Sensitivity of nucleation phenomena on range of interaction potential

Theoretical and computational investigations of nucleation have been plagued by the sensitivity of the phase diagram to the range of the interaction potential. As the surface tension depends strongly on the range of interaction potential and as the classical nucleation theory (CNT) predicts the free energy barrier to be directly proportional to the cube of the surface tension, one expects a strong sensitivity of nucleation barrier to the range of the potential; however, CNT leaves many aspects unexplored. We find for gas-liquid nucleation in Lennard-Jones system that on increasing the range of interaction the kinetic spinodal (KS) (where the mechanism of nucleation changes from activated to barrierless) shifts deeper into the metastable region. Therefore the system remains metastable for larger value of supersaturation and this allows one to explore the high metastable region without encountering the KS. On increasing the range of interaction, both the critical cluster size and pre-critical minima in the free energy surface of kth largest cluster, at respective kinetic spinodals, shift towards smaller cluster size. In order to separate surface tension contribution to the increase in the barrier from other non-trivial factors, we introduce a new scaling form for surface tension and use it to capture both the temperature and the interaction range dependence of surface tension. Surprisingly, we find only a weak non-trivial contribution from other factors to the free energy barrier of nucleation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3685835]

PAMAM Dendrimer-Drug Interactions: Effect of pH on the Binding and Release Pattern

Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine (PAMAM) dendrimer using the docking method. We have computed the potential of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with drug molecules using umbrella sampling. From our calculated PMF values, we observe that soluble drugs (Sal and Ala) have lower energy barriers than insoluble drugs (Pbz and Prim). The order of ease of release pattern for these drugs from G5 protonated PAMAM dendrimer was found to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs (Prim and Pbz), because of larger size, we observe much nonpolar contribution, and thus, their larger energy barriers can be reasoned to van der Waals contribution. From the hydrogen bonding analysis of the four PAMAM drug complexes under study, we found intermolecular hydrogen bonding to show less significant contribution to the free energy barrier. Another interesting feature appears while calculating the PMF profile of G5NP (nonprotonated)-PAMAM Pbz and G5NP (nonprotonated)-PAMAM-Sal complex. The PMF was found to be less when the drug is bound to nonprotonated dendrimer compared to the protonated dendrimer. Our results suggest that encapsulation of the drug molecule into the host PAMAM dendrimer should be carried out at higher pH values (near pH 10). When such complex enters the human body, the pH is around 7.4 and at that physiological pH, the dendrimer holds the drug tightly. Hence the release of drug can occur at a controlled rate into the bloodstream. Thus, our findings provide a microscopic picture of the encapsulation and controlled release of drugs in the case of dendrimer-based host-guest systems.

Deorphanization of Malonyl CoA:ACP Transacylase Drug Target in Plasmodium falciparum (PfFabD) Using Bacterial Antagonists: A Piggyback' Approach for Antimalarial Drug Discovery

Quest for new drug targets in Plasmodium sp. has underscored malonyl CoA:ACP transacylase (PfFabD) of fatty acid biosynthetic pathway in apicoplast. In this study, a piggyback approach was employed for the receptor deorphanization using inhibitors of bacterial FabD enzymes. Due to the lack of crystal structure, theoretical model was constructed using the structural details of homologous enzymes. Sequence and structure analysis has localized the presence of two conserved pentapeptide motifs: GQGXG and GXSXG and five key invariant residues viz., Gln109, Ser193, Arg218, His305 and Gln354 characteristic of FabD enzyme. Active site mapping of PfFabD using substrate molecules has disclosed the spatial arrangement of key residues in the cavity. As structurally similar molecules exhibit similar biological activities, signature pharmacophore fingerprints of FabD antagonists were generated using 0D-3D descriptors for molecular similarity-based cluster analysis and to correlate with their binding profiles. It was observed that antagonists showing good geometrical fitness score were grouped in cluster-1, whereas those exhibiting high binding affinities in cluster-2. This study proves important to shed light on the active site environment to reveal the hotspot for binding with higher affinity and to narrow down the virtual screening process by searching for close neighbors of the active compounds.

