Diffusion of pentane isomers in faujasite-type zeolites : NMR and molecular dynamics study

Diffusion of pentane isomers in zeolites NaX has been investigated using pulsed field gradient nuclear magnetic resonance (PFG-NMR) and molecular dynamics (MD) techniques respectively. Temperature and concentration dependence of diffusivities have been studied. The diffusivities obtained from NMR are roughly an order of magnitude smaller than those obtained from MD. The dependence of diffusivity on loading at high temperatures exhibits a type I behavior according to the classification of Karger and Pfeifer 1]. NMR diffusivities of the isomers exhibit the order D(n-pentane) > D(isopentane) > D(neopentane). The results from MD suggest that the diffusivities of the isomers follow the order D(n-pentane) < D(isopentane) < D(neopentane). The activation energies from NMR show E-a(n-pentane) < E-a(isopentane) < E-a(neopentane) whereas those from MD suggest the order E-a(n-pentane) > (isopentane) > E-a(neopentane). The latter follows the predictions of levitation effect whereas those of NMR appears to be due to the presence of defects in the zeolite crystals. The differences between diffusivities estimated by NMR and MD are attributed to the longer time and length scales sampled by the NMR technique, as compared to MD. (C) 2012 Elsevier Inc. All rights reserved.

Molecular dynamics simulations of PPI dendrimer-drug complexes

Dendrimeric nanoparticles are potential drug delivery devices which can enhance the solubility of hydrophobic drugs, thus increasing their bioavailability and sustained release action. A quantitative understanding of the dendrimer-drug interactions can give valuable insight into the solubility and release profile of hydrophobic drug molecules in various solvent conditions. Fully atomistic molecular dynamics (MD) simulations have been performed to study the interactions of G5 PPIEDA (G5 ethylenediamine cored poly(propylene imine)) dendrimer and two well known drugs (Famotidine and Indomethacin) at different pH conditions. The study suggested that at low pH the dendrimer-drug complexes are thermodynamically unstable as compared to neutral and high pH conditions. Calculated Potential of Mean Force (PMF) by umbrella sampling showed that the release of drugs from the dendrimer at low pH is spontaneous, median release at neutral pH and slow release at high pH. In addition, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculations were also performed at each umbrella sampling window to identify the various energy contributions. To understand the effect of dendrimer chemistry and topology on the solubility and release profile of drugs, this study is extended to explore the solubility and release profile of phenylbutazone drug complexed with G3 poly(amidoamine) and G4 diaminobutane cored PPI dendrimers. The results indicate that the pH-induced conformational changes in dendrimer, ionization states, dendrimer type and pK(a) of the guest molecules influence the free energy barrier and stability of complexation, and thus regulate drug loading, solubility and release.

Data assimilation using ensemble transform Kalman filter (ETKF) in ROMS model for Indian Ocean

Study of Oceans dynamics and forecast is crucial as it influences the regional climate and other marine activities. Forecasting oceanographic states like sea surface currents, Sea surface temperature (SST) and mixed layer depth at different time scales is extremely important for these activities. These forecasts are generated by various ocean general circulation models (OGCM). One such model is the Regional Ocean Modelling System (ROMS). Though ROMS can simulate several features of ocean, it cannot reproduce the thermocline of the ocean properly. Solution to this problem is to incorporates data assimilation (DA) in the model. DA system using Ensemble Transform Kalman Filter (ETKF) has been developed for ROMS model to improve the accuracy of the model forecast. To assimilate data temperature and salinity from ARGO data has been used as observation. Assimilated temperature and salinity without localization shows oscillations compared to the model run without assimilation for India Ocean. Same was also found for u and v-velocity fields. With localization we found that the state variables are diverging within the localization scale.

Relation Between the Diffusivity, Viscosity, and Ionic Radius of LiCl in Water, Methanol, and Ethylene Glycol: A Molecular Dynamics Simulation

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several; structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent solvent interaction is important in EG while solute solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes we show that there is a relation between the void and neck radius on e one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (lambda(0)) of TMA(+), while in water in EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in lambda(0) as a function ionic radius is seen for Br- in water EG but for the larger ClO4- ion in methanol. The relation between the void and neck distribution and the variation in lambda(0) with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Inference for the Component and System Lifetime Distribution of a k-unit Parallel System Based on System Data

In this paper, we consider the inference for the component and system lifetime distribution of a k-unit parallel system with independent components based on system data. The components are assumed to have identical Weibull distribution. We obtain the maximum likelihood estimates of the unknown parameters based on system data. The Fisher information matrix has been derived. We propose -expectation tolerance interval and -content -level tolerance interval for the life distribution of the system. Performance of the estimators and tolerance intervals is investigated via simulation study. A simulated dataset is analyzed for illustration.

