Search results for: molecular beam epitaxy

Authors: Danesh Nourzadeh, Sepideh Khorshid, Shiro Takada, Khosrow Bargi

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In this paper, transversal vibration of buried pipelines during loading induced by underground explosions is analyzed. The pipeline is modeled as an infinite beam on an elastic foundation, so that soil-structure interaction is considered by means of transverse linear springs along the pipeline. The pipeline behavior is assumed to be ideal elasto-plastic which an ultimate strain value limits the plastic behavior. The blast loading is considered as a point load, considering the affected length at some point of the pipeline, in which the magnitude decreases exponentially with time. A closed-form solution for the quasi-static problem is carried out for both elastic and elasticperfect plastic behaviors of pipe materials. At the end, a comparative study on steel and polyethylene pipes with different sizes buried in various soil conditions, affected by a predefined underground explosion is conducted, in which effect of each parameter is discussed.

Keywords: Beam on elastic foundation, Buried pipelines, External explosion, Non-linear quasi-static solution.

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Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

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Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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Authors: Shagufta Tabassum

Abstract:

The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. Here we discuss the basic calibration and normalization procedure for TDR measurements. Our aim is to explain different types of error occur during TDR measurements and how to minimize it.

Keywords: time domain reflectometry measurement technique, cable and connector loss, oscilloscope loss, normalization technique

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Authors: A. Aljohani, M. Orif

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The concentration of polycyclic aromatic hydrocarbons (PAH) in clams (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: Bivalves, biomonitoring, hydrocarbons, PAHs.

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Authors: Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira, Marta A. S. Perez, Irina S. Moreira, António J. M.Ribeiro, Ana R. A. P. Neves, Maria J. Ramos, Pedro A. Fernandes

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In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

Keywords: Enzyme, Molecular Dynamics, Protein, Quantum Mechanics.

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Authors: Meng-Hao Tsai, Tsuei-Chiang Huang

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Interior brick-infill partitions are usually considered as non-structural components, and only their weight is accounted for in practical structural design. In this study, the brick-infill panels are simulated by compression struts to clarify their effect on the progressive collapse potential of an earthquake-resistant RC building. Three-dimensional finite element models are constructed for the RC building subjected to sudden column loss. Linear static analyses are conducted to investigate the variation of demand-to-capacity ratio (DCR) of beam-end moment and the axial force variation of the beams adjacent to the removed column. Study results indicate that the brick-infill effect depends on their location with respect to the removed column. As they are filled in a structural bay with a shorter span adjacent to the column-removed line, more significant reduction of DCR may be achieved. However, under certain conditions, the brick infill may increase the axial tension of the two-span beam bridging the removed column.

Keywords: Progressive collapse, brick-infill partition, compression strut.

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Authors: Vikas Rastogi, Vipan Kumar, Loveleen Kumar Bhagi

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The present work deals with the structural analysis of turbine blades and modeling of turbine blades. A common failure mode for turbine machines is high cycle of fatigue of compressor and turbine blades due to high dynamic stresses caused by blade vibration and resonance within the operation range of the machinery. In this work, proper damping system will be analyzed to reduce the vibrating blade. The main focus of the work is the modeling of under platform damper to evaluate the dynamic analysis of turbine-blade vibrations. The system is analyzed using Bond graph technique. Bond graph is one of the most convenient ways to represent a system from the physical aspect in foreground. It has advantage of putting together multi-energy domains of a system in a single representation in a unified manner. The bond graph model of dry friction damper is simulated on SYMBOLS-shakti® software. In this work, the blades are modeled as Timoshenko beam. Blade Vibrations under different working conditions are being analyzed numerically.

Keywords: Turbine blade vibrations, Friction dampers, Timoshenko Beam, Bond graph modeling.

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Authors: Suchi Barua, Narottam Das, Sven Nordholm, Mohammad Razaghi

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This paper presents nonlinear pulse propagation characteristics for different input optical pulse shapes with various input pulse energy levels in semiconductor optical amplifiers. For simulation of nonlinear pulse propagation, finite-difference beam propagation method is used to solve the nonlinear Schrödinger equation. In this equation, gain spectrum dynamics, gain saturation are taken into account which depends on carrier depletion, carrier heating, spectral-hole burning, group velocity dispersion, self-phase modulation and two photon absorption. From this analysis, we obtained the output waveforms and spectra for different input pulse shapes as well as for different input energies. It shows clearly that the peak position of the output waveforms are shifted toward the leading edge which due to the gain saturation of the SOA for higher input pulse energies. We also analyzed and compared the normalized difference of full-width at half maximum for different input pulse shapes in the SOA.

