Process-dependent magnetic properties of Co-doped ZnO in bulk and thin film form

Structural, optical and magnetic studies of Co-doped ZnO have been carried out for bulk as well as thin films. The magnetic studies revealed the superparamagnetic nature for low-temperature synthesized samples, indicating the presence of cobalt metallic clusters, and this is supported by the optical studies. For the high-temperature sintered samples one obtains paramagnetism. The optical studies reveal the presence of Co2+ ions in the tetrahedral sites indicating proper doping. Interestingly, the films deposited by laser ablation from the paramagnetic target showed room temperature ferromagnetism. It appears that the magnetic nature of this system is process dependent.

Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein

Acyl carrier protein (ACIP) plays a central role in many metabolic processes inside the cell, and almost 4% of the total enzymes inside the cell require it as a cofactor. Here, we report self-acylation properties in ACPs from Plasmodium falciparum and Brassica napus that are essential components of type II fatty acid biosynthesis (FAS II), disproving the existing notion that this phenomenon is restricted only to ACPs involved in polyketide biosynthesis. We also provide strong evidence to suggest that catalytic self-acylation is intrinsic to the individual ACP. Mutational analysis of these ACPs revealed the key residue(s) involved in this phenomenon. We also demonstrate that these FAS 11 ACPs exhibit a high degree of selectivity for self-acylation employing only dicarboxylic acids as substrates. A plausible mechanism for the self-acylation reaction is also proposed.

Observation of a thermally reversing window in bulk Ge15Te85-xInx glasses

Alternating differential scanning calorimetry measurements have been undertaken on the Ge15Te85-xInx (1 <= x <= 11) series of glasses. It is found that there is a marginal decrease in the glass transition temperature (T-g) in the composition range 1 <= x <= 3. Above x = 3, a monotonic increase is seen in T-g which indicates a continuous build-up in network connectivity and absence of any nanophase separation. The non-reversing heat flow (Delta H-NR) has been found to exhibit a broad trough between the compositions x = 3 and 7, which clearly indicates the presence of a thermally reversing window in Ge15Te85-xInx glasses in the composition range 3 <= x <= 7.

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

In uplink OFDMA, carrier frequency offsets (CFO) and/or timing offsets (TO) of other users with respect to a desired user can cause multiuser interference (MUI). In practical uplink OFDMA systems (e.g., IEEE 802.16e standard), effect of this MUI is made acceptably small by requiring that frequency/timing alignment be achieved at the receiver with high precision (e.g., CFO must be within 1 % of the subcarrier spacing and TO must be within 1/8th of the cyclic prefix duration in IEEE 802.16e), which is realized using complex closed-loop frequency/timing correction between the transmitter and the receiver. An alternate open-loop approach to handle the MUI induced by large CFOs and TOs is to employ interference cancellation techniques at the receiver. In this paper, we first analytically characterize the degradation in the average output signal-to-interference ratio (SIR) due to the combined effect of large CFOs and TOs in uplink OFDMA. We then propose a parallel interference canceller (PIC) for the mitigation of interference due to CFOs and TOs in this system. We show that the proposed PIC effectively mitigates the performance loss due to CFO/TO induced interference in uplink OFDMA.

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.

Simplified theory of optical nonlinearities in spin-polarized bulk GaAs

Apart from their intrinsic physical interest, spin-polarized many-body effects are expected to be important to the working of spintronic devices. A vast literature exists on the effects of a spin-unpolarized electron-hole plasma on the optical properties of a semiconductor. Here, we include the spin degree of freedom to model optical absorption of circularly polarized light by spin-polarized bulk GaAs. Our model is easy to implement and does not require elaborate numerics, since it is based on the closed-form analytical pair-equation formula that is valid in 3d. The efficacy of our approach is demonstrated by a comparison with recent experimental data.

Characterization of the interaction of lipid A and lipopolysaccharide with human serum albumin: implications for an endotoxin carrier function for albumin

The interactions of lipid A and lipopolysaccharide (LPS) with human serum albumin (HSA) were examined using fluorescence methods. Lipid A binds HSA with a stoichiometry of 2:1 with dissociation constants of 1.0 µM and 6.0 µM for the high- and low-affinity interactions, respectively. Lipid A displaces HSA-bound dansylsarcosine competitively, but not HSA-bound warfarin, suggesting that domain III-A, and not domain 11-A, is a lipid A binding site. Domain I does not contribute a site for lipid A. Based on these data, and the structural similarity between subdomains III-A and III-B, it is proposed that these two regions of HSA represent the high- and low-affinity sites of interaction of lipid A. Whole LPS also binds HSA, displacing dansylsarcosine, and its lipid A moiety appears to be the interaction site. However, there are differences between LPS and free lipid A. Polymyxin B forms ternary complexes with LPS bound to HSA, suggesting that the regions on LPS recognized by HSA and polymyxin B are different. The observed affinity of lipid A for HSA and mass action effects due to its abundance in the circulation would imply a major LPS carrier function for HSA.

