Search results for: Molecular electronics

Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

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Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Zubair Ahmad, M. H. Sayyad, M. Yaseen, M. Ali

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In this work, an organic compound 5,10,15,20- Tetrakis(3,5-di-tertbutylphenyl)porphyrinatocopper(II) (TDTBPPCu) is studied as an active material for thin film electronic devices. To investigate the electrical properties of TDTBPPCu, junction of TDTBPPCu with heavily doped n-Si and Al is fabricated. TDTBPPCu film was sandwiched between Al and n-Si electrodes. Various electrical parameters of TDTBPPCu are determined. The current-voltage characteristics of the junction are nonlinear, asymmetric and show rectification behavior, which gives the clue of formation of depletion region. This behavior indicates the potential of TDTBPPCu for electronics applications. The current-voltage and capacitance-voltage techniques are used to find the different electronic parameters.

Keywords: P-type, organic semiconductor, Electricalcharacteristics

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Authors: Chanin Park, Sundarapandian Thangapandian, Yuno Lee, Minky Son, Shalini John, Young-sik Sohn, Keun Woo Lee

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Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.

Keywords: Renin inhibitor, Molecular dynamics simulation, Structure-based pharmacophore modeling

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Authors: Raed A. Amro

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Standard packaging and interconnection technologies of power devices have difficulties meeting the increasing thermal demands of new application fields of power electronics devices. Main restrictions are the decreasing reliability of bond-wires and solder layers with increasing junction temperature. In the last few years intensive efforts have been invested in developing new packaging and interconnection solutions which may open a path to future application of power devices. In this paper, the main failure mechanisms of power devices are described and principle of new packaging and interconnection concepts and their power cycling reliability are presented.

Keywords: Power electronics devices, Reliability, Power Cycling, Low-temperature joining technique (LTJT)

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Authors: Zoja Raud, Valery Vodovozov

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Modelling and simulation provide effective way to acquire engineering experience. An active approach to modelling and simulation proposed in the paper involves, beside the compulsory part directed by the traditional step-by-step instructions, the new optional part basing on the human’s habits to design thus stimulating the efforts towards success in active learning. Computer exercises as a part of engineering curriculum incorporate a set of effective activities. In addition to the knowledge acquired in theoretical training, the described educational arrangement helps to develop problem solutions, computation skills, and experimentation performance along with enhancement of practical experience and qualification.

Keywords: Modelling, simulation, engineering education, electronics, active learning.

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Authors: Jeong-Won Kang

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Graphene, a single-atom sheet, has been considered as the most promising material for making future nanoelectromechanical systems as well as purely electrical switching with graphene transistors. Graphene-based devices have advantages in scaled-up device fabrication due to the recent progress in large area graphene growth and lithographic patterning of graphene nanostructures. Here we investigated its mechanical responses of circular graphene nanoflake under the nanoindentation using classical molecular dynamics simulations. A correlation between the load and the indentation depth was constructed. The nanoindented force in this work was applied to the center point of the circular graphene nanoflake and then, the resonance frequency could be tuned by a nanoindented depth. We found the hardening or the softening of the graphene nanoflake during its nanoindented-deflections, and such properties were recognized by the shift of the resonance frequency. The calculated mechanical parameters in the force-vs-deflection plot were in good agreement with previous experimental and theoretical works. This proposed schematics can detect the pressure via the deflection change or/and the resonance frequency shift, and also have great potential for versatile applications in nanoelectromechanical systems.

Keywords: Graphene, pressure sensor, circular graphene nanoflake, molecular dynamics.

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Authors: Raju Bhukya, DVLN Somayajulu

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Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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Authors: Jianwei Zhang, Dazhi Jiang, Huaxin Peng, Chunqi Wang

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Stress-strain curve of inter-tube connected carbon nanotube (CNT) reinforced polymer composite under axial loading generated from molecular dynamics simulation is presented. Comparison of the response to axial mechanical loading between this composite system with composite systems reinforced by long, continuous CNTs (replicated via periodic boundary conditions) and short, discontinuous CNTs has been made. Simulation results showed that the inter-tube connection improved the mechanical properties of short discontinuous CNTs dramatically. Though still weaker than long CNT/polymer composite, more remarkable increase in the stiffness relative to the polymer was observed in the inter-tube connected CNT/polymer composite than in the discontinuous CNT/polymer composite. The manually introduced bridge break process resulted in a stress-strain curve of ductile fracture mode, which is consistent with the experimental result.