Keywords: Finite-difference beam propagation method, pulse shape, pulse propagation, semiconductor optical amplifier.

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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: B. Mohebi, N. Asadi, F. Kazemi

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Inelastic deformation of the brace in Special Concentrically Braced Frame (SCBF) creates inelastic damages on gusset plate connections such as buckling at edges. In this study, to improve the seismic performance of SCBFs connections, an analytical study was undertaken. To improve the gusset plate connection, this study proposes using ‎edge’s stiffeners in both sides of gusset plate.‎ For this purpose, in order to examine edge’s stiffeners effect on gusset plate connections, two groups of modeling with and without considering edge’s stiffener and different types of braces were modeled using ABAQUS software. The results show that considering the edge’s stiffener reduces the equivalent plastic strain values at a connection region of gusset plate with beam and column, which can improve the seismic performance of gusset plate. Furthermore, considering the edge’s stiffeners significantly decreases the strain concentration at regions where gusset plates have been connected to beam and column. Moreover, considering 2t_pl distance causes reduction in the plastic strain.

Keywords: Special concentrically braced frame, gusset plate, edge’s stiffener, seismic performance.

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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: N. Bakradze, N. Gagelidze, T. Dumbadze, L. Amiranashvili, A. D. L. Batako

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Cereals are considered as a strategic product in human life and their demand is increasing with the growth of world population. Increasing wheat production is important for the country. One of the ways to solve the problem is to develop and implement new, environmentally and economically acceptable technologies. Such technologies include pre-sowing treatment of seed with a laser and associative nitrogen-fixing bacteria - Azospirillum brasilense. In the region there are the wheat varieties - Dika and Lomtagora, which are among the most common in Georgia. Dika is a frost-resistant wheat, with a high ability to adapt to the environment, resistant to falling and it is sown in highlands. Lomtagora 126 differs with its winter and drought resistance, and it has a great ability to germinate. Lomtagora is characterized by a strong root system and a high budding capacity. It is an early variety, fall-resistant, easy to thresh and suitable for mechanized harvesting with large and red grains. This paper presents some preliminary experimental results where a continuous CO2 laser with a power of 25-40 W was used to radiate grains at a flow rate of 10 and 15 cm/sec. The treatment was carried out on grains of the Triticum aestivum L. var. Lutescens (local variety name - Lomtagora 126), and Triticum carthlicum Nevski (local variety name - Dika). Here the grains were treated with A. brasilense isolate (108-109 CFU/ml), which was isolated from the rhizosphere of wheat. It was observed that the germination of the wheat was not significantly influenced by either laser or bacteria treatment. The results of our research show that combined treatment with laser and A. brasilense significantly influenced the germination of wheat. In the case of the Lomtagora 126 variety, grains were exposed to the beam on a speed of 10 cm/sec, only slightly improved the growth for 38-day seedlings, in case of exposition of grains with a speed of 15 cm/sec - by 23%. Treatment of seeds with A. brasilense in both exposed and non-exposed variants led to an improvement in the growth of seedlings, with A. brasilense alone - by 22%, and with combined treatment of grains - by 29%. In the case of the Dika variety, only exposure led to growth by 8-9%, and the combined treatment - by 10-15%, in comparison with the control variant. Superior effect on growth of seedlings of different varieties was achieved with the combinations of laser treatment on grains in a beam of 15 cm/sec (radiation power 30-40 W) and in addition of A. brasilense - nitrogen fixing bacteria. Therefore, this is a promising application of A. brasilense as active agents of bacterial fertilizers due to their ability of molecular nitrogen fixation in cereals in combination with laser irradiation: choosing a proper strain gives a good ability to colonize roots of agricultural crops, providing a high nitrogen-fixing ability and the ability to mobilize soil phosphorus, and laser treatment stimulates natural processes occurring in plant cells, will increase the yield.

