stress-level-based method of stress characteristics compares better with experimental data. Finally, the end-bearing capacity of driven piles in sand was expressed in terms of a general expression with the addition of a new factor that accounts for different factors contributing to the bearing capacity. The influence of the soil nonassociative flow rule has also been included to achieve more realistic results.

SIR Analysis and Interference Cancellation in Uplink OFDMA with Large Carrier Frequency/Timing Offsets

In uplink orthogonal frequency division multiple access (OFDMA), large timing offsets (TO) and/or carrier frequency offsets (CFO) of other users with respect to a desired user can cause significant multiuser interference (MUI). In this letter, we analytically characterize the degradation in the average output signal-to-interference ratio (SIR) due to the combined effect of both TOs as well as CFOs in uplink OFDMA. Specifically, we derive closed-form expressions for the average SIR at the DFT output in the presence of large CFOs and TOs. The analyticalexpressions derived for the signal and various interference terms at the DFT output are used to devise an interference cancelling receiver to mitigate the effect of CFO/TO-induced interferences.

Conformational Analysis and Electronic Structure of Monothiodiacetamide: Normal Coordinate Analysis and Molecular Orbital Study

The infrared spectra of monothiodiacetamide (MTDA, CHaCONHCSCH3) and its N-deuterated compound in solution, solid state and at low temperature are measured. Normal coordinate analysis for the planar vibrations of MTDAd o and -dl have been performed for the two most probable cis-trans-CONHCSor -CSNHCO-conformers using a simple Urey-Bradley force function. The conformation of MTDA derived from the vibrational spectra is supported by the all valence CNDO/2 molecular orbital method. The vibrational assignments and the electronic structure of MTDA are also given.

Theoretical studies on Beta-lactam antibiotics VI: Conformational analysis and structure-activity relationships of penicillin sulfoxides and cephalosporins

Conformational energy calculations were carried out on penicillin α-and Β-sulfoxides and δ2- and δ3-cephalosporins, in order to identify the structural features governing their biological activity. Results on penicillin Β-sulfoxide indicated that in its favoured conformation, the orientation of the aminoacyl group was different from the one required for biological activity. Penicillin α sulfoxide, like penicillin sulfide, favoured two conformations of nearly equal energies, but separated by a much higher energy barrier. The reduced activity of the sulfoxides despite the nonplanarity of their lactam peptide indicated that the orientations of the aminoacyl and carboxyl groups might also govern biological activity. δ3-cephalosporins favoured two conformations of nearly equal energies, whereas δ2-cephalosporins favoured only one conformation. The lactam peptide was moderately nonplanÄr in the former, but nearly planar in the latter. The differences in the.preferred orientations of the carboxyl group between penicillins and cephalosporins were correlated with the resistance of cephalosporins to penicillinases.

Analysis And Design Of Two Layered Ultra Wide Band Filter

Design of an Ultra Wide Band (UWB) filter over 3.1 GHz to 10.6 GHz using broad side coupled and spur lines in microstrip medium suitable for UWB communications has been presented in this paper. Parameters of broad side coupled lines have been appropriately chosen to achieve ultra wide band response. Spur lines have been incorporated at the input and output feed lines of the filter to improve the stop band rejection characteristics of the filter. Filter has been analyzed based on circuit models and full wave simulations. Experimental results of the filter designed using the proposed structure has been verified against the results obtained from circuit models and full wave simulations. The results match satisfactorily. Stop band rejection of better than 20 dB was obtained over the frequencies of 13 GHz to 18.2 GHz. Overall size of the filter is 40 x 18 x 0.787 mm(3).

Karnaugh map analysis and synthesis of threshold functions

A unate function can easily be identified on a Karnaugh map from the well-known property that it cons ist s only ofess en ti al prime implicante which intersect at a common implicant. The additional property that the plot of a unate function F(x, ... XII) on a Karnaugh map should possess in order that F may also be Ivrealizable (n';:; 6) has been found. It has been sh own that the I- realizability of a unate function F corresponds to the ' compac tness' of the plot of F. No resort to tho inequalities is made, and no pre-processing such as positivizing and ordering of the given function is required.

Automatic Road Extraction using High Resolution Satellite Image Based on Texture Progressive Analysis and Normalized Cut Method

In this paper the approach for automatic road extraction for an urban region using structural, spectral and geometric characteristics of roads has been presented. Roads have been extracted based on two levels: Pre-processing and road extraction methods. Initially, the image is pre-processed to improve the tolerance by reducing the clutter (that mostly represents the buildings, parking lots, vegetation regions and other open spaces). The road segments are then extracted using Texture Progressive Analysis (TPA) and Normalized cut algorithm. The TPA technique uses binary segmentation based on three levels of texture statistical evaluation to extract road segments where as, Normalizedcut method for road extraction is a graph based method that generates optimal partition of road segments. The performance evaluation (quality measures) for road extraction using TPA and normalized cut method is compared. Thus the experimental result show that normalized cut method is efficient in extracting road segments in urban region from high resolution satellite image.

