Detection of Target DNA using Photo-Reactive Protoporphyrin Moeity on a Nanocomposite Substrate

Detection of pathogens from infected biological samples through conventional process involves cell lysis and purification. The main objective of this work is to minimize the time and sample loss, as well as to increase the efficiency of detection of biomolecules. Electrical lysis of medical sample is performed in a closed microfluidic channel in a single integrated platform where the downstream analysis of the sample is possible. The device functions involve, in a sequence, flow of lysate from lysis chamber passed through a thermal denaturation counter where dsDNA is denatured to ssDNA, which is controlled by heater unit. A functionalized binding chamber of ssDNA is prepared by using ZnO nanorods as the matrix and functionalized with bifunctional carboxylic acid, 16-(2-pyridyldithiol) hexadecanoic acid (PDHA) which is further attached to a linker molecule 1-ethyl-3-(3-dimethylaminopropyl) (EDC). Linker moeity is then covalently bound to photoreactive protoporphyrin (PPP) molecule. The photolabile molecule protoporphyrin interacts with -NH2 labeled single stranded DNA (ssDNA) which thus acts as a probe to detect complimentary ssDNA from target organisms. Thereafter the bound DNA with protoporphyrin is exposed to an LED of particular wavelength for a definite period of time and DNA was eluted and analyzed. UV/Vis spectroscopic analysis at 260/280 nm wavelength confirms the purity and peak at 260 nm is reconfirmed for the elution of target DNA. Quantitative and qualitative data obtained from the current experiments show highly selective detection of biomolecule such as DNA which have large number of future applications in Point-of-Care devices.

Designing Novel Sulphate-based Ceramic Materials as Insertion Host Compounds for Secondary Batteries

Rechargeable batteries have propelled the wireless revolution and automobiles market over the past 25 years. Developing better batteries with improved energy density demands unveiling of new cathode ceramic materials with suitable diffusion channels and open framework structure. In this pursuit of achieving higher energy density, one approach is to realize enhanced redox voltage of insertion of ceramic compounds. This can be accomplished by incorporating highly electronegative anions in the cathode ceramics. Building on this idea, recently various sulphate- based compounds have been reported as high voltage cathode materials. The current article highlights the use of sulphate (SO4) based cathodes to realize the highest ever Fe3+/Fe2+ redox potentials in Li-ion batteries (LiFeSO4F fluorosulphate: 3.9V vs Li/Li+) and Na-ion batteries (Na2Fe2(SO4)(3) polysulphate: 3.8V vs Na/Na+). These sulphate-based cathode ceramic compounds pave way for newer avenues to design better batteries for future applications.

Cell-targeted regulation of gene expression through synthetic RNA devices

The ability to interface with and program cellular function remains a challenging research frontier in biotechnology. Although the emerging field of synthetic biology has recently generated a variety of gene-regulatory strategies based on synthetic RNA molecules, few strategies exist through which to control such regulatory effects in response to specific exogenous or endogenous molecular signals. Here, we present the development of an engineered RNA-based device platform to detect and act on endogenous protein signals, linking these signals to the regulation of genes and thus cellular function.

We describe efforts to develop an RNA-based device framework for regulating endogenous genes in human cells. Previously developed RNA control devices have demonstrated programmable ligand-responsive genetic regulation in diverse cell types, and we attempted to adapt this class of cis-acting control elements to function in trans. We divided the device into two strands that reconstitute activity upon hybridization. Device function was optimized using an in vivo model system, and we found that device sequence is not as flexible as previously reported. After verifying the in vitro activity of our optimized design, we attempted to establish gene regulation in a human cell line using additional elements to direct device stability, structure, and localization. The significant limitations of our platform prevented endogenous gene regulation.