Simplified theory of optical nonlinearities in spin-polarized bulk GaAs

Apart from their intrinsic physical interest, spin-polarized many-body effects are expected to be important to the working of spintronic devices. A vast literature exists on the effects of a spin-unpolarized electron-hole plasma on the optical properties of a semiconductor. Here, we include the spin degree of freedom to model optical absorption of circularly polarized light by spin-polarized bulk GaAs. Our model is easy to implement and does not require elaborate numerics, since it is based on the closed-form analytical pair-equation formula that is valid in 3d. The efficacy of our approach is demonstrated by a comparison with recent experimental data.

Backbone chemical shift assignments of the acyl-acyl carrier protein intermediates of the fatty acid biosynthesis pathway of Plasmodium falciparum

We report the backbone chemical shift assignments of the acyl-acyl carrier protein (ACP) intermediates of the fatty acid biosynthesis pathway of Plasmodium falciparum. The acyl-ACP intermediates butyryl (C4), -octanoyl (C8), -decanoyl (C10), -dodecanoyl (C12) and -tetradecanoyl (C14)-ACPs display marked changes in backbone HN, Cα and Cβ chemical shifts as a result of acyl chain insertion into the hydrophobic core. Chemical shift changes cast light on the mechanism of expansion of the acyl carrier protein core.

Structural Insights into the Acyl Intermediates of the Plasmodium falciparum Fatty Acid Synthesis Pathway THE MECHANISM OF EXPANSION OF THE ACYL CARRIER PROTEIN CORE

Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in C-alpha and C-beta of Ser-37 in tetradecanoyl-ACP. C-13, N-15-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C-8)- and dodecanoyl (C-12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C-14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pK(a) value for the carboxylate, similar to 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.

Solution structures of conformationally equilibrium forms of holo-acyl carrier protein (PfACP) from Plasmodium falciparum provides insight into the mechanism of activation of ACPs

Acyl Carrier Protein (ACP) from the malaria parasite, Plasmodium falciparum (PfACP) in its holo form is found to exist in two conformational states in solution. Unique 3D solution structures of holo-PfACP have been determined for both equilibrium conformations, using high-resolution NMR methods. Twenty high-resolution solution structures for each of the two forms of holo-PfACP have been determined on the basis of 1226 and 1218 unambiguously assigned NOEs (including NOEs between 4 '-phosphopantetheine prosthetic group (4 '-PP) and protein), 55 backbone dihedral angles and 26 hydrogen bonds. The atomic rmsd values of the determined structures of two equilibrium forms, about the mean coordinates of the backbone and heavy atoms, are 0.48 +/- 0.09 and 0.92 +/- 0.10 and 0.49 +/- 0.08 and 0.97 +/- 0.11 angstrom, respectively. The interaction of 4 '-PP with the polypeptide backbone is reported here for the first time for any of the ACPs. The structures of holo-PfACP consist of three well-defined helices that are tightly packed. The structured regions of the molecule are stabilized by extensive hydrophobic interactions. The difference between the two forms arises from a reorientation of the 4 '-PP group. The enthalpy difference between the two forms, although small, implies that a conformational switch is essential for the activation of holo-ACP. Sequence and structures of holo-PfACP have been compared with those of the ACPs from type I and type II fatty acid biosynthesis pathways (FAS), in particular with the ACP from rat and the butyryl-ACP from E. coli. The PfACP structure, thus determined has several novel features hitherto not seen in other ACPs.

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from R falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and R falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.

Simplified theory of carrier back-scattering in semiconducting carbon nanotubes: A Kane's model approach

We present a simplified yet analytical formulation of the carrier backscattering coefficient for zig-zag semiconducting single walled carbon nanotubes under diffusive regime. The electron-phonon scattering rate for longitudinal acoustic, optical, and zone-boundary phonon emissions for both inter- and intrasubband transition rates have been derived using Kane's nonparabolic energy subband model.The expressions for the mean free path and diffusive resistance have been formulated incorporating the aforementioned phonon scattering. Appropriate overlap function in Fermi's golden rule has been incorporated for a more general approach. The effect of energy subbands on low and high bias zones for the onset of longitudinal acoustic, optical, and zone-boundary phonon emissions and absorption have been analytically addressed. 90% transmission of the carriers from the source to the drain at 400 K for a 5 mu m long nanotube at 105 V m(-1) has been exhibited. The analytical results are in good agreement with the available experimental data. (c) 2010 American Institute of Physics.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.