Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum

The beta-hydroxyacyl-acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ is available in hexameric (active) and dimeric (inactive) forms. However, PfFabZ has not been crystallized with any bound inhibitors until now. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of four of these complexes. This is the first report on any FabZ enzyme with active site inhibitors that interact directly with the catalytic residues. Inhibitor binding not only stabilized the substrate binding loop but also revealed that the substrate binding tunnel has an overall shape of ``U''. In the crystal structures, residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed. Thus, Phe169, merely by changing its side chain conformation, appears to be controlling the length of the tunnel to make it suitable for accommodating longer substrates. The volume of the substrate binding tunnel is determined by the sequence as well as by the conformation of the substrate binding loop region and varies between organisms for accommodating fatty acids of different chain lengths. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. (C) 2011 Elsevier Inc. All rights reserved.

Temperature dependence of the energy gap and free carrier absorption in bulk InAs0.05Sb0.95 single crystals

Temperature dependence of the energy gap and free carrier absorption in a high-quality InAs0.05Sb0.95 single crystal was studied between 90 K and 430 K through the absorption spectra. At this alloy concentration, the room-temperature energy gap was measured to be 0.15 eV. Varshni- and the Bose–Einstein-type fit parameters were obtained from the measured temperature dependence of the energy gap, and the latter gave the zero-temperature gap to be 0.214 eV. It was found that although Weider’s empirical formula for the dependence of the energy gap on temperature and the alloy concentration agrees with the value of the gap at room temperature, it is inaccurate in describing its temperature dependence. From the free carrier absorption measurements, the phonon limited cross section of 7.35×10−16 cm2 at 15 μm was deduced at room temperature.

Macromolecular Transport Through Porous Arterial Walls

Arteries are heterogeneous, composite structures that undergo large cyclic deformations during blood transport. Presence, build-up and consequent rupture of blockages in blood vessels, called atherosclerotic plaques, lead to disruption in the blood flow that can eventually be fatal. Abnormal lipid profile and hypertension are the main risk factors for plaque progression. Treatments span from pharmacological methods, to minimally invasive balloon angioplasty and stent procedures, and finally to surgical alternatives. There is a need to understand arterial disease progression and devise methods to detect, control, treat and manage arterial disease through early intervention. Local delivery through drug eluting stents also provide an attractive option for maintaining vessel integrity and restoring blood flow while releasing controlled amount of drug to reduce and alleviate symptoms. Development of drug eluting stents is hence interesting albeit challenging because it requires an integration of knowledge of mechanical properties with material transport of drug through the arterial wall to produce a desired biochemical effect. Although experimental models are useful in studying such complex multivariate phenomena, numerical models of mass transport in the vessel have proved immensely useful to understand and delineate complex interactions between chemical species, physical parameters and biological variables. The goals of this review are to summarize literature based on studies of mass transport involving low density lipoproteins in the arterial wall. We also discuss numerical models of drug elution from stents in layered and porous arterial walls that provide a unique platform that can be exploited for the design of novel drug eluting stents.

BER Analysis of Uplink OFDMA in the Presence of Carrier Frequency and Timing Offsets on Rician Fading Channels

In orthogonal frequency-division multiple access (OFDMA) on the uplink, the carrier frequency offsets (CFOs) and/or timing offsets (TOs) of other users with respect to a desired user can cause multiuser interference (MUI). Analytically evaluating the effect of these CFO/TO-induced MUI on the bit error rate (BER) performance is of interest. In this paper, we analyze the BER performance of uplink OFDMA in the presence of CFOs and TOs on Rician fading channels. A multicluster multipath channel model that is typical in indoor/ultrawideband and underwater acoustic channels is considered. Analytical BER expressions that quantify the degradation in BER due to the combined effect of both CFOs and TOs in uplink OFDMA with M-state quadrature amplitude modulation (QAM) are derived. Analytical and simulation BER results are shown to match very well. The derived BER expressions are shown to accurately quantify the performance degradation due to nonzero CFOs and TOs, which can serve as a useful tool in OFDMA system design.