Study on the detection efficiency of gaseous photomultipliers

Efficient photon detection in gaseous photomultipliers require maximum photoelectron yield from the photocathode surface and also detection of them. In this work we have investigated the parameters that affect the photoelectron yield from the photocathode surface and methods to improve them thus ensuring high detection efficiency of the gaseous photomultiplier. The parameters studied are the electric field at the photocathode surface, surface properties of photocathode and pressure of gas mixture inside the gaseous photomultiplier. It was observed that optimized electric field at the photocathode ensures high detection efficiency. Lower pressure of filled gas increases the photoelectron yield from the photocathode surface but reduces the focusing probability of electrons inside the electron multiplier. Also evacuation for longer duration before gas filling increases the photoelectron yield.

Deformation-induced grain growth and twinning in nanocrystalline palladium thin films

The microstructure and mechanical properties of nanocrystalline Pd films prepared by magnetron sputtering have been investigated as a function of strain. The films were deposited onto polyimide substrates and tested in tensile mode. In order to follow the deformation processes in the material, several samples were strained to defined straining states, up to a maximum engineering strain of 10%, and prepared for post-mortem analysis. The nanocrystalline structure was investigated by quantitative automated crystal orientation mapping (ACOM) in a transmission electron microscope (TEM), identifying grain growth and twinning/detwinning resulting from dislocation activity as two of the mechanisms contributing to the macroscopic deformation. Depending on the initial twin density, the samples behaved differently. For low initial twin densities, an increasing twin density was found during straining. On the other hand, starting from a higher twin density, the twins were depleted with increasing strain. The findings from ACOM-TEM were confirmed by results from molecular dynamics (MD) simulations and from conventional and in-situ synchrotron X-ray diffraction (CXRD, SXRD) experiments.

Design and Evaluation of a Robust Optical Beam-Interruption-Based Vehicle Classifier System

This paper presents the design and development of a novel optical vehicle classifier system, which is based on interruption of laser beams, that is suitable for use in places with poor transportation infrastructure. The system can estimate the speed, axle count, wheelbase, tire diameter, and the lane of motion of a vehicle. The design of the system eliminates the need for careful optical alignment, whereas the proposed estimation strategies render the estimates insensitive to angular mounting errors and to unevenness of the road. Strategies to estimate vehicular parameters are described along with the optimization of the geometry of the system to minimize estimation errors due to quantization. The system is subsequently fabricated, and the proposed features of the system are experimentally demonstrated. The relative errors in the estimation of velocity and tire diameter are shown to be within 0.5% and to change by less than 17% for angular mounting errors up to 30 degrees. In the field, the classifier demonstrates accuracy better than 97.5% and 94%, respectively, in the estimation of the wheelbase and lane of motion and can classify vehicles with an average accuracy of over 89.5%.

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Confinement induced stochastic sensing of charged coronene and perylene aggregates in alpha-hemolysin nanochannels

Biological nanopores provide optimum dimensions and an optimal environment to study early aggregation kinetics of charged polyaromatic molecules in the nano-confined regime. It is expected that probing early stages of nucleation will enable us to design a strategy for supramolecular assembly and biocrystallization processes. Specifically, we have studied translocation dynamics of coronene and perylene based salts, through the alpha-hemolysin (alpha-HL) protein nanopore. The characteristic blocking events in the time-series signal are a function of concentration and bias voltage. We argue that different blocking events arise due to different aggregation processes as captured by all atomistic molecular dynamics (MD) simulations. These confinement induced aggregations of polyaromatic chromophores during the different stages of translocation are correlated with the spatial symmetry and charge distribution of the molecules.

Small-scale mechanical testing of materials

Small-scale mechanical testing of materials has gained prominence in the last decade or so due to the continuous miniaturization of components and devices in everyday application. This review describes the various micro-fabrication processes associated with the preparation of miniaturized specimens, geometries of test specimens and the small scale testing techniques used to determine the mechanical behaviour of materials at the length scales of a few hundred micro-meters and below. This is followed by illustrative examples in a selected class of materials. The choice of the case studies is based on the relevance of the materials used in today's world: evaluation of mechanical properties of thermal barrier coatings (TBCs), applied for enhanced high temperature protection of advanced gas turbine engine components, is essential since its failure by fracture leads to the collapse of the engine system. Si-based substrates, though brittle, are indispensible for MEMS/NEMS applications. Biological specimens, whose response to mechanical loads is important to ascertain their role in diseases and to mimic their structure for attaining high fracture toughness and impact resistance. An insight into the mechanisms behind the observed size effects in metallic systems can be exploited to achieve excellent strength at the nano-scale. A future outlook of where all this is heading is also presented.

