Multiple conformational states in crystals and in solution in alpha gamma hybrid peptides. Fragility of the C-12 helix in short sequences

The conformational properties of foldamers generated from alpha gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible coil formational space. This model sequence was anticipated to be a short segment of the alpha gamma C-12 helix, stabilized by three successive 4 -> 1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C-12 hydrogen bonds were obtained at the N-terminus, while a novel C-17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C-9 and C-7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C-12 and C-9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i)<-> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C-12 helix conformation. Lengthening of the (alpha gamma)(n) sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alpha gamma C-12 helix. These results establish that conformational fragility is manifested in short hybrid alpha gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.

Improved switching frequency variation control of hysteresis controlled voltage source inverter-fed IM drives using current error space vector

A constant switching frequency current error space vector-based hysteresis controller for two-level voltage source inverter-fed induction motor (IM) drives is proposed in this study. The proposed controller is capable of driving the IM in the entire speed range extending to the six-step mode. The proposed controller uses the parabolic boundary, reported earlier, for vector selection in a sector, but uses simple, fast and self-adaptive sector identification logic for sector change detection in the entire modulation range. This new scheme detects the sector change using the change in direction of current error along the axes jA, jB and jC. Most of the previous schemes use an outer boundary for sector change detection. So the current error goes outside the boundary six times during sector change, in one cycle,, introducing additional fifth and seventh harmonic components in phase current. This may cause sixth harmonic torque pulsations in the motor and spread in the harmonic spectrum of phase voltage. The proposed new scheme detects the sector change fast and accurately eliminating the chance of introducing additional fifth and seventh harmonic components in phase current and provides harmonic spectrum of phase voltage, which exactly matches with that of constant switching frequency voltage-controlled space vector pulse width modulation (VC-SVPWM)-based two-level inverter-fed drives.

Amino acid sequence of the winged bean (Psophocarpus tetragonolobus) basic lectin. Adenine binding and identification of the active-site tryptophan residue

The complete amino acid sequence of winged bean basic agglutinin (WBA I) was obtained by a combination of manual and gas-phase sequencing methods. Peptide fragments for sequence analyses were obtained by enzymatic cleavages using trypsin and Staphylococcus aureus V8 endoproteinase and by chemical cleavages using iodosobenzoic acid, hydroxylamine, and formic acid. COOH-terminal sequence analysis of WBA I and other peptides was performed using carboxypeptidase Y. The primary structure of WBA I was homologous to those of other legume lectins and more so to Erythrina corallodendron. Interestingly, the sequence shows remarkable identities in the regions involved in the association of the two monomers of E. corallodendron lectin. Other conserved regions are the double metal-binding site and residues contributing to the formation of the hydrophobic cavity and the carbohydrate-binding site. Chemical modification studies both in the presence and absence of N-acetylgalactosamine together with sequence analyses of tryptophan-containing tryptic peptides demonstrate that tryptophan 133 is involved in the binding of carbohydrate ligands by the lectin. The location of tryptophan 133 at the active center of WBA I for the first time subserves to explain a role for one of the most conserved residues in legume lectins.

Velocity-Space Contours of Collision Integrals

Based on the recently found closed-form expressions of the Boltzmann collision integrals in a rigid-sphere gas for multi-Maxwellian distributions, a few typical sets of contour surfaces of the integrals in the space of molecular velocities are presented. These show graphically the tendency toward equilibrium under the influence of collisions. A brief preliminary comparison with Monte Carlo results is also given.