High sensitivity low field magnetically gated resistive switching in CoFe2O4/La0.66Sr0.34MnO3 heterostructure

The phenomenon of resistive switching (RS) has been demonstrated in several non-magnetic and some magnetic oxide systems, however the ``magnetic'' aspect of magnetic oxides has not been emphasized especially in terms of low field tunability. In our work, we examined the CoFe2O4/La0.66Sr0.34MnO3 all-magnetic oxide interface system for RS and discovered a very sharp (bipolar) transition at room temperature that can be gated with high sensitivity by low magnetic fields (similar to 0-100 mT). By using a number of characterizations, we show that this is an interface effect, which may open up interesting directions for manipulation of the RS phenomenon. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4707373]

Combining adiabatic and Hartmann-Hahn cross-polarization for sensitivity enhancement in solid state separated local field 2D-NMR experiments of partially ordered systems

In this Letter, we examine magnetization in double- and zero-quantum reservoirs of an ensemble of spin-1/2 nuclei and describe their role in determining the sensitivity of a class of separated local field NMR experiments based on Hartmann-Hahn cross-polarization. We observe that for the liquid crystal system studied, a large dilute spin-polarization, obtained initially by the use of adiabatic cross-polarization, can enhance the sensitivity of the above experiment. The signal enhancement factors, however, are found to vary and depend on the local dynamics. The experimental results have been utilized to obtain the local order-parameters of the system. (C) 2012 Elsevier B. V. All rights reserved.

Measurement of effective permeability of reinforcement mats using sensitivity analysis

A methodology using sensitivity analysis is proposed to measure the effective permeability which includes the interaction of the resin and the reinforcement. Initially, mold-filling experiments were performed at isothermal conditions on the test specimen and the positions of the flow front were tracked with time using a flow visualization method. Following this, mold-filling experiments were simulated using a commercial software to obtain the positions of the flow front with time at the process conditions used for experiments. Several iterations were performed using different trial values of the permeability until the experimentally tracked and simulated positions of the flow front with time were matched. Finally, the value of the permeability thus obtained was validated by comparing the positions obtained by performing the experiments at different process conditions with the positions obtained by simulating the experiments. In this study, woven roving and chopped strand mats of E-class glass fiber and unsaturated polyester resin were used for the experiments. From the results, it was found that the measured permeabilities were consistent with varying process conditions. POLYM. COMPOS., 2012. (c) 2012 Society of Plastics Engineers

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Sensitivity of polyvinylidene fluoride films to mechanical vibration modes and impact after optimizing stretching conditions

The β-phase of polyvinylidene fluoride (PVDF) is well known for its piezoelectric properties. PVDF films have been developed using solvent cast method. The films thus produced are in α-phase. The α-phase is transformed to piezoelectric β-phase when the film is hot-stretched with various different stretching factors at various different temperatures. The films are then characterized in terms of their mechanical properties and surface morphological changes during the transformation from α- to β-phases by using X-ray diffraction, differential scanning calorimeter, Raman spectra, Infrared spectra, tensile testing, and scanning electron microscopy. The films showed increased crystallinity with stretching at temperature up to 80°C. The optimum conditions to achieve β-phase have been discussed in detail. The fabricated PVDF sensors have been tested for free vibration and impact on plate structure, and its response is compared with conventional piezoelectric wafer type sensor. The resonant and antiresonant peaks in the frequency response of PVDF sensor match well with that of lead zirconate titanate wafer sensors. Effective piezoelectric properties and the variations in the frequency response spectra due to free vibration and impact loading conditions are reported. POLYM. ENG. SCI., 2012. © 2012 Society of Plastics Engineers.

Conformational Polymorphism in a Non-steroidal Anti-inflammatory Drug, Mefenamic Acid

For several years, the non-steroidal anti-inflammatory drug mefenamic acid, MA, has been known to exist as dimorphs (I and II). We report a new metastable polymorph (III) of MA obtained during attempted co-crystallization experiments and establish its stability relationship with existing forms. At elevated temperatures I and III convert to II, as evident from DSC experiments. On the basis of the lattice energy calculations in conjunction with thermal analysis, the stability order is proposed to be I > II > III at ambient conditions, whereas at elevated temperature the order is II > I > III. In either condition III is a metastable form and hence transforms to I at ambient conditions and to II at higher temperatures. Also we report the structural studies of a DMF solvate and a cytosine complex.

Monsoon sensitivity to aerosol direct radiative forcing in the community atmosphere model