Keywords: laser treatment, Azospirillum brasilense, seeds, wheat varieties, Lomtagora, Dika

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Authors: Sadegh Masoudi, Ali Asghar Yousefi, Somayeh Nourollahi, Fatemeh Noughani

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Two different testicular tissues have to be distinguished in regard to radiation damage: first the seminiferous tubules, corresponding to the sites of spermatogenesis, which are extremely radiosensitive. Second the testosterone secreting Leydig cells, which are considered to be less radiosensitive. This study aims to estimate testicular dose and the associated risks for infertility and hereditary effects from Abdominal and pelvic irradiation. Radiotherapy was simulated on a humanoid phantom using a 15 MV photon beam. Testicular dose was measured for various field sizes and tissue thicknesses along beam axis using an ionization chamber and TLD. For transmission Factor Also common method of measuring the absorbed dose distribution and electron contamination in the build-up region of high-energy beams for radiation therapy is by means of parallel-plate Ionisation chambers. Gonadal dose was reduced by placing lead cups around the testes supplemented by a field edge block. For a tumor dose of 100 cGy, testicular dose was 2.96-8.12 cGy depending upon the field size and the distance from the inferior field edge. The treatment at parameters, the presence of gonad shield and the somatometric characteristics determine whether testicular dose can exceed 1 Gy which allows a complete recovery of spermatogenesis.

Keywords: Absorbed Dose, Abdominal and pelvic, gonads men, Radiotherapy.

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Authors: Jin Y. Park, Jeong Wan Lee

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An experimental and analytical research on shear buckling of a comparably large polymer composite I-section is presented. It is known that shear buckling load of a large span composite beam is difficult to determine experimentally. In order to sensitively detect shear buckling of the tested I-section, twenty strain rosettes and eight displacement sensors were applied and attached on the web and flange surfaces. The tested specimen was a pultruded composite beam made of vinylester resin, E-glass, carbon fibers and micro-fillers. Various coupon tests were performed before the shear buckling test to obtain fundamental material properties of the Isection. An asymmetric four-point bending loading scheme was utilized for the shear test. The loading scheme resulted in a high shear and almost zero moment condition at the center of the web panel. The shear buckling load was successfully determined after analyzing the obtained test data from strain rosettes and displacement sensors. An analytical approach was also performed to verify the experimental results and to support the discussed experimental program.

Keywords: Strain sensor, displacement sensor, shear buckling, polymer composite I-section, asymmetric loading.

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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: K. Karuppasamy

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In this paper, analysis of an infinite beam resting on multilayer tensionless extensible geosynthetic reinforced granular fill-poor soil system overlying soft soil strata under moving load with constant velocity is presented. The beam is subjected to a concentrated load moving with constant velocity. The upper reinforced granular bed is modeled by a rough membrane embedded in Pasternak shear layer overlying a series of compressible nonlinear winkler springs representing the underlying the very poor soil. The multilayer tensionless extensible geosynthetic layer has been assumed to deform such that at interface the geosynthetic and the soil have some deformation. Nonlinear behaviour of granular fill and the very poor soil has been considered in the analysis by means of hyperbolic constitutive relationships. Governing differential equations of the soil foundation system have been obtained and solved with the help of appropriate boundary conditions. The solution has been obtained by employing finite difference method by means of Gauss-Siedal iterative scheme. Detailed parametric study has been conducted to study the influence of various parameters on the response of soil–foundation system under consideration by means of deflection and bending moment in the beam and tension mobilized in the geosynthetic layer. These parameters include magnitude of applied load, velocity of load, damping, ultimate resistance of poor soil and granular fill layer. Range of values of parameters has been considered as per Indian Railway conditions. This study clearly observed that the comparisons of multilayer tensionless extensible geosynthetic reinforcement with poor foundation soil and magnitude of applied load, relative compressibility of granular fill and ultimate resistance of poor soil has significant influence on the response of soil–foundation system.

Keywords: Infinite beams, multilayer tensionless extensible geosynthetic, granular layer, moving load, nonlinear behavior of poor soil.

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Authors: Umair Baig, Kohei Nagai

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At highly congested reinforcement regions, which is common at beam-column joint area, clear spacing between parallel bars becomes less than maximum normal aggregate size (20mm) which has not been addressed in any design code and specifications. Limited clear spacing between parallel bars (herein after thin cover) is one of the causes which affect anchorage performance. In this study, an experimental investigation was carried out to understand anchorage performance of reinforcement in Self-Compacting Concrete (SCC) and Normal Concrete (NC) at highly congested regions under uni-axial tensile loading.  Column bar was pullout whereas; beam bars were offset from column reinforcement creating thin cover as per site condition. Two different sizes of coarse aggregate were used for NC (20mm and 10mm). Strain gauges were also installed along the bar in some specimens to understand the internal stress mechanism. Test results reveal that anchorage performance is affected at highly congested reinforcement region in NC with maximum aggregate size 20mm whereas; SCC and Small Aggregate (10mm) gives better structural performance. 