Keywords: Carbon nanotube, inter-tube connection, molecular dynamics, stress-strain curve

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

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A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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Authors: S. Desouky, A. Al sabagh , M. Betiha, A. Badawi, A. Ghanem, S. Khalil

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Two Amphiphilic catalysts, iron (III) dodecylbenzene sulfonate and nickel (II) dodecylbenzene sulfonate, were synthesized and used in the catalytic aquathermolysis of heavy crude oil to reduce its viscosity. The prepared catalysts exhibited good performance in the aquathermolysis and the viscosity is reduced by ~ 78.9 % for Egyptian heavy crude oil. The chemical and physical properties of heavy oil both before and after reaction were investigated by FT-IR, dynamic viscosity, molecular weight and SARA analysis. The results indicated that the content of resin, asphaltene, average molecular weight and sulfur content of heavy oil is reduced after the catalytic aquathermolysis.

Keywords: Amphiphilic catalyst, Aquathermolysis, Heavy oil, Viscosity reduction.

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Authors: Archana S. Nanoty, A. R. Chudasama

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Three-phase induction machines are today a standard for industrial electrical drives. Cost, reliability, robustness and maintenance free operation are among the reasons these machines are replacing dc drive systems. The development of power electronics and signal processing systems has eliminated one of the greatest disadvantages of such ac systems, which is the issue of control. With modern techniques of field oriented vector control, the task of variable speed control of induction machines is no longer a disadvantage. The need to increase system performance, particularly when facing limits on the power ratings of power supplies and semiconductors, motivates the use of phase number other than three, In this paper a novel scheme of connecting two, three phase induction motors in parallel fed by two inverters; viz. VSI and CSI and their vector control is presented.

Keywords: Field oriented control, multiphase induction motor, power electronics converter.

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Authors: Zone-Ching Lin, Meng-Hua Lin, Ying-Chih Hsu

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This paper uses quasi-steady molecular statics model and diamond tool to carry out simulation temperature rise of nanoscale orthogonal cutting single-crystal silicon. It further qualitatively analyzes temperature field of silicon workpiece without considering heat transfer and considering heat transfer. This paper supposes that the temperature rise of workpiece is mainly caused by two heat sources: plastic deformation heat and friction heat. Then, this paper develops a theoretical model about production of the plastic deformation heat and friction heat during nanoscale orthogonal cutting. After the increased temperature produced by these two heat sources are added up, the acquired total temperature rise at each atom of the workpiece is substituted in heat transfer finite difference equation to carry out heat transfer and calculates the temperature field in each step and makes related analysis.

Keywords: Quasi-steady molecular statics, Nanoscale orthogonal cutting, Finite difference, Temperature.

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Authors: Tudor Petreuş, Andrei Neamţu, Cristina Dascălu, Paul Dan Sîrbu, Carmen E. Cotrutz

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Matrix metalloproteinases (MMP) are a class of structural and functional related enzymes involved in altering the natural elements of the extracellular matrix. Most of the MMP structures are cristalographycally determined and published in WorldWide ProteinDataBank, isolated, in full structure or bound to natural or synthetic inhibitors. This study proposes an algorithm to replace missing crystallographic structures in PDB database. We have compared the results of a chosen docking algorithm with a known crystallographic structure in order to validate enzyme sites reconstruction there where crystallographic data are missing.

Keywords: matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.

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Authors: Permphan Dharmasaroja

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Acute disseminated encephalomyelitis (ADEM) has been reported to develop after a hymenoptera sting, but its pathogenesis is not known in detail. Myelin basic protein (MBP)- specific T cells have been detected in the blood of patients with ADEM, and a proportion of these patients develop multiple sclerosis (MS). In an attempt to understand the mechanisms underlying ADEM, molecular mimicry between hymenoptera venom peptides and the human immunodominant MBP peptide was scrutinized, based on the sequence and structural similarities, whether it was the root of the disease. The results suggest that the three wasp venom peptides have low sequence homology with the human immunodominant MBP residues 85-99. Structural similarity analysis among the three venom peptides and the MS-related HLA-DR2b (DRA, DRB1*1501)-associated immunodominant MHC binding/TCR contact residues 88-93, VVHFFK showed that hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and antigen 5 residues 109-114 showed a high degree of similarity 83.3%, 100%, and 83.3% respectively. In conclusion, some wasp venom peptides, particularly phospholipase A1, may potentially act as the molecular motifs of the human 3HLA-DR2b-associated immunodominant MBP88-93, and possibly present a mechanism for induction of wasp sting-associated ADEM.