Aerosol forcing remains a dominant uncertainty in climate studies. The impact of aerosol direct radiative forcing on Indian monsoon is extremely complex and is strongly dependent on the model, aerosol distribution and characteristics specified in the model, modelling strategy employed as well as on spatial and temporal scales. The present study investigates (i) the aerosol direct radiative forcing impact on mean Indian summer monsoon when a combination of quasi-realistic mean annual cycles of scattering and absorbing aerosols derived from an aerosol transport model constrained with satellite observed Aerosol Optical Depth (AOD) is prescribed, (ii) the dominant feedback mechanism behind the simulated impact of all-aerosol direct radiative forcing on monsoon and (iii) the relative impacts of absorbing and scattering aerosols on mean Indian summer monsoon. We have used CAM3, an atmospheric GCM (AGCM) that has a comprehensive treatment of the aerosol-radiation interaction. This AGCM has been used to perform climate simulations with three different representations of aerosol direct radiative forcing due to the total, scattering aerosols and black carbon aerosols. We have also conducted experiments without any aerosol forcing. Aerosol direct impact due to scattering aerosols causes significant reduction in summer monsoon precipitation over India with a tendency for southward shift of Tropical Convergence Zones (TCZs) over the Indian region. Aerosol forcing reduces surface solar absorption over the primary rainbelt region of India and reduces the surface and lower tropospheric temperatures. Concurrent warming of the lower atmosphere over the warm oceanic region in the south reduces the land-ocean temperature contrast and weakens the monsoon overturning circulation and the advection of moisture into the landmass. This increases atmospheric convective stability, and decreases convection, clouds, precipitation and associated latent heat release. Our analysis reveals a defining negative moisture-advection feedback that acts as an internal damping mechanism spinning down the regional hydrological cycle and leading to significant circulation changes in response to external radiative forcing perturbations. When total aerosol loading (both absorbing and scattering aerosols) is prescribed, dust and black carbon aerosols are found to cause significant atmospheric heating over the monsoon region but the aerosol-induced weakening of meridional lower tropospheric temperature gradient (leading to weaker summer monsoon rainfall) more than offsets the increase in summer-time rainfall resulting from the atmospheric heating effect of absorbing aerosols, leading to a net decrease of summer monsoon rainfall. Further, we have carried out climate simulations with globally constant AODs and also with the constant AODs over the extended Indian region replaced by realistic AODs. Regional aerosol radiative forcing perturbations over the Indian region is found to have impact not only over the region of loading but over remote tropical regions as well. This warrants the need to prescribe realistic aerosol properties in strategic regions such as India in order to accurately assess the aerosol impact.

Silver nanoparticles modified nanocapsules for ultrasonically activated drug delivery

Novel ultrasound-sensitive nanocapsules were designed via layer-by-layer assembly (LbL) of polyelectrolytes for remote activated release of biomolecules/drug. Nanocapsules embedded with silver nanoparticles in the walls were synthesized by alternate assembly of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on silica template followed by nanoparticle synthesis and subsequent template removal thus yielding nanocapsules. The silver NPs were synthesized in situ within the capsule walls under controlled conditions. The nanocapsules were found to be well dispersed and the silver NPs were evenly distributed within the shell. FITC-dextran permeated easily into the capsules containing silver NP's due to the pores generated during the formation of NP's. When the loaded nanocapsules were sonicated, the presence of the silver NPs in the shell structure led to rupturing of the shell into smaller fragments thus releasing the FITC-dextran. Such nanocapsules have the potential to be used as drug delivery vehicles and offer the scope for further development in the areas of modern medicine, material science, and biochemistry. (C) 2012 Elsevier B.V. All rights reserved.

Two orders of magnitude increase in metal piezoresistor sensitivity through nanoscale inhomogenization

Metal-based piezoresistive sensing devices could find a much wider applicability if their sensitivity to mechanical strain could be substantially improved. Here, we report a simple method to enhance the strain sensitivity of metal films by over two orders of magnitude and demonstrate it on specially designed microcantilevers. By locally inhomogenizing thin gold films using controlled electromigration, we have achieved a logarithmic divergence in the strain sensitivity with progressive microstructural modification. The enhancement in strain sensitivity could be explained using non-universal tunneling-percolation transport. We find that the Johnson noise limited signal-to-noise ratio is an order of magnitude better than silicon piezoresistors. This method creates a robust platform for engineering low resistance, high gauge factor metallic piezoresistors that may have profound impact on micro and nanoscale self-sensing technology. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4761817]

Tuning the Sensitivity of a Metal-Based Piezoresistive Sensor Using Electromigration

We report a simple method to enhance the piezoresistive sensitivity of a gold film by more than 30 times and demonstrate it using a microcantilever resonator. Our method depends on controlled electromigration that we use to tune the resistance and sensitivity of the piezoresistive sensor. We attribute the enhancement in strain sensitivity to the creation of an inhomogeneous conduction medium at a predefined location by directed and controlled electromigration. We understand this phenomenon with tunneling-percolation model, which was originally hypothesized to explain nonuniversal percolation behavior of composite materials. 2012-0174]

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

Near-infrared light-responsive graphene oxide composite multilayer capsules: a novel route for remote controlled drug delivery

A novel and simple route for near-infrared (NIR)-light controlled release of drugs has been demonstrated using graphene oxide (GO) composite microcapsules based on the unique optical properties of GO. Upon NIR-laser irradiation, the microcapsules were ruptured in a point-wise fashion due to local heating which in turn triggers the light-controlled release of the encapsulated anticancer drug doxorubicin (Dox) from these capsules.