Keywords: Anchorage capacity, bond, Normal Concrete, self-compacting concrete.

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Authors: Yeo Kyeong Lee, Hae Won Min, Ji Yeon Kang, Hee Sun Kim, Yeong Soo Shin

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In recent years, fire accidents have been steadily increased and the amount of property damage caused by the accidents has gradually raised. Damaging building structure, fire incidents bring about not only such property damage but also strength degradation and member deformation. As a result, the building structure undermines its structural ability. Examining the degradation and the deformation is very important because reusing the building is more economical than reconstruction. Therefore, engineers need to investigate the strength degradation and member deformation well, and make sure that they apply right rehabilitation methods. This study aims at evaluating deformation characteristics of fire damaged and rehabilitated normal strength concrete beams through both experiments and finite element analyses. For the experiments, control beams, fire damaged beams and rehabilitated beams are tested to examine deformation characteristics. Ten test beam specimens with compressive strength of 21MPa are fabricated and main test variables are selected as cover thickness of 40mm and 50mm and fire exposure time of 1 hour or 2 hours. After heating, fire damaged beams are air-recurred for 2 months and rehabilitated beams are repaired with polymeric cement mortar after being removed the fire damaged concrete cover. All beam specimens are tested under four points loading. FE analyses are executed to investigate the effects of main parameters applied to experimental study. Test results show that both maximum load and stiffness of the rehabilitated beams are higher than those of the fire damaged beams. In addition, predicted structural behaviors from the analyses also show good rehabilitation effect and the predicted load-deflection curves are similar to the experimental results. For the further, the proposed analytical method can be used to predict deformation characteristics of fire damaged and rehabilitated concrete beams without suffering from time and cost consuming of experimental process.

Keywords: Fire, Normal strength concrete, Rehabilitation, Reinforced concrete beam.

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Authors: Andrey V. Osipov, Sergey A. Kukushkin, Andrey V. Luk’yanov

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A method is developed for the solid-phase synthesis of epitaxial layers when the substrate itself is involved into a topochemical reaction and the reaction product grows in the interior of substrate layer. It opens up new possibilities for the relaxation of the elastic energy due to the attraction of point defects formed during the topochemical reaction in anisotropic media. The presented method of silicon carbide (SiC) formation employs a topochemical reaction between the single-crystalline silicon (Si) substrate and gaseous carbon monoxide (CO). The corresponding theory of interaction of point dilatation centers in anisotropic crystals is developed. It is eliminated that the most advantageous location of the point defects is the direction (111) in crystals with cubic symmetry. The single-crystal SiC films with the thickness up to 200 nm have been grown on Si (111) substrates owing to the topochemical reaction with CO. Grown high-quality single-crystal SiC films do not contain misfit dislocations despite the huge lattice mismatch value of ~20%. Also the possibility of growing of thick wide-gap semiconductor films on these templates SiC/Si(111) and, accordingly, its integration into Si electronics, is demonstrated. Finally, the ab initio theory of SiC formation due to the topochemical reaction has been developed.

Keywords: Epitaxy, silicon carbide, topochemical reaction, wide-bandgap semiconductors.

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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: Bing Lu, Shuang Li, Hongyuan Zhou

Abstract:

The steel-concrete hybrid structure has been extensively employed in high-rise buildings and super high-rise buildings. The light gauge steel-concrete hybrid structure, including light gauge steel structure and concrete hybrid structure, is a type of steel-concrete hybrid structure, which possesses some advantages of light gauge steel structure and concrete hybrid structure. The seismic behavior and loss assessment of three high-rise buildings with three different concrete hybrid structures were investigated through finite element software. The three concrete hybrid structures are reinforced concrete column-steel beam (RC-S) hybrid structure, concrete-filled steel tube column-steel beam (CFST-S) hybrid structure, and tubed concrete column-steel beam (TC-S) hybrid structure. The nonlinear time-history analysis of three high-rise buildings under 80 earthquakes was carried out. After simulation, it indicated that the seismic performances of three high-rise buildings were superior. Under extremely rare earthquakes, the maximum inter-story drifts of three high-rise buildings are significantly lower than 1/50. The inter-story drift and floor acceleration of high-rise building with CFST-S hybrid structure were bigger than those of high-rise buildings with RC-S hybrid structure, and smaller than those of high-rise building with TC-S hybrid structure. Then, based on the time-history analysis results, the post-earthquake repair cost ratio and repair time of three high-rise buildings were predicted through an economic performance analysis method proposed in FEMA-P58 report. Under frequent earthquakes, basic earthquakes and rare earthquakes, the repair cost ratio and repair time of three high-rise buildings were less than 5% and 15 days, respectively. Under extremely rare earthquakes, the repair cost ratio and repair time of high-rise buildings with TC-S hybrid structure were the most among three high rise buildings. Due to the advantages of CFST-S hybrid structure, it could be extensively employed in high-rise buildings subjected to earthquake excitations.