We next describe the development of a protein-responsive RNA-based regulatory platform. Employing various design strategies, we demonstrated functional devices that both up- and downregulate gene expression in response to a heterologous protein in a human cell line. The activity of our platform exceeded that of a similar, small-molecule-responsive platform. We demonstrated the ability of our devices to respond to both cytoplasmic- and nuclear-localized protein, providing insight into the mechanism of action and distinguishing our platform from previously described devices with more restrictive ligand localization requirements. Finally, we demonstrated the versatility of our device platform by developing a regulatory device that responds to an endogenous signaling protein.

The foundational tool we present here possesses unique advantages over previously described RNA-based gene-regulatory platforms. This genetically encoded technology may find future applications in the development of more effective diagnostic tools and targeted molecular therapy strategies.

Parallel optical negabinary signed-digit computing: algorithm and optical implementation

Negabinary is a component of the positional number system. A complete set of negabinary arithmetic operations are presented, including the basic addition/subtraction logic, the two-step carry-free addition/subtraction algorithm based on negabinary signed-digit (NSD) representation, parallel multiplication, and the fast conversion from NSD to the normal negabinary in the carry-look-ahead mode. All the arithmetic operations can be performed with binary logic. By programming the binary reference bits, addition and subtraction can be realized in parallel with the same binary logic functions. This offers a technique to perform space-variant arithmetic-logic functions with space-invariant instructions. Multiplication can be performed in the tree structure and it is simpler than the modified signed-digit (MSD) counterpart. The parallelism of the algorithms is very suitable for optical implementation. Correspondingly, a general-purpose optical logic system using an electron trapping device is suggested. Various complex logic functions can be performed by programming the illumination of the data arrays without additional temporal latency of the intermediate results. The system can be compact. These properties make the proposed negabinary arithmetic-logic system a strong candidate for future applications in digital optical computing with the development of smart pixel arrays. (C) 1999 Society of Photo-Optical Instrumentation Engineers. [S0091-3286(99)00803-X].

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.

Uma técnica híbrida para geração de rotas em espaço geográfico com obstáculos.

Este trabalho está inserido no campo da Geomática e se concentra, mais especificamente, no estudo de métodos para exploração e seleção de rotas em espaços geográficos sem delimitação prévia de vias trafegáveis. As atividades que poderiam se beneficiar de estudos desse tipo estão inseridas em áreas da engenharia, logística e robótica. Buscou-se, com as pesquisas realizadas nesse trabalho, elaborar um modelo computacional capaz de consultar as informações de um terreno, explorar uma grande quantidade de rotas viáveis e selecionar aquelas rotas que oferecessem as melhores condições de trajetória entre dois pontos de um mapa. Foi construído um sistema a partir do modelo computacional proposto para validar sua eficiência e aplicabilidade em diferentes casos de estudo. Para que esse sistema fosse construído, foram combinados conceitos de sistemas baseados em agentes, lógica nebulosa e planejamento de rotas em robótica. As informações de um terreno foram organizadas, consumidas e apresentadas pelo sistema criado, utilizando mapas digitais. Todas as funcionalidades do sistema foram construídas por meio de software livre. Como resultado, esse trabalho de pesquisa disponibiliza um sistema eficiente para o estudo, o planejamento ou a simulação de rotas sobre mapas digitais, a partir de um módulo de inferência nebuloso aplicado à classificação de rotas e um módulo de exploração de rotas baseado em agentes autônomos. A perspectiva para futuras aplicações utilizando o modelo computacional apresentado nesse trabalho é bastante abrangente. Acredita-se que, a partir dos resultados alcançados, esse sistema possa ajudar a reduzir custos e automatizar equipamentos em diversas atividades humanas.

