Acidic pH induced STM1485 gene is essential for intracellular replication of Salmonella

During the course of infection, Salmonella has to face several potentially lethal environmental conditions, one such being acidic pH. The ability to sense and respond to the acidic pH is crucial for the survival and replication of Salmonella. The physiological role of one gene (STM1485) involved in this response, which is upregulated inside the host cells (by 90- to 113-fold) is functionally characterized in Salmonella pathogenesis. In vitro, the DSTM1485 neither exhibited any growth defect at pH 4.5 nor any difference in the acid tolerance response. The DSTM1485 was compromised in its capacity to proliferate inside the host cells and complementation with STM1485 gene restored its virulence. We further demonstrate that the surface translocation of Salmonella pathogenicity island-2 (SPI-2) encoded translocon proteins, SseB and SseD were reduced in the DSTM1485. The increase in co-localization of this mutant with lysosomes was also observed. In addition, the DSTM1485 displayed significantly reduced competitive indices (CI) in spleen, liver and mesenteric lymph nodes in murine typhoid model when infected by intra-gastric route. Based on these results, we conclude that the acidic pH induced STM1485 gene is essential for intracellular replication of Salmonella.

Electrical breakdown of carbon nanotube devices and the predictability of breakdown position

We have investigated electrical transport properties of long (>10 mu m) multiwalled carbon nanotubes (NTs) by dividing individuals into several segments of identical length. Each segment has different resistance because of the random distribution of defect density in an NT and is corroborated by Raman studies. Higher is the resistance, lower is the current required to break the segments indicating that breakdown occurs at the highly resistive segment/site and not necessarily at the middle. This is consistent with the one-dimensional thermal transport model. We have demonstrated the healing of defects by annealing at moderate temperatures or by current annealing. To strengthen our mechanism, we have carried out electrical breakdown of nitrogen doped NTs (NNTs) with diameter variation from one end to the other. It reveals that the electrical breakdown occurs selectively at the narrower diameter region. Overall, we believe that our results will help to predict the breakdown position of both semiconducting and metallic NTs. Copyright 2012 Author(s). This article is distributed under a Creative Commons Attribution 3.0 Unported License. http://dx.doi.org/10.1063/1.4720426]

Non-monotonic, distance-dependent relaxation of water in reverse micelles: Propagation of surface induced frustration along hydrogen bond networks

Layer-wise, distance-dependent orientational relaxation of water confined in reverse micelles (RM) is studied using theoretical and computational tools. We use both a newly constructed ``spins on a ring'' (SOR) Ising-type model (with Shore-Zwanzig rotational dynamics) and atomistic simulations with explicit water. Our study explores the effect of reverse micelle size and role of intermolecular correlations, compromised by the presence of a highly polar surface, on the distance (from the interface) dependence of water relaxation. The ``spins on a ring'' model can capture some aspects of distance dependence of relaxation, such as acceleration of orientational relaxation at intermediate layers. In atomistic simulations, layer-wise decomposition of hydrogen bond formation pattern clearly reveals that hydrogen bond arrangement of water at a certain distance away from the surface can remain frustrated due to the interaction with the polar surface head groups. This layer-wise analysis also reveals the presence of a non-monotonic slow relaxation component which can be attributed to this frustration effect and which is accentuated in small to intermediate size RMs. For large size RMs, the long time component decreases monotonically from the interface to the interior of the RMs with slowest relaxation observed at the interface. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4732095]

Interaction of nucleic acids with carbon nanotubes and dendrimers

Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

Temperature Dependent Photoluminescence Studies in Hg0.2Cd0.8Te Nanorods Synthesized by Solvothermal Method

Hg0.2Cd0.8Te nanorods were synthesized via solvothermal route using an air-stable Na2Te-O-3. The structural and morphological studies were done by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The diameters of the nanorods were found to be 20-50 nm. The growth of the nanorods were facilitated due to the use of CTAB as surfactant. The temperature dependent photoluminescence (PL) studies between 10-300 K show three prominent PL bands in 0.5-0.7 eV and are attributed to defect centers. The features like temperature independent peak energy and quite sensitive PL intensity which shows a thermal quenching behavior indicate that the defects are related to the compositional disorder.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Geometrically non-linear dynamics of composite four-bar mechanisms