Keywords: seismic behavior, loss assessment, light gauge steel, concrete hybrid structure, high-rise building, time-history analysis

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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: Jihad S. Daba, Jean-Pierre Dubois, Georges El Soury

Abstract:

Fifth generation wireless networks guarantee significant capacity enhancement to suit more clients and services at higher information rates with better reliability while consuming less power. The deployment of massive multiple-input-multiple-output technology guarantees broadband wireless networks with the use of base station antenna arrays to serve a large number of users on the same frequency and time-slot channels. In this work, we evaluate the performance of massive multiple-input-multiple-output systems (MIMO) systems in 5^th generation cellular networks in terms of capacity and bit error rate. Several cases were considered and analyzed to compare the performance of massive MIMO systems while varying the number of antennas at both transmitting and receiving ends. We found that, unlike classical MIMO systems, reducing the number of transmit antennas while increasing the number of antennas at the receiver end provides a better solution to performance enhancement. In addition, enhanced orthogonal frequency division multiplexing and beam division multiple access schemes further improve the performance of massive MIMO systems and make them more reliable.

Keywords: Beam division multiple access, D2D communication, enhanced OFDM, fifth generation broadband, massive MIMO.

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Authors: A. Selmi

Abstract:

Free vibration analysis of homogenous and axially functionally graded simply supported beams within the context of Euler-Bernoulli beam theory is presented in this paper. The material properties of the beams are assumed to obey the linear law distribution. The effective elastic modulus of the composite was predicted by using the rule of mixture. Here, the complexities which appear in solving differential equation of transverse vibration of composite beams which limit the analytical solution to some special cases are overcome using a relatively new approach called the Differential Transformation Method. This technique is applied for solving differential equation of transverse vibration of axially functionally graded beams. Natural frequencies and corresponding normalized mode shapes are calculated for different Young’s modulus ratios. MATLAB code is designed to solve the transformed differential equation of the beam. Comparison of the present results with the exact solutions proves the effectiveness, the accuracy, the simplicity, and computational stability of the differential transformation method. The effect of the Young’s modulus ratio on the normalized natural frequencies and mode shapes is found to be very important.

Keywords: Differential transformation method, functionally graded material, mode shape, natural frequency.

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

Abstract:

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: Rudy Djamaluddin, Yasser Bachtiar, Rita Irmawati, Abd. Madjid Akkas, Rusdi Usman Latief

Abstract:

The aesthetic qualities and the versatility of reinforced concrete have made it a popular choice for many architects and structural engineers. Therefore, the exploration of natural materials such as gravels and sands as well as lime-stone for cement production is increasing to produce a concrete material. The exploration must affect to the environment. Therefore, the using of the concrete materials should be as efficient as possible. According to its natural behavior of the concrete material, it is strong in compression and weak in tension. Therefore the contribution of the tensile stresses of the concrete to the flexural capacity of the beams is neglected. However, removing of concrete on tension zone affects to the decreasing of flexural capacity. Introduce the strut action of truss structures may an alternative to solve the decreasing of flexural capacity. A series of specimens were prepared to clarify the effect of the truss structures in the concrete beams without concrete on the tension zone. Results indicated that the truss system is necessary for the external reinforced concrete beams. The truss system of concrete beam without concrete on tension zone (BR) could develop almost same capacity to the normal beam (BN). It can be observed also that specimens BR has lower number of cracks than specimen BN. This may be caused by the fact that there was no bonding effect on the tensile reinforcement on specimen BR to distribute the cracks.

Keywords: External Reinforcement, Truss, Concrete Beams.

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

Abstract:

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

Abstract:

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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