Investigation of biodegradable and biocompatible castor oil poly(mannitol-citric-sebacate) polyester as a drug carrier

Castor oil-based poly(mannitol-citric sebacate) was synthesized by simple, catalyst-free melt condensation process using monomers having potential to be metabolized in vivo. The polymer was characterized using various techniques and the tensile and hydration properties of the polymers were also determined. The biocompatibility of the polymer was tested using human foreskin fibroblasts cells. The in vitro degradation studies show that the time for complete degradation of the polymer was more than 21 days. The usage of castor oil polyester as a drug carrier was analysed by doping the polymer with 5-fluorouracil model drug and the release rate was studied by varying the percentage loading of drugs and the pH of the PBS solution medium. The cumulative drug-release profiles exhibited a biphasic release with an initial burst release and cumulative 100% release within 42 h. To understand the role of the polymer as a drug carrier in the release behaviour, drug-release studies were conducted with another drug, isoniazid. The release behaviour of isoniazid drug from the same polymer matrix followed an nth order kinetic model and 100% cumulative release was achieved after 12 days. The variation in the release behaviour for two model drugs from the same polymer matrix suggests a strong interaction between the polymer and the drug molecule.

Carrier-transport studies of III-nitride/Si3N4/Si isotype heterojunctions

GaN/Si3N4/n-Si and InN/Si3N4/n-Si heterojunctions (HJs) were fabricated using plasma-assisted molecular beam epitaxy for a comparison study. Single-crystalline wurtzite structures of GaN and InN epilayers were confirmed by high-resolution X-ray diffraction and thickness of ultrathin Si3N4 layer was measured by transmission electron microscopy. n-GaN/Si3N4/n-Si HJs show diode-like rectifying current-voltage (I-V) characteristic, while n-InN/Si3N4/n-Si HJs show symmetric nonlinear I-V behavior. The I-V characteristics of both HJs were discussed in terms of the band diagram of HJs and the carrier transport mechanism. The activation energies of carrier conduction were estimated to be similar to 29 meV for GaN/Si3N4/Si and similar to 95 meV for InN/Si3N4/Si HJs. (C) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Cyclodextrin functionalized magnetic iron oxide nanocrystals: a host-carrier for magnetic separation of non-polar molecules and arsenic from aqueous media

A single-step magnetic separation procedure that can remove both organic pollutants and arsenic from contaminated water is clearly a desirable goal. Here we show that water dispersible magnetite nanoparticles prepared by anchoring carboxymethyl-beta-cyclodextrin (CMCD) cavities to the surface of magnetic nanoparticles are suitable host carriers for such a process. Monodisperse, 10 nm, spherical magnetite, Fe3O4, nanocrystals were prepared by the thermal decomposition of FeOOH. Trace amounts of antiferromagnet, FeO, present in the particles provides an exchange bias field that results in a high superparamagnetic blocking temperature and appreciable magnetization values that facilitate easy separation of the nanocrystals from aqueous dispersions on application of modest magnetic fields. We show here that small molecules like naphthalene and naphthol can be removed from aqueous media by forming inclusion complexes with the anchored cavities of the CMCD-Fe3O4 nanocrystals followed by separation of the nanocrystals by application of a magnetic field. The adsorption properties of the iron oxide surface towards As ions are unaffected by the CMCD capping so it too can be simultaneously removed in the separation process. The CMCD-Fe3O4 nanocrystals provide a versatile platform for magnetic separation with potential applications in water remediation.

Analysis of Conformational Variation in Macromolecular Structural Models

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.

Designing carboxymethyl cellulose based layer-by-layer capsules as a carrier for protein delivery

Stable hollow microcapsules composed of sodium carboxymethyl cellulose (CMC) and poly (allylamine hydrochloride) (PAH) were produced by layer-by-layer adsorption of polyelectrolytes onto CaCO 3 microparticles. Subsequently the core was removed by addition of chelating agents for calcium ions. Zeta potential studies showed charge reversal with deposition of successive polyelectrolyte layers, indicating that the alternate electrostatic adsorption of polyelectrolytes of opposite charge was successfully achieved. The size and surface morphology of the capsules was characterized by various microscopy techniques. The pH responsive loading behavior was elucidated by confocal laser scanning microscopy (CLSM) studies using fluorescence labeled dextran (FITC-dextran) and labeled BSA (FITC-BSA). CLSM images confirmed the open (pH ≤ 6) and closed state (pH ≥ 7) of the capsules. A model drug bovine serum albumin (BSA) was spontaneously loaded below its isoelectric point into hollow microcapsules, where BSA is positively charged. The loading of the BSA into the microcapsules was found to be dependent on the feeding concentration and pH of the medium. 65 of the loaded BSA was released over 7h of which about 34 was released in the first hour. These findings demonstrate that (CMC/PAH) 2 hollow capsules can be further exploited as a potential drug delivery system.

