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  • Articles  (250)
  • Latest Papers from Table of Contents or Articles in Press  (250)
  • Molecular Diversity Preservation International  (194)
  • American Institute of Physics (AIP)  (56)
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  • Articles  (250)
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  • 1
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    In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis (2020)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2020-09-03
    Description: Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general treatment strategies) to treat this emerging pathogen. Iron is a crucial transition metal for N. meningitidis. Proteomic analysis data could be valuable for vaccine design. Here, we conduct a comparative study using computational bioinformatic tools to identify the most effective iron-regulated outer membrane proteins (OMPs) as immunogenic targets for a potential vaccine against N. meningitidis. The basic properties of N. meningitidis OMPs are explored for flexibility, solubility, hydrophilicity, beta-turns, and overall antigenic probability. Results of our study suggest that iron-regulated OMPs are flexible and soluble in water with high densities of conformational B-cell epitopes. As such, they can be recommended as a novel candidate for a vaccine against N. meningitidis both in vitro and in vivo.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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  • 2
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    The Fate of Chemical Pollutants with Soil Properties and Processes in the Climate Change Paradigm—A Review (2018)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2018-09-01
    Description: Heavy metal(loid)s and organic contaminants are two major groups of pollutants in soils. The fate and exposure of such pollutants in soil depends on their chemical properties, speciation, and soil properties. Soil properties and processes that control the toxicological aspects of pollutants include temperature, moisture, organic matter, mineral fractions, and microbial activities. These processes are vulnerable to climate change associated with global warming, including increased incidences of extreme rainfall, extended dry periods, soil erosion, and a rise in sea level. Here we explain evidence that relates to the effects of climate change-driven soil processes on the mobility, transport, and storage of pollutants in soil. The review found that changes in climate could increase human exposure to soil contaminants mainly due to processes involving soil organic carbon (SOC), surface runoff, redox state, and microbial community. However, uncertainties remain in relation to the extent of contaminant toxicity to human health, which is linked to global change drivers.
    Electronic ISSN: 2571-8789
    Topics: Biology , Chemistry and Pharmacology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Physics
    Published by Molecular Diversity Preservation International
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  • 3
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    Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana (2020)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2020-12-09
    Description: Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
    Electronic ISSN: 2073-4425
    Topics: Biology
    Published by Molecular Diversity Preservation International
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  • 4
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    Life Cycle Sustainability Assessment of Alternative Energy Sources for the Western Australian Transport Sector (2020)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2020-07-10
    Description: Environmental obligation, fuel security, and human health issues have fuelled the search for locally produced sustainable transport fuels as an alternative to liquid petroleum. This study evaluates the sustainability performance of various alternative energy sources, namely, ethanol, electricity, electricity-gasoline hybrid, and hydrogen, for Western Australian road transport using a life cycle sustainability assessment (LCSA) framework. The framework employs 11 triple bottom line (TBL) sustainability indicators and uses threshold values for benchmarking sustainability practices. A number of improvement strategies were devised based on the hotspots once the alternative energy sources failed to meet the sustainability threshold for the determined indicators. The proposed framework effectively addresses the issue of interdependencies between the three pillars of sustainability, which was an inherent weakness of previous frameworks. The results show that the environment-friendly and socially sustainable energy options, namely, ethanol-gasoline blend E55, electricity, electricity-E10 hybrid, and hydrogen, would need around 0.02, 0.14, 0.10, and 0.71 AUD/VKT of financial support, respectively, to be comparable to gasoline. Among the four assessed options, hydrogen shows the best performance for the environmental and social bottom line when renewable electricity is employed for hydrogen production. The economic sustainability of hydrogen fuel is, however, uncertain at this stage due to the high cost of hydrogen fuel cell vehicles (HFCVs). The robustness of the proposed framework warrants its application in a wide range of alternative fuel assessment scenarios locally as well as globally.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Molecular Diversity Preservation International
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  • 5
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    Effect of fast drifting electrons on electron temperature measurement with a triple Langmuir probe (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-08-13
    Description: Triple Langmuir Probe (TLP) is a widely used diagnostics for instantaneous measurement of electron temperature and density in low temperature laboratory plasmas as well as in edge region of fusion plasma devices. Presence of a moderately energetic flowing electron component, constituting only a small fraction of the bulk electrons, is also a generally observed scenario in plasma devices, where plasmas are produced by electron impact ionization of neutrals. A theoretical analysis of its effect on interpretation of the TLP data for bulk electron temperature measurement is presented here assuming electron velocity distribution is not deviating substantially from a Maxwellian. The study predicts conventional expression from standard TLP theory to give overestimated value of bulk electron temperature. Correction factor is significant and largely depends on population density, temperature, and energy of the fast component. Experimental verification of theoretical results is obtained in the magnetized plasma linear experimental device of Saha Institute of Nuclear Physics where plasma is produced by an electron cyclotron resonance method and known to have a fast flowing electron component.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Fabrication of novel cryomill for synthesis of high purity metallic nanoparticles (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-08-26