Mersey Estuary baseline survey. Analysis of macroinfaunal samples, literature review and database production

This is the Mersey Estuary baseline survey: Analysis of macroinfaunal samples, literature review and database production report produced by the Environment Agency North West in 2002. This report presents an ecological review of the Mersey estuary along with an extensive bibliography of the available environmental literature for this system. The central objective of this programme has been to provide the information necessary to support the Environment Agency's review of existing and future consents (for discharges, abstractions etc) in the Mersey estuary. This review of consents was required because the Mersey had been designated as a Special Protection Area (SPA) under the EC Birds Directive. Therefore under Regulation 50 of the Conservation, the Environment Agency was responsible for reviewing any extant consent, or future applications, which may directly or indirectly, affected this SPA.

Avaliação do potencial fotoprotetor de extratos de musgos e investigação de seus riscos toxicológicos

A radiação ultravioleta (UV) induz diversos efeitos nocivos nos organismos e a quantidade desta radiação que atinge a biosfera é afetada pela concentração de ozônio, latitude, altitude, clima e reflexão especular. As respostas de briófitas em relação aos efeitos da radiação UV e a presença de compostos que absorvem esta radiação têm sido estudadas. Sanionia uncinata, Holomitriopsis laevifolia e Leucobryum laevifolium são espécies de musgos encontrados em locais expostos a alta incidência de radiação UV e com habitats distintos. Considerando que as respostas de musgos contra os efeitos da radiação UV e seus mecanismos de proteção ainda são pouco caracterizados, o objetivo deste estudo foi investigar o potencial fotoprotetor e possíveis riscos toxicológicos associados aos extratos dos musgos S. uncinata, proveniente da Antártica e H. laevifolia e L. laevifolium, proveniente do Amazonas. Seus extratos metanólico (EM), aquoso (EA), hidroalcoólico (EH) e etanólico (EE) foram estudados com a caracterização química por absorção ao UV e visível e pela cromatografia líquida de alta eficiência; quantificação do índice total de compostos fenólicos; determinação da capacidade captadora do radical 2,2-difenil-1-picril-hidrazila a fim de avaliar as atividades antioxidantes; avaliação do potencial de fotoproteção cutânea pela determinação do fator de proteção solar; avaliações do potencial mutagênico e citototóxico, através do ensaio de Salmonella/microssoma, utilizando as cepas TA97, TA98, TA100, TA102 e TA104; do potencial fotomutagênico através do ensaio de fotomutagenicidade, usando as cepas TA102 e TA104; e investigação dos efeitos genotóxicos e fotogenotóxicos, pelo ensaio de micronúcleo e fotomicronúcleo, respectivamente, usando diferentes linhagens celulares estabelecidas. Foram encontradas atividades fotoprotetoras e antioxidantes e observou-se que os extratos se apresentaram singulares devido a sua composição química. Os resultados fotoprotetores, além dos mutagênicos/fotomutagênicos, genotóxicos/fotogenotóxicos e suas respectivas avaliações citotóxicas também permitiram selecionar extratos e suas concentrações, como promissores candidatos em fotoproteção Assim, os EA e EH de H. laevifolia e L. laevifolium apresentam, no geral, os resultados mais significativos, tornando-se potenciais para avaliações refinadas em fotoproteção e na separação de componentes que possam levar a futuras aplicações como antioxidantes e protetores solares ou como adjuvantes.

Uma Simulação computacional do passeio aleatório simples

Em 1828 foi observado um fenômeno no microscópio em que se visualizava minúsculos grãos de pólen mergulhados em um líquido em repouso que mexiam-se de forma aleatória, desenhando um movimento desordenado. A questão era compreender este movimento. Após cerca de 80 anos, Einstein (1905) desenvolveu uma formulação matemática para explicar este fenômeno, tratado por movimento Browniano, teoria cada vez mais desenvolvida em muitas das áreas do conhecimento, inclusive recentemente em modelagem computacional. Objetiva-se pontuar os pressupostos básicos inerentes ao passeio aleatório simples considerando experimentos com e sem problema de valor de contorno para melhor compreensão ao no uso de algoritmos aplicados a problemas computacionais. Foram explicitadas as ferramentas necessárias para aplicação de modelos de simulação do passeio aleatório simples nas três primeiras dimensões do espaço. O interesse foi direcionado tanto para o passeio aleatório simples como para possíveis aplicações para o problema da ruína do jogador e a disseminação de vírus em rede de computadores. Foram desenvolvidos algoritmos do passeio aleatório simples unidimensional sem e com o problema do valor de contorno na plataforma R. Similarmente, implementados para os espaços bidimensionais e tridimensionais,possibilitando futuras aplicações para o problema da disseminação de vírus em rede de computadores e como motivação ao estudo da Equação do Calor, embora necessita um maior embasamento em conceitos da Física e Probabilidade para dar continuidade a tal aplicação.