Friction Stir-Welded Dissimilar Aluminum Alloys: Microstructure, Mechanical Properties, and Physical State

A356 and 6061 aluminum alloys were joined by friction stir welding at constant tool rotational rate with different tool-traversing speeds. Thermomechanical data of welding showed that increment in tool speed reduced the pseudo heat index and temperature at weld nugget (WN). On the other hand, volume of material within extrusion zone, strain rate, and Zenner Hollomon parameter were reduced with decrease in tool speed. Optical microstructure of WN exhibited nearly uniform dispersion of Si-rich particles, fine grain size of 6061 Al alloy, and disappearance of second phase within 6061 Al alloy. With enhancement in welding speed, matrix grain size became finer, yet size of Si-rich particles did not reduce incessantly. Size of Si-rich particles was governed by interaction time between tool and substrate. Mechanical property of WN was evaluated. It has been found that the maximum joint efficiency of 116% with respect to that of 6061 alloy was obtained at an intermediate tool-traversing speed, where matrix grain size was significantly fine and those of Si-rich particles were substantially small.

Is The Burden of Medical Education Affecting Ethics of Medical Treatment?

A substantial number of medical students in India have to bear an enormous financial burden for earning a bachelor's degree in medicine referred to as MBBS (bachelor of medicine and bachelor of surgery). This degree program lasts for four and one-half years followed by one year of internship. A postgraduate degree, such as MD, has to be pursued separately on completion of a MBBS. Every medical college in India is part of a hospital where the medical students get clinical exposure during the course of their study. All or at least a number of medical colleges in a given state are affiliated to a university that mainly plays a role of an overseeing authority. The medical colleges usually have no official interaction with other disciplines of education such as science and engineering, perhaps because of their independent location and absence of emphasis on medical research. However, many of the medical colleges are adept in imparting high-quality and sound training in medical practices including diagnostics and treatment. The medical colleges in India are generally of two types, i.e., government owned and private. Since only a limited number of seats are available across India in the former category of colleges, only a small fraction of aspiring candidates can find admission in these colleges after performing competitively in the relevant entrance tests. A major advantage of studying in these colleges is the nominal tuition fees that have to be paid. On the other hand, a large majority of would-be medical graduates have to seek admission in the privately run medical institutes in which the tuition and other related fees can be mind boggling when compared to their public counterparts. Except for candidates of exceptionally affluent background, the only alternative for fulfilling the dream of becoming a doctor is by financing one's study through hefty bank loans that may take years to pay back. It is often heard from patients that they are asked by doctors to undergo a plethora of diagnostic tests for apparently minor illnesses, which may financially benefit those prescribing the tests. The present paper attempts to throw light on the extent of disparity in cost of a medical education between state-funded and privately managed medical colleges in India; the average salary of a new medical graduate, which is often ridiculously low when compared to what is offered in entry-level engineering and business jobs; and the possible repercussions of this apparently unjust economic situation regarding the exploitation of patients.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Micromechanisms of fracture and strengthening in free-standing Pt-aluminide bond coats under tensile loading

Free-standing Pt-aluminide (PtAl) bond coats exhibit a linear stress strain response under tensile loading and undergo brittle cleavage fracture at temperatures below the brittle-to-ductile transition temperature (BDTT). Above the BDTT, these coatings show yielding and fail in a ductile manner. In this paper, the various micromechanisms affecting the tensile fracture stress (FS) below the BDTT and yield strength (YS) above the BDTT in a PtAl bond coat have been ascertained and quantified at various temperatures. The micromechanisms have been identified by carrying out microtensile testing of stand-alone PtAl coating specimens containing different levels of Pt at temperatures between room temperature and 1100 degrees C and correlation of the corresponding fracture mechanisms with the deformation substructure in the coating. An important aspect of the influence of Pt on the tensile behavior, slip characteristics, FS/YS and BDTT in the PtAl coating has also been examined. The addition of Pt enhances the FS of the coating by Pt solid solution strengthening and imparts a concomitant increase in fracture toughness and yet causes a significant increase in the BDTT of the coating. Published by Elsevier Ltd. on behalf of Acta Materialia Inc.