Low PAPR full-diversity space-frequency codes for MIMO-OFDM systems

Use of precoding transforms such as Hadamard Transforms and Phase Alteration for Peak to Average Power Ratio (PAPR) reduction in OFDM systems are well known. In this paper we propose use of Inverse Discrete Fourier Transform (IDFT) and Hadamard transform as precoding transforms in MIMO-OFDM systems to achieve low peak to average power ratio (PAPR). We show that while our approach using IDFT does not disturb the diversity gains of the MIMO-OFDM systems (spatial, temporal and frequency diversity gains), it offers a better trade-off between PAPR reduction and ML decoding complexity compared to that of the Hadamard transform precoding. We study in detail the amount of PAPR reduction achieved for the following two recently proposed full-diversity Space-Frequency coded MIMO-OFDM systems using both the IDFT and the Hadamard transform: (i) W. Su. Z. Safar, M. Olfat, K. J. R. Liu (IEEE Trans. on Signal Processing, Nov. 2003), and (ii) W. Su, Z. Safar, K. J. R. Liu (IEEE Trans. on Information Theory, Jan. 2005).

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

Detection,amplification and sequence homology of sodC in clinical isolates of Salmonella sp

Background & objectives: Periplasmic copper and zinc superoxide dismutase (Cu,Zn-SOD or SodC) is an important component of the antioxidant shield which protects bacteria from the phagocytic oxidative burst. Cu,Zn-SODs protect Gram-negative bacteria against oxygen damage which have also been shown to contribute to the pathogenicity of these bacterial species. We report the presence of SodC in drug resistant Salmonella sp. isolated from patients suffering from enteric fever. Further sodC was amplified, cloned into Escherichia coli and the nucleotide sequence and amino acid sequence homology were compared with the standard strain Salmonella Typhimurium 14028. Methods: Salmonella enterica serovar Typhi (S. Typhi) and Salmonellaenterica serovar Paratyphi (S. Paratyphi) were isolated and identified from blood samples of the patients. The isolates were screened for the presence of Cu, Zn-SOD by PAGE using KCN as inhibitor of Cu,Zn-SOD. The gene (sodC) was amplified by PCR, cloned and sequenced. The nucleotide and amino acid sequences of sodC were compared using CLUSTAL X.Results: SodC was detected in 35 per cent of the Salmonella isolates. Amplification of the genomic DNA of S. Typhi and S. Paratyphi with sodC specific primers resulted in 519 and 515 bp amplicons respectively. Single mutational difference at position 489 was observed between thesodC of S. Typhi and S. Paratyphi while they differed at 6 positions with the sodC of S. Typhimurium 14028. The SodC amino acid sequences of the two isolates were homologous but 3 amino acid difference was observed with that of standard strain S. Typhimurium 14028.Interpretation & conclusions: The presence of SodC in pathogenic bacteria could be a novel candidate as phylogenetic marker.

BER analysis of space-time block codes from generalized complex orthogonal designs for M-PSK

In this paper, we present an analysis for the bit error rate (BER) performance of space-time block codes (STBC) from generalized complex orthogonal designs for M-PSK modulation. In STBCs from complex orthogonal designs (COD), the norms of the column vectors are the same (e.g., Alamouti code). However, in generalized COD (GCOD), the norms of the column vectors may not necessarily be the same (e.g., the rate-3/5 and rate-7/11 codes by Su and Xia in [1]). STBCs from GCOD are of interest because of the high rates that they can achieve (in [2], it has been shown that the maximum achievable rate for STBCs from GCOD is bounded by 4/5). While the BER performance of STBCs: from COD (e.g., Alamouti code) can be simply obtained from existing analytical expressions for receive diversity with the same diversity order by appropriately scaling the SNR, this can not be done for STBCs from GCOD (because of the unequal norms of the column vectors). Our contribution in this paper is that we derive analytical expressions for the BER performance of any STBC from GCOD. Our BER analysis for the GCOD captures the performance of STBCs from COD as special cases. We validate our results with two STBCs from GCOD reported by Su and Xia in [1], for 5 and 6 transmit antennas (G(5) and G(6) in [1]) with rates 7/11 and 3/5, respectively.