Grain boundaries in multi-seeded melt-grown superconductors

Future applications of high temperature superconductors require bulk materials of a complex shape. The multi-seeded-melt-growth process (MSMG) represents a promising technique for obtaining qualitatively well oriented bulk materials with different kinds of shape. In the MSMG process, several seeds are placed on a precursor pellet, from which the growth of the bulk starts. A certain problem of the MSMG process is that grain boundaries become inevitable when the growth fronts of two neighboring seeds collide. These grain boundaries are responsible for a reduction of the critical currents and pose a problem for high current applications. By polishing the sample step by step, the influence of the grain boundaries was investigated by scanning Hall probe measurements and by the magnetoscan technique. Additionally, optical microscopy and electron microscopy were employed to investigate the details of the microstructure. © 2005 IEEE.

Plasmonic nanostructure enhanced graphene-based photodetectors

Graphene exhibits electrical and optical properties promising for future applications in ultra-fast photonics[1]. High carrier mobility and Fermi velocity[2, 3] combined with its constant absorption over the visible wavelength range to the near-infrared[4] potentially allow its application for photodetection over a broad wavelength spectrum, operating at high frequencies. However, absorption being 2.3% per monolayer[4], responsiv-ity of these devices is rather low[5, 6]. Here we show that by combining graphene-based photodetectors with metal-nanostructures, plasmonic effects lead to an increased respon-sivity. © 2011 by the Author(s); licensee Accademia Peloritana dei Pericolanti, Messina, Italy.

Application of scalar dissipation rate model to siemens DLE combustors

The standard design process for the Siemens Industrial Turbomachinery, Lincoln, Dry Low Emissions combustion systems has adopted the Eddy Dissipation Model with Finite Rate Chemistry for reacting computational fluid dynamics simulations. The major drawbacks of this model have been the over-prediction of temperature and lack of species data limiting the applicability of the model. A novel combustion model referred to as the Scalar Dissipation Rate Model has been developed recently based on a flamelet type assumption. Previous attempts to adopt the flamelet philosophy with alternative closure models have failed, with the prediction of unphysical phenomenon. The Scalar Dissipation Rate Model (SDRM) was developed from a physical understanding of scalar dissipation rate, signifying the rate of mixing of hot and cold fluids at scales relevant to sustain combustion, in flames and was validated using direct numerical simulations data and experimental measurements. This paper reports on the first industrial application of the SDRM to SITL DLE combustion system. Previous applications have considered ideally premixed laboratory scale flames. The industrial application differs significantly in the complexity of the geometry, unmixedness and operating pressures. The model was implemented into ANSYS-CFX using their inbuilt command language. Simulations were run transiently using Scale Adaptive Simulation turbulence model, which switches between Large Eddy Simulation and Unsteady Reynolds Averaged Navier Stokes using a blending function. The model was validated in a research SITL DLE combustion system prior to being applied to the actual industrial geometry at real operating conditions. This system consists of the SGT-100 burner with a glass square-sectioned combustor allowing for detailed diagnostics. This paper shows the successful validation of the SDRM against time averaged temperature and velocity within measurement errors. The successful validation allowed application of the SDRM to the SGT-100 twin shaft at the relevant full load conditions. Limited validation data was available due to the complexity of measurement in the real geometry. Comparison of surface temperatures and combustor exit temperature profiles showed an improvement compared to EDM/FRC model. Furthermore, no unphysical phenomena were predicted. This paper presents the successful application of the SDRM to the industrial combustion system. The model shows a marked improvement in the prediction of temperature over the EDM/FRC model previously used. This is of significant importance in the future applications of combustion CFD for understanding of hardware mechanical integrity, combustion emissions and dynamics of the flame. Copyright © 2012 by ASME.