Effect of carrier concentration of InN on the transport behavior of InN/GaN heterostructure based Schottky junctions

We present the study involving the dependence of carrier concentration of InN films, grown on GaN templates using the plasma assisted molecular beam epitaxy system, on growth temperature. The influence of InN carrier concentration on the electrical transport behavior of InN/GaN heterostructure based Schottky junctions is also discussed. The optical absorption edge of InN film was found to be strongly dependent on carrier concentration, and was described by Kane's k.p model, with non-parabolic dispersion relation for carrier in the conduction band. The position of the Fermi-level in InN films was modulated by the carrier concentration in the InN films. The barrier height of the heterojunctions as estimated from I-V characteristic was also found to be dependent on the carrier concentration of InN. (C) 2012 Elsevier Ltd. All rights reserved.

High field carrier transport in graphene: Insights from fast current transient

In this work, we observe gate tunable negative differential conductance (NDC) and current saturation in single layer and bilayer graphene transistor at high source-drain field, which arise due to the interplay among (1) self-heating, (2) hot carrier injection, and (3) drain induced minority carrier injection. The magnitude of the NDC is found to be reduced for a bilayer, in agreement with its weaker carrier-optical phonon coupling and less efficient hot carrier injection. The contributions of different mechanisms to the observed results are decoupled through fast transient measurements with nanosecond resolution. The findings provide insights into high field transport in graphene. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4754103]

Probing ultrafast carrier dynamics, nonlinear absorption and refraction in core-shell silicon nanowires

We investigate the relaxation dynamics of photogenerated carriers in silicon nanowires consisting of a crystalline core and a surrounding amorphous shell, using femtosecond time-resolved differential reflectivity and transmission spectroscopy at 3.15 eV and 1.57 eV photon energies. The complex behaviour of the differential transmission and reflectivity transients is the mixed contributions from the crystalline core and the amorphous silicon on the nanowire surface and the substrate where competing effects of state-filling and photoinduced absorption govern the carrier dynamics. Faster relaxation rates are observed on increasing the photogenerated carrier density. Independent experimental results on crystalline silicon-on-sapphire (SOS) help us in separating the contributions from the carrier dynamics in crystalline core and the amorphous regions in the nanowire samples. Further, single-beam z-scan nonlinear transmission experiments at 1.57 eV in both open- and close-aperture configurations yield two-photon absorption coefficient beta (similar to 3 cm/GW) and nonlinear refraction coefficient gamma (-2.5 x 10 (-aEuro parts per thousand 4) cm(2)/GW).

MODELING HETEROSTRUCTURES WITH SCHRODINGER-POISSON-NAVIER ITERATIVE SCHEMES, EFFECT OF CARRIER CHARGE, AND INFLUENCE OF ELECTROMECHANICAL COUPLING

This paper presents a detailed investigation of the erects of piezoelectricity, spontaneous polarization and charge density on the electronic states and the quasi-Fermi level energy in wurtzite-type semiconductor heterojunctions. This has required a full solution to the coupled Schrodinger-Poisson-Navier model, as a generalization of earlier work on the Schrodinger-Poisson problem. Finite-element-based simulations have been performed on a A1N/GaN quantum well by using both one-step calculation as well as the self-consistent iterative scheme. Results have been provided for field distributions corresponding to cases with zero-displacement boundary conditions and also stress-free boundary conditions. It has been further demonstrated by using four case study examples that a complete self-consistent coupling of electromechanical fields is essential to accurately capture the electromechanical fields and electronic wavefunctions. We have demonstrated that electronic energies can change up to approximately 0.5 eV when comparing partial and complete coupling of electromechanical fields. Similarly, wavefunctions are significantly altered when following a self-consistent procedure as opposed to the partial-coupling case usually considered in literature. Hence, a complete self-consistent procedure is necessary when addressing problems requiring more accurate results on optoelectronic properties of low-dimensional nanostructures compared to those obtainable with conventional methodologies.