This work intends to demonstrate the importance of a geometrically nonlinear cross-sectional analysis of certain composite beam-based four-bar mechanisms in predicting system dynamic characteristics. All component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically non-linear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and non-linear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional non-linearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the non-linear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the non-linear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict multi-body dynamic responses more quickly and accurately than would otherwise be possible. The analysis methodology can be viewed as a three-step procedure: First, the cross-sectional properties of each bar of the mechanism is determined analytically based on an asymptotic procedure, starting from Classical Laminated Shell Theory (CLST) and taking advantage of its thin strip geometry. Second, the dynamic response of the non-linear, flexible four-bar mechanism is simulated by treating each bar as a 1-D beam, discretized using finite elements, and employing energy-preserving and -decaying time integration schemes for unconditional stability. Finally, local 3-D deformations and stresses in the entire system are recovered, based on the 1-D responses predicted in the previous step. With the model, tools and procedure in place, we identify and investigate a few four-bar mechanism problems where the cross-sectional non-linearities are significant in predicting better and critical system dynamic characteristics. This is carried out by varying stacking sequences (i.e. the arrangement of ply orientations within a laminate) and material properties, and speculating on the dominating diagonal and coupling terms in the closed-form non-linear beam stiffness matrix. A numerical example is presented which illustrates the importance of 2-D cross-sectional non-linearities and the behavior of the system is also observed by using commercial software (I-DEAS + NASTRAN + ADAMS). (C) 2012 Elsevier Ltd. All rights reserved.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

Structure of a carbon nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report a microscopic picture of the carbon nanotube (6,5)-dendrimer complex for PAMAM dendrimers of generations 2 to 4. We study the compact wrapping conformations of the dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. A high degree of wrapping for the non-protonated dendrimer is observed as compared to the protonated dendrimer. For comparison, we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with the nanotube. The results of the distance of closest approach as well as the number of close contacts between the nanotube and the dendrimer reveal that the PAMAM dendrimer interacts strongly as compared to the PETIM dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on the CNT will make it soluble and the dendrimer can act as an efficient dispersing agent for the nanotubes.

Interaction of CdSe and ZnO nanocrystals with electron-donor and -acceptor molecules

Interaction of CdSe and ZnO nanocrystals with electron-donating tetrathiafulvalene (TTF) and electron-withdrawing tetracyanoethylene (TCNE) has been investigated. Isothermal calorimetry shows CdSe nanocrystals interact more strongly with TCNE than TTF. Interaction of larger CdSe nanocrystals with TCNE causes a red-shift in the band-edge emission because of agglomeration, while the smaller CdSe nanocrystals, exhibiting stronger interaction with TCNE modify the optical gap of the nanocrystal. Luminescence of CdSe gets quenched sharply after addition of both TTF and TCNE. ZnO nanocrystals also exhibit luminescence quenching to lesser extent. Defect-emission of ZnO nanocrystals gets red or blue-shifted after interaction with TTF or TCNE respectively. (C) 2012 Elsevier B. V. All rights reserved.

Wave propagation in a porous composite beam: Porosity determination, location and quantification

A wave-based method is developed to quantify the defect due to porosity and also to locate the porous regions, in a composite beam-type structure. Wave propagation problem for a porous laminated composite beam is modeled using spectral finite element method (SFEM), based on the modified rule of mixture approach, which is used to include the effect of porosity on the stiffness and density of the composite beam structure. The material properties are obtained from the modified rule of mixture model, which are used in a conventional SFEM to develop a new model for solving wave propagation problems in porous laminated composite beam. The influence of the porosity content on the group speed and also the effect of variation in theses parameters on the time responses are studied first, in the forward problem. The change in the time responses with the change in the porosity of the structure is used as a parameter to find the porosity content in a composite beam. The actual measured response from a structure and the numerically obtained time responses are used for the estimation of porosity, by solving a nonlinear optimization problem. The effect of the length of the porous region (in the propagation direction), on the time responses, is studied. The damage force indicator technique is used to locate the porous region in a beam and also to find its length, using the measured wave propagation responses. (C) 2012 Elsevier Ltd. All rights reserved.

A simple method of synthesis and optical properties of Mn doped ZnO nanocups

A combination of chemical and thermal annealing techniques has been employed to synthesize a rarely reported nanocup structure of Mn doped ZnO with good yield. Nanocup structures are obtained by thermally annealing the powder samples consisting of nanosheets, synthesized chemically at room temperature, isochronally in a furnace at 200-500 degrees C temperature range for 2 h. Strong excitonic absorption in the UV and photoluminescence (PL) emission in UV-visible regions are observed in all the samples at room temperature. The sample obtained at 300 degrees C annealing temperature exhibits strong PL emission in the UV due to near-band-edge emission along with very week defect related emissions in the visible regions. The synthesized samples have been found to be exhibiting stable optical properties for 10 months which proved the unique feature of the presented technique of synthesis of nanocup structures. (C) 2012 Elsevier B.V. All rights reserved.