Keywords: central nervous system, Hymenoptera, myelin basicprotein, molecular mimicry.

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Authors: Babak Safaei, A. M. Fattahi

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In the present study we have investigated axial buckling characteristics of nanocomposite beams reinforced by single-walled carbon nanotubes (SWCNTs). Various types of beam theories including Euler-Bernoulli beam theory, Timoshenko beam theory and Reddy beam theory were used to analyze the buckling behavior of carbon nanotube-reinforced composite beams. Generalized differential quadrature (GDQ) method was utilized to discretize the governing differential equations along with four commonly used boundary conditions. The material properties of the nanocomposite beams were obtained using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long- (10,10) SWCNT composites which were embedded by amorphous polyethylene matrix. Then the results obtained directly from MD simulations were matched with those calculated by the mixture rule to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results were presented to indicate the influences of nanotube volume fractions and end supports on the critical axial buckling loads of nanocomposite beams relevant to long- and short-nanotube composites.

Keywords: Nanocomposites, molecular dynamics simulation, axial buckling, generalized differential quadrature (GDQ).

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Authors: Ilya Kavalchuk, Mehdi Seyedmahmoudian, Ben Horan, Aman Than Oo, Alex Stojcevski

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The power electronic components within Electric Vehicles (EV) need to operate in several important modes. Some modes directly influence safety, while others influence vehicle performance. Given the variety of functions and operational modes required of the power electronics, it needs to meet efficiency requirements to minimize power losses. Another challenge in the control and construction of such systems is the ability to support bidirectional power flow. This paper considers the construction, operation, and feasibility of available converters for electric vehicles with feasible configurations of electrical buses and loads. This paper describes logic and control signals for the converters for different operations conditions based on the efficiency and energy usage bases.

Keywords: Electric Vehicles, Electrical Machines Control, Power Electronics, Powerflow Regulations.

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.

Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.

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Authors: Amin Eisazadeh, Khairul Anuar Kassim, Hadi Nur

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The expansive nature of soils containing high amounts of clay minerals can be altered through chemical stabilization, resulting in a material suitable for construction purposes. The primary objective of this investigation was to study the changes induced in the molecular structure of phosphoric acid stabilized bentonite and lateritic soil using Nuclear Magnetic Resonance (NMR) and Fourier Transform Infrared (FTIR) spectroscopy. Based on the obtained data, it was found that a surface alteration mechanism was the main reason responsible for the improvement of treated soils. Furthermore, the results indicated that the Al present in the octahedral layer of clay minerals were more amenable to chemical attacks and also partly responsible for the formation of new products.

Keywords: Bentonite, Laterite clay, Molecularcharacterization, Phosphoric acid, Stabilization

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Surrogate model has received increasing attention for use in detecting damage of structures based on vibration modal parameters. However, uncertainties existing in the measured vibration data may lead to false or unreliable output result from such model. In this study, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The kriging technique allows one to genuinely quantify the surrogate error, therefore it is chosen as metamodeling technique. Enhanced version of ideal gas molecular movement (EIGMM) algorithm is used as main algorithm for model updating. The developed approach is applied to detect simulated damage in numerical models of 72-bar space truss and 120-bar dome truss. The simulation results show the proposed method can perform well in probability-based damage detection of structures with less computational effort compared to direct finite element model.

Keywords: Enhanced ideal gas molecular movement, Kriging, probability-based damage detection, probability of damage existence, surrogate modeling, uncertainty quantification.

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Authors: Amanda M. Tadini, Houssam Hajjoul, Gustavo Nicolodelli, Stéphane Mounier, Célia R. Montes, Débora M. B. P. Milori

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Soil organic matter (SOM) plays an important role in maintaining soil productivity and accounting for the promotion of biological diversity. The main components of the SOM are the humic substances which can be fractionated according to its solubility in humic acid (HA), fulvic acids (FA) and humin (HU). The determination of the chemical properties of organic matter as well as its interaction with metallic species is an important tool for understanding the structure of the humic fractions. Fluorescence spectroscopy has been studied as a source of information about what is happening at the molecular level in these compounds. Specially, soils of Amazon region are an important ecosystem of the planet. The aim of this study is to understand the molecular and structural composition of HA samples from Spodosol of Amazonia using the fluorescence Emission-Excitation Matrix (EEM) and Time Resolved Fluorescence Spectroscopy (TRFS). The results showed that the samples of HA showed two fluorescent components; one has a more complex structure and the other one has a simpler structure, which was also seen in TRFS through the evaluation of each sample lifetime. Thus, studies of this nature become important because it aims to evaluate the molecular and structural characteristics of the humic fractions in the region that is considered as one of the most important regions in the world, the Amazon.