    Description: The successful preparation of free standing metal nanoparticles with high purity in bulk quantity is the pre-requisite for any potential application. This is possible by using ball milling at cryogenic temperature. However, the most of ball mills available in the market do not allow preparing high purity metal nanoparticles by this route. In addition, it is not possible to carry out in situ measurements of process parameters as well as diagnostic of the process. In the present investigation, we present a detailed study on the fabrication of a cryomill, which is capable of avoiding contaminations in the product. It also provides in situ measurements and diagnostic of the low temperature milling process. Online monitoring of the milling temperature and observation of ball motion are the important aspects in the newly designed mill. The nanoparticles prepared using this fabricated mill have been found to be free standing and also free from contaminations.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Effect of superheat and electric field on saturated film boiling (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-05-11
    Description: The objective of this investigation is to study the influence of superheat temperature and applied uniform electric field across the liquid-vapor interface during film boiling using a coupled level set and volume of fluid algorithm. The hydrodynamics of bubble growth, detachment, and its morphological variation with electrohydrodynamic forces are studied considering the medium to be incompressible, viscous, and perfectly dielectric at near critical pressure. The transition in interfacial instability behavior occurs with increase in superheat, the bubble release being periodic both in space and time. Discrete bubble growth occurs at a smaller superheat whereas vapor columns form at the higher superheat values. Destabilization of interfacial motion due to applied electric field results in decrease in bubble separation distance and increase in bubble release rate culminating in enhanced heat transfer rate. A comparison of maximum bubble height owing to application of different intensities of electric field is performed at a smaller superheat. The change in dynamics of bubble growth due to increasing superheat at a high intensity of electric field is studied. The effect of increasing intensity of electric field on the heat transfer rate at different superheats is determined. The boiling characteristic is found to be influenced significantly only above a minimum critical intensity of the electric field.
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 8
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    Effect of potassium doping on electronic structure and thermoelectric properties of topological crystalline insulator (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-05-10
    Description: Topological crystalline insulator (TCI), Pb 0.6 Sn 0.4 Te, exhibits metallic surface states protected by crystal mirror symmetry with negligibly small band gap. Enhancement of its thermoelectric performances needs tuning of its electronic structure particularly through engineering of its band gap. While physical perturbations tune the electronic structure of TCI by breaking of the crystal mirror symmetry, chemical means such as doping have been more attractive recently as they result in better thermoelectric performance in TCIs. Here, we demonstrate that K doping in TCI, Pb 0.6 Sn 0.4 Te, breaks the crystal mirror symmetry locally and widens electronic band gap, which is confirmed by direct electronic absorption spectroscopy and electronic structure calculations. K doping in Pb 0.6 Sn 0.4 Te increases p -type carrier concentration and suppresses the bipolar conduction via widening a band gap, which collectively boosts the thermoelectric figure of merit (ZT) to 1 at 708 K.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 9
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    Interface structure in nanoscale multilayers near continuous-to-discontinuous regime (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-07-28
    Description: Interfacial atomic diffusion, reaction, and formation of microstructure in nanoscale level are investigated in W/B 4 C multilayer (ML) system as functions of thickness in ultrathin limit. Hard x-ray reflectivity (XRR) and x-ray diffuse scattering in conjunction with x-ray absorption near edge spectroscopy (XANES) in soft x-ray and hard x-ray regimes and depth profiling x-ray photoelectron spectroscopy (XPS) have been used to precisely evaluate detailed interfacial structure by systematically varying the individual layer thickness from continuous-to-discontinuous regime. It is observed that the interfacial morphology undergoes an unexpected significant modification as the layer thickness varies from continuous-to-discontinuous regime. The interfacial atomic diffusion increases, the physical density of W layer decreases and that of B 4 C layer increases, and further more interestingly the in-plane correlation length decreases substantially as the layer thickness varies from continuous-to-discontinuous regime. This is corroborated using combined XRR and x-ray diffused scattering analysis. XANES and XPS results show formation of more and more tungsten compounds at the interfaces as the layer thickness decreases below the percolation threshold due to increase in the contact area between the elements. The formation of compound enhances to minimize certain degree of disorder at the interfaces in the discontinuous region that enables to maintain the periodic structure in ML. The degree of interfacial atomic diffusion, interlayer interaction, and microstructure is correlated as a function of layer thickness during early stage of film growth.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Designing pH induced fold switch in proteins (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-05-14
    Description: This work investigates the computational design of a pH induced protein fold switch based on a self-consistent mean-field approach by identifying the ensemble averaged characteristics of sequences that encode a fold switch. The primary challenge to balance the alternative sets of interactions present in both target structures is overcome by simultaneously optimizing two foldability criteria corresponding to two target structures. The change in pH is modeled by altering the residual charge on the amino acids. The energy landscape of the fold switch protein is found to be double funneled. The fold switch sequences stabilize the interactions of the sites with similar relative surface accessibility in both target structures. Fold switch sequences have low sequence complexity and hence lower sequence entropy. The pH induced fold switch is mediated by attractive electrostatic interactions rather than hydrophobic-hydrophobic contacts. This study may provide valuable insights to the design of fold switch proteins.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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