Low-thermal-budget solution processing of thin films of zinc ferrite and other complex oxides

Further miniaturization of magnetic and electronic devices demands thin films of advanced nanomaterials with unique properties. Spinel ferrites have been studied extensively owing to their interesting magnetic and electrical properties coupled with stability against oxidation. Being an important ferrospinel, zinc ferrite has wide applications in the biological (MRI) and electronics (RF-CMOS) arenas. The performance of an oxide like ZnFe2O4 depends on stoichiometry (defect structure), and technological applications require thin films of high density, low porosity and controlled microstructure, which depend on the preparation process. While there are many methods for the synthesis of polycrystalline ZnFe2O4 powder, few methods exist for the deposition of its thin films, where prolonged processing at elevated temperature is not required. We report a novel, microwave-assisted, low temperature (<100°C) deposition process that is conducted in the liquid medium, developed for obtaining high quality, polycrystalline ZnFe2O4 thin films on technologically important substrates like Si(100). An environment-friendly solvent (ethanol) and non-hazardous oxide precursors (β-diketonates of Zn and Fe in 1:2 molar ratio), forming a solution together, is subjected to irradiation in a domestic microwave oven (2.45 GHz) for a few minutes, leading to reactions which result in the deposition of ZnFe2O4 films on Si (100) substrates suspended in the solution. Selected surfactants added to the reactant solution in optimum concentration can be used to control film microstructure. The nominal temperature of the irradiated solution, i.e., film deposition temperature, seldom exceeds 100°C, thus sharply lowering the thermal budget. Surface roughness and uniformity of large area depositions (50x50 mm2) are controlled by tweaking the concentration of the mother solution. Thickness of the films thus grown on Si (100) within 5 min of microwave irradiation can be as high as several microns. The present process, not requiring a vacuum system, carries a very low thermal budget and, together with a proper choice of solvents, is compatible with CMOS integration. This novel solution-based process for depositing highly resistive, adherent, smooth ferrimagnetic films on Si (100) is promising to RF engineers for the fabrication of passive circuit components. It is readily extended to a wide variety of functional oxide films.

Shear bands mediate cavitation in brittle metallic glasses

Recent experimental studies have revealed nanoscale cavities and periodic corrugations on the fracture surfaces of brittle metallic glasses. How such cavitation in these materials leads to brittle failure remains unclear. Here we show, using atomistic and continuum finite element simulations, that a shear band can mediate cavity nucleation and coalescence owing to plastic flow confinement caused by material softening. This leads to brittle fracture as cavities nucleate and coalesce within a shear band, causing the crack to extend along it. (c) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Application of a modified jogged-screw model for creep of titanium aluminides: evaluation of the key substructural parameters

A modification of the jogged-screw model has been adopted recently by the authors to explain observations of 1/2[110]-type jogged-screw dislocations in equiaxed Ti-48Al under creep conditions. The aim of this study has been to verify and validate the parameters and functional dependencies that have been assumed in this previous work. The original solution has been reformulated to take into account the finite length of the moving jog. This is a better approximation of the tall jog. The substructural model parameters have been further investigated in light of the Finite Length Moving Line (FLML) source approximation. The original model assumes that the critical jog height (beyond which the jog is not dragged) is inversely proportional to the applied stress. By accounting for the fact that there are three competing mechanisms (jog dragging, dipole dragging, dipole bypass) possible, we can arrive at a modified critical jog height. The critical jog height was found to be more strongly stress dependent than assumed previously. The original model assumes the jog spacing to be invariant over the stress range. However, dynamic simulation using a line tension model has shown that the jog spacing is inversely proportional to the applied stress. This has also been confirmed by TEM measurements of jog spacings over a range of stresses. Taylor's expression assumed previously to provide the dependence of dislocation density on the applied stress, has now been confirmed by actual dislocation density measurements. Combining all of these parameters and dependencies, derived both from experiment and theory, leads to an excellent prediction of creep rates and stress exponents. The further application of this model to other materials, and the important role of atomistic and dislocation dynamics simulations in its continued development is also discussed.