Design and market considerations for axial flux superconducting electric machine design

In this paper, the authors investigate a number of design and market considerations for an axial flux superconducting electric machine design that uses high temperature superconductors. The axial flux machine design is assumed to utilise high temperature superconductors in both wire (stator winding) and bulk (rotor field) forms, to operate over a temperature range of 65-77 K, and to have a power output in the range from 10s of kW up to 1 MW (typical for axial flux machines), with approximately 2-3 T as the peak trapped field in the bulk superconductors. The authors firstly investigate the applicability of this type of machine as a generator in small- and medium-sized wind turbines, including the current and forecasted market and pricing for conventional turbines. Next, a study is also carried out on the machine's applicability as an in-wheel hub motor for electric vehicles. Some recommendations for future applications are made based on the outcome of these two studies. Finally, the cost of YBCO-based superconducting (2G HTS) wire is analysed with respect to competing wire technologies and compared with current conventional material costs and current wire costs for both 1G and 2G HTS are still too great to be economically feasible for such superconducting devices.

Direct temperature mapping of nanoscale plasmonic devices.

Side by side with the great advantages of plasmonics in nanoscale light confinement, the inevitable ohmic loss results in significant joule heating in plasmonic devices. Therefore, understanding optical-induced heat generation and heat transport in integrated on-chip plasmonic devices is of major importance. Specifically, there is a need for in situ visualization of electromagnetic induced thermal energy distribution with high spatial resolution. This paper studies the heat distribution in silicon plasmonic nanotips. Light is coupled to the plasmonic nanotips from a silicon nanowaveguide that is integrated with the tip on chip. Heat is generated by light absorption in the metal surrounding the silicon nanotip. The steady-state thermal distribution is studied numerically and measured experimentally using the approach of scanning thermal microscopy. It is shown that following the nanoscale heat generation by a 10 mW light source within a silicon photonic waveguide the temperature in the region of the nanotip is increased by ∼ 15 °C compared with the ambient temperature. Furthermore, we also perform a numerical study of the dynamics of the heat transport. Given the nanoscale dimensions of the structure, significant heating is expected to occur within the time frame of picoseconds. The capability of measuring temperature distribution of plasmonic structures at the nanoscale is shown to be a powerful tool and may be used in future applications related to thermal plasmonic applications such as control heating of liquids, thermal photovoltaic, nanochemistry, medicine, heat-assisted magnetic memories, and nanolithography.

Study of GaN growth on ultra-thin Si membranes

10 mu m-thick ultra-thin Si (111) membranes for GaN epi-layers growth were successfully fabricated on silicon-on-insulator (SOI) substrate by backside etching the handle Si and buried oxide (BOX) layer. Then 1 mu m-thick GaN layers were deposited on these Si membranes by metal-organic chemical vapor deposition (MOCVD). The crack-free areas of 250 mu m, x 250 mu m were obtained on the GaN layers due to the reduction of thermal stress by using these ultra-thin Si membranes, which was further confirmed by the photoluminescence (PL) spectra and the simulation results from the finite element method calculation by using the software of ANSYS. In this paper, a newly developed approach was demonstrated to utilize micromechanical structures for GaN growth, which would improve the material quality of the epi-layers and facilitate GaN-based micro electro-mechanical system (MEMS) fabrication, especially the pressure sensor, in the future applications. (C) 2008 Elsevier Ltd. All rights reserved.