Reduction of Torque Ripple in Induction Motor Drives Using an AdvancedHybrid PWM Technique

A voltage source inverter-fed induction motor produces a pulsating torque due to application of nonsinusoidal voltages. Torque pulsation is strongly influenced by the pulsewidth modulation (PWM) method employed. Conventional space vector PWM (CSVPWM) is known to result in less torque ripple than sine-triangle PWM. This paper aims at further reduction in the pulsating torque by employing advanced bus-clamping switching sequences, which apply an active vector twice in a subcycle. This paper proposes a hybrid PWM technique which employs such advanced bus-clamping sequences in conjunction with a conventional switching sequence. The proposed hybrid PWM technique is shown to reduce the torque ripple considerably over CSVPWM along with a marginal reduction in current ripple.

Space-charge limited conduction in doped polypyrrole devices

Doping dependent current-voltage (I-V) and capacitance-voltage (C-V) measurements were carried out on polypyrrole devices in metal-polymer-metal sandwich structure. Temperature dependent I-V measurements infer that space-charge limited conduction (SCLC) with exponential trap distribution is appropriate for the moderately doped samples, whereas trap-free SCLC is observed in lightly doped samples. Trap densities and energies are estimated, the effective mobility is calculated using the Poole-Frenkel model, and the mobility exhibits thermally activated behavior. Frequency dependent capacitance-voltage characteristics show a peak near zero bias voltage, which implies that these devices are symmetric with a negligible barrier height at the metal-polymer interface. Low frequency capacitance measurements have revealed a negative capacitance at higher voltages due to the processes associated with the injection and redistribution of space-charges. (C) 2010 American Institute of Physics.

The Line Spectral Frequency Model of a Finite-Length Sequence

The line spectral frequency (LSF) of a causal finite length sequence is a frequency at which the spectrum of the sequence annihilates or the magnitude spectrum has a spectral null. A causal finite-length sequencewith (L + 1) samples having exactly L-LSFs, is referred as an Annihilating (AH) sequence. Using some spectral properties of finite-length sequences, and some model parameters, we develop spectral decomposition structures, which are used to translate any finite-length sequence to an equivalent set of AH-sequences defined by LSFs and some complex constants. This alternate representation format of any finite-length sequence is referred as its LSF-Model. For a finite-length sequence, one can obtain multiple LSF-Models by varying the model parameters. The LSF-Model, in time domain can be used to synthesize any arbitrary causal finite-length sequence in terms of its characteristic AH-sequences. In the frequency domain, the LSF-Model can be used to obtain the spectral samples of the sequence as a linear combination of spectra of its characteristic AH-sequences. We also summarize the utility of the LSF-Model in practical discrete signal processing systems.

Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

Approximation of solutions to fractional integral equation

In this paper we shall study a fractional integral equation in an arbitrary Banach space X. We used the analytic semigroups theory of linear operators and the fixed point method to establish the existence and uniqueness of solutions of the given problem. We also prove the existence of global solution. The existence and convergence of the Faedo–Galerkin solution to the given problem is also proved in a separable Hilbert space with some additional assumptions on the operator A. Finally we give an example to illustrate the applications of the abstract results.

A non-orthogonal distributed space-time coded protocol - Part 1:Signal model and design criteria

In this two-part series of papers, a generalized non-orthogonal amplify and forward (GNAF) protocol which generalizes several known cooperative diversity protocols is proposed. Transmission in the GNAF protocol comprises of two phases - the broadcast phase and the cooperation phase. In the broadcast phase, the source broadcasts its information to the relays as well as the destination. In the cooperation phase, the source and the relays together transmit a space-time code in a distributed fashion. The GNAF protocol relaxes the constraints imposed by the protocol of Jing and Hassibi on the code structure. In Part-I of this paper, a code design criteria is obtained and it is shown that the GNAF protocol is delay efficient and coding gain efficient as well. Moreover GNAF protocol enables the use of sphere decoders at the destination with a non-exponential Maximum likelihood (ML) decoding complexity. In Part-II, several low decoding complexity code constructions are studied and a lower bound on the Diversity-Multiplexing Gain tradeoff of the GNAF protocol is obtained.