Splitting Algorithms for Fast Relay Selection: Generalizations, Analysis, and a Unified View

Relay selection for cooperative communications promises significant performance improvements, and is, therefore, attracting considerable attention. While several criteria have been proposed for selecting one or more relays, distributed mechanisms that perform the selection have received relatively less attention. In this paper, we develop a novel, yet simple, asymptotic analysis of a splitting-based multiple access selection algorithm to find the single best relay. The analysis leads to simpler and alternate expressions for the average number of slots required to find the best user. By introducing a new contention load' parameter, the analysis shows that the parameter settings used in the existing literature can be improved upon. New and simple bounds are also derived. Furthermore, we propose a new algorithm that addresses the general problem of selecting the best Q >= 1 relays, and analyze and optimize it. Even for a large number of relays, the scalable algorithm selects the best two relays within 4.406 slots and the best three within 6.491 slots, on average. We also propose a new and simple scheme for the practically relevant case of discrete metrics. Altogether, our results develop a unifying perspective about the general problem of distributed selection in cooperative systems and several other multi-node systems.

Genome-wide analysis and experimentation of plant serine/threonine/tyrosine-specific protein kinases

Protein tyrosine phosphorylation plays an important role in cell growth, development and oncogenesis. No classical protein tyrosine kinase has hitherto been cloned from plants. Does protein tyrosine kinase exist in plants? To address this, we have performed a genomic survey of protein tyrosine kinase motifs in plants using the delineated tyrosine phosphorylation motifs from the animal system. The Arabidopsis thaliana genome encodes 57 different protein kinases that have tyrosine kinase motifs. Animal non-receptor tyrosine kinases, SRC, ABL, LYN, FES, SEK, KIN and RAS have structural relationship with putative plant tyrosine kinases. In an extended analysis, animal receptor and non-receptor kinases, Raf and Ras kinases, mixed lineage kinases and plant serine/threonine/tyrosine (STY) protein kinases, form a well-supported group sharing a common origin within the superfamily of STY kinases. We report that plants lack bona fide tyrosine kinases, which raise an intriguing possibility that tyrosine phosphorylation is carried out by dual-specificity STY protein kinases in plants. The distribution pattern of STY protein kinase families on Arabidopsis chromosomes indicates that this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats. Genome-wide analysis is supported by the functional expression and characterization of At2g24360 and phosphoproteomics of Arabidopsis. Evidence for tyrosine phosphorylated proteins is provided by alkaline hydrolysis, anti-phosphotyrosine immunoblotting, phosphoamino acid analysis and peptide mass fingerprinting. These results report the first comprehensive survey of genome-wide and tyrosine phosphoproteome analysis of plant STY protein kinases.

Homomorphic Analysis and Modeling of ECG Signals

Homomorphic analysis and pole-zero modeling of electrocardiogram (ECG) signals are presented in this paper. Four typical ECG signals are considered and deconvolved into their minimum and maximum phase components through cepstral filtering, with a view to study the possibility of more efficient feature selection from the component signals for diagnostic purposes. The complex cepstra of the signals are linearly filtered to extract the basic wavelet and the excitation function. The ECG signals are, in general, mixed phase and hence, exponential weighting is done to aid deconvolution of the signals. The basic wavelet for normal ECG approximates the action potential of the muscle fiber of the heart and the excitation function corresponds to the excitation pattern of the heart muscles during a cardiac cycle. The ECG signals and their components are pole-zero modeled and the pole-zero pattern of the models can give a clue to classify the normal and abnormal signals. Besides, storing only the parameters of the model can result in a data reduction of more than 3:1 for normal signals sampled at a moderate 128 samples/s

Weighted subspace methods and spatial smoothing: analysis and comparison

The effect of using a spatially smoothed forward-backward covariance matrix on the performance of weighted eigen-based state space methods/ESPRIT, and weighted MUSIC for direction-of-arrival (DOA) estimation is analyzed. Expressions for the mean-squared error in the estimates of the signal zeros and the DOA estimates, along with some general properties of the estimates and optimal weighting matrices, are derived. A key result is that optimally weighted MUSIC and weighted state-space methods/ESPRIT have identical asymptotic performance. Moreover, by properly choosing the number of subarrays, the performance of unweighted state space methods can be significantly improved. It is also shown that the mean-squared error in the DOA estimates is independent of the exact distribution of the source amplitudes. This results in a unified framework for dealing with DOA estimation using a uniformly spaced linear sensor array and the time series frequency estimation problems.

Kinematic analysis and design of articulated manipulators with joint motion constraints

For an articulated manipulator with joint rotation constraints, we show that the maximum workspace is not necessarily obtained for equal link lengths but is also determined by the range and mean positions of the joint motions. We present expressions for sectional area, workspace volume, overlap volume and work area in terms of link ratios, mean positions and ranges of joint motion. We present a numerical procedure to obtain the maximum rectangular area that can be embedded in the workspace of an articulated manipulator with joint motion constraints. We demonstrate the use of analytical expressions and the numerical plots in the kinematic design of an articulated manipulator with joint rotation constraints.

Pipelined ring algorithm for matrix multiplication on transputer networks: performance analysis and estimation

A parallel matrix multiplication algorithm is presented, and studies of its performance and estimation are discussed. The algorithm is implemented on a network of transputers connected in a ring topology. An efficient scheme for partitioning the input matrices is introduced which enables overlapping computation with communication. This makes the algorithm achieve near-ideal speed-up for reasonably large matrices. Analytical expressions for the execution time of the algorithm have been derived by analysing its computation and communication characteristics. These expressions are validated by comparing the theoretical results of the performance with the experimental values obtained on a four-transputer network for both square and irregular matrices. The analytical model is also used to estimate the performance of the algorithm for a varying number of transputers and varying problem sizes. Although the algorithm is implemented on transputers, the methodology and the partitioning scheme presented in this paper are quite general and can be implemented on other processors which have the capability of overlapping computation with communication. The equations for performance prediction can also be extended to other multiprocessor systems.