Keywords: Amazonian soil, characterization, fluorescence, humic acid, lifetime.

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Authors: R. Hocine, K. Belkacemi, A. Boukortt, A. Boudjemai

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When designing satellites, one of the major issues aside for designing its primary subsystems is to devise its thermal. The thermal management of satellites requires solving different sets of issues with regards to modelling. If the satellite is well conditioned all other parts of the satellite will have higher temperature no matter what. The main issue of thermal modelling for satellite design is really making sure that all the other points of the satellite will be within the temperature limits they are designed. The insertion of power electronics in aerospace technologies is becoming widespread and the modern electronic systems used in space must be reliable and efficient with thermal management unaffected by outer space constraints. Many advanced thermal management techniques have been developed in recent years that have application in high power electronic systems. This paper presents a Three-Dimensional Modal Transmission Line Matrix (3D-TLM) implementation of transient heat flow in space power electronics. In such kind of components heat dissipation and good thermal management are essential. Simulation provides the cheapest tool to investigate all aspects of power handling. The 3DTLM has been successful in modeling heat diffusion problems and has proven to be efficient in terms of stability and complex geometry. The results show a three-dimensional visualisation of self-heating phenomena in the device affected by outer space constraints, and will presents possible approaches for increasing the heat dissipation capability of the power modules.

Keywords: Thermal management, conduction, heat dissipation, CTE, ceramic, heat spreader, nodes, 3D-TLM.

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Authors: Y. Saylan, F. Yılmaz, A. Denizli

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In this study, we have focused our attention on combining of molecular imprinting into nanofilms and QCM nanosensor approaches and producing QCM nanosensor for anti- CCP, chosen as model protein, using anti-CCP imprinted nanofilms. The nonimprinted nanosensor was also prepared to evaluate the selectivity of the imprinted nanosensor. Anti-CCP imprinted QCM nanosensor was tested for real time detection of anti-CCP from aqueous solution. The kinetic and affinity studies were determined by using anti-CCP solutions with different concentrations. The responses related with mass shifts (%m) and frequency shifts (%f) were used to evaluate adsorption properties. To show the selectivity of the anti-CCP imprinted QCM nanosensor, competitive adsorption of anti-CCP and IgM was investigated. The results indicate that anti- CCP imprinted QCM nanosensor has higher adsorption capabilities for anti-CCP than for IgM, due to selective cavities in the polymer structure.

Keywords: Anti-CCP, molecular imprinting, QCM nanosensor, rheumatoid arthritis.

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Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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Authors: Atitaya Singchai, Nooduan Muangsan, Thitiporn Machikowa

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Sunflower oil with high oleic acid content is most desirable because of its high oxidative stability. Screening sunflower of high oleic acid using conventional method is laborious and time consuming. Therefore, the use of molecular markers as a screening tool is promising. The objective of this research was to evaluate SSR primers for high oleic acid content in sunflower. Two sunflower lines, 5A and PI 649855 were used as the representative of low and high oleic acid sunflowers, respectively, and thirty seven SSR markers were used to identify oleic acid content trait. The results revealing 10 SSR primers showed polymorphic between high and low oleic acid lines and thus were informative. With these primers, therefore, it is possible to identify the genetic markers associated with high oleic acid trait in sunflower genotypes. 

Keywords: Microsatellite, Helianthus annuus L., fatty acid composition, molecular markers.

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Authors: F. S. Abtahi, M. Koohi Hbibi, M. Khodaei Motlagh

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Bean common mosaic necrosis virus (BCMNV) is a potyvirus with a worldwide distribution. This virus causes serious economic losses in Iran in many leguminoses. During 20008, samples were collected from soybeans fields in Tehran Province. Four isolates (S1, S2 and S3) were inoculated on 15 species of Cucurbitaceae, Chenopodiaceae, Solanacae and Leguminosae. Chenopodium quinoa and C. amaranticolor. Did not developed any symptoms.all isolates caused mosaic symptoms on Phaseolus vulgaris cv. Red Kidney and P. vulgaris cv. Bountiful. The molecular weights of coat protein using SDS-PAGE and western blotting were estimated at 33 kDa. Reverse transcription polymerase chain reaction (RT-PCR) was performed using one primer pairs designed by L. XU et al. An approximately 920 bp fragment was amplified with a specific primer.

Keywords: ELISA, RT-PCR, SDS-PAGE, BCMNV.

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Authors: G. Khatisashvili, M. Gordeziani, G. Adamia, E. Kvesitadze, T. Sadunishvili, G. Kvesitadze

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The ability of agricultural and decorative plants to absorb and detoxify TNT and RDX has been studied. All tested 8 plants, grown hydroponically, were able to absorb these explosives from water solutions: Alfalfa > Soybean > Chickpea> Chikling vetch >Ryegrass > Mung bean> China bean > Maize. Differently from TNT, RDX did not exhibit negative influence on seed germination and plant growth. Moreover, some plants, exposed to RDX containing solution were increased in their biomass by 20%. Study of the fate of absorbed [1-14ðí]-TNT revealed the label distribution in low and high-molecular mass compounds, both in roots and above ground parts of plants, prevailing in the later. Content of 14ðí in lowmolecular compounds in plant roots are much higher than in above ground parts. On the contrary, high-molecular compounds are more intensively labeled in aboveground parts of soybean. Most part (up to 70%) of metabolites of TNT, formed either by enzymatic reduction or oxidation, is found in high molecular insoluble conjugates. Activation of enzymes, responsible for reduction, oxidation and conjugation of TNT, such as nitroreductase, peroxidase, phenoloxidase and glutathione S-transferase has been demonstrated. Among these enzymes, only nitroreductase was shown to be induced in alfalfa, exposed to RDX. The increase in malate dehydrogenase activities in plants, exposed to both explosives, indicates intensification of Tricarboxylic Acid Cycle, that generates reduced equivalents of NAD(P)H, necessary for functioning of the nitroreductase. The hypothetic scheme of TNT metabolism in plants is proposed.

Keywords: Higher plants, TNT, RDX, transformation.

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structureprocess- property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: Biosensor, design, DNA, molecular dynamics simulation.

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Authors: H. Hashim, B. F. Usher

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InGaAsN and GaAsN epitaxial layers with similar nitrogen compositions in a sample were successfully grown on a GaAs (001) substrate by solid source molecular beam epitaxy. An electron cyclotron resonance nitrogen plasma source has been used to generate atomic nitrogen during the growth of the nitride layers. The indium composition changed from sample to sample to give compressive and tensile strained InGaAsN layers. Layer characteristics have been assessed by high-resolution x-ray diffraction to determine the relationship between the lattice constant of the GaAs1-yNy layer and the fraction x of In. The objective was to determine the In fraction x in an InxGa1-xAs1-yNy epitaxial layer which exactly cancels the strain present in a GaAs1-yNy epitaxial layer with the same nitrogen content when grown on a GaAs substrate.

Keywords: Indium, molecular beam epitaxy, nitrogen, straincancellation.

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Authors: M. Wannaborworn, B. Jongsomjit, T. Shiono

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Copolymerization of ethylene with 1-hexene was carried out using two ansa-fluorenyl titanium derivative complexes. The substituent effect on the catalytic activity, monomer reactivity ratio and polymer property was investigated. It was found that the presence of t-Bu groups on fluorenyl ring exhibited remarkable catalytic activity and produced polymer with high molecular weight. However, these catalysts produce polymer with narrow molecular weight distribution, indicating the characteristic of single-site metallocene catalyst. Based on 13C NMR, we can observe that monomer reactivity ratio was affected by catalyst structure. The rH values of complex 2 were lower than that of complex 1 which might be result from the higher steric hindrance leading to a reduction of 1- hexene insertion step.

Keywords: Constrained geometry catalyst, linear low density polyethylene, copolymerization, reactivity ratio

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Authors: K. Massila, R. D. Stein, S. M. Suhaizan, A. A. Azlianor

Abstract:

A number of mass spectrometry applications are already available as web-based and windows-based systems to calculate isotope pattern and to display the mass spectrum based on the specific molecular formula besides providing necessary information. These applications were evaluated and compared with our new alternative application called Theoretical Isotope Generator (TIG) in terms of its functionality and features provided to prove this new application is working better and performing well. TIG provides extra features than others, complete with several functionality such as drawing, normalizing and zooming the generated graph that convey with the molecular information in a number of formats by providing the details of the calculation and molecules. Thus, any chemist, students, lecturers and researchers from anywhere could use TIG to gain related information on molecules and their relative intensity.

Keywords: Isotope pattern calculator, mass number, massspectrum, relative intensity.

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