Search results for: molecular mobility

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: 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: Trevor Kroeger, Hayden Williams, Edward Holzinger, David Coleman, Brian Haberman

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The network connectivity of medical devices is increasing at a rapid rate. Many medical devices, such as vital sign monitors, share information via wireless or wired connections. However, these connectivity options suffer from a variety of well-known limitations. Wireless connectivity, especially in the unlicensed radio frequency bands, can be disrupted. Such disruption could be due to benign reasons, such as a crowded spectrum, or to malicious intent. While wired connections are less susceptible to interference, they inhibit the mobility of the medical devices, which could be critical in a variety of scenarios. This work explores the application of Light Fidelity (Li-Fi) communication to enhance the security, performance, and mobility of medical devices in connected healthcare scenarios. A simple bridge for connected devices serves as an avenue to connect traditional medical devices to the Li-Fi network. This bridge was utilized to conduct bandwidth tests on a small Li-Fi network installed into a Mock-ICU setting with a backend enterprise network similar to that of a hospital. Mobile and stationary tests were conducted to replicate various different situations that might occur within a hospital setting. Results show that in room Li-Fi connectivity provides reasonable bandwidth and latency within a hospital like setting.

Keywords: Hospital, light fidelity, Li-Fi, medical devices, security.

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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: Yuyun Wabula, B. J. Dewancker

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In the past decade, the social networking app has been growing very rapidly. Geolocation data is one of the important features of social media that can attach the user's location coordinate in the real world. This paper proposes the use of geolocation data from the Twitter social media application to gain knowledge about urban dynamics, especially on human mobility behavior. This paper aims to explore the relation between geolocation Twitter with the existence of people in the urban area. Firstly, the study will analyze the spread of people in the particular area, within the city using Twitter social media data. Secondly, we then match and categorize the existing place based on the same individuals visiting. Then, we combine the Twitter data from the tracking result and the questionnaire data to catch the Twitter user profile. To do that, we used the distribution frequency analysis to learn the visitors’ percentage. To validate the hypothesis, we compare it with the local population statistic data and land use mapping released by the city planning department of Makassar local government. The results show that there is the correlation between Twitter geolocation and questionnaire data. Thus, integration the Twitter data and survey data can reveal the profile of the social media users.

Keywords: Geolocation, Twitter, distribution analysis, human mobility.

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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: 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: José M. Cantera, Miguel Jiménez, Genoveva López, Javier Soriano

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With the advent of emerging personal computing paradigms such as ubiquitous and mobile computing, Web contents are becoming accessible from a wide range of mobile devices. Since these devices do not have the same rendering capabilities, Web contents need to be adapted for transparent access from a variety of client agents. Such content adaptation is exploited for either an individual element or a set of consecutive elements in a Web document and results in better rendering and faster delivery to the client device. Nevertheless, Web content adaptation sets new challenges for semantic markup. This paper presents an advanced components platform, called SMC, enabling the development of mobility applications and services according to a channel model based on the principles of Services Oriented Architecture (SOA). It then goes on to describe the potential for integration with the Semantic Web through a novel framework of external semantic annotation that prescribes a scheme for representing semantic markup files and a way of associating Web documents with these external annotations. The role of semantic annotation in this framework is to describe the contents of individual documents themselves, assuring the preservation of the semantics during the process of adapting content rendering. Semantic Web content adaptation is a way of adding value to Web contents and facilitates repurposing of Web contents (enhanced browsing, Web Services location and access, etc).

Keywords: Semantic web, ubiquitous and mobile computing, web content transcoding. semantic mark-up, mobile computing, middleware and services.

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Authors: Anirudh Sunil Warrier, Saba Al-Rubaye, Dimitrios Panagiotakopoulos, Gokhan Inalhan, Antonios Tsourdos

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The demand for increased data transfer rate and network traffic capacity has given rise to the concept of heterogeneous networks. Heterogeneous networks are wireless networks, consisting of devices using different underlying radio access technologies (RAT). For Unmanned Aerial Vehicles (UAVs) this enhanced data rate and network capacity are even more critical especially in their applications of medicine, delivery missions and military. In an urban heterogeneous network environment, the UAVs must be able switch seamlessly from one base station (BS) to another for maintaining a reliable link. Therefore, seamless handover in such urban environments has become a major challenge. In this paper, a scheme to achieve seamless handover is developed, an algorithm based on Received Signal Strength (RSS) criterion for network selection is used and Entropy Weighted Method (EWM) is implemented for decision making. Seamless handover using EWM decision-making is demonstrated successfully for a UAV moving across fifth generation (5G) and long-term evolution (LTE) networks via a simulation level analysis. Thus, a solution for UAV-5G communication, specifically the mobility challenge in heterogeneous networks is solved and this work could act as step forward in making UAV-5G architecture integration a possibility.

Keywords: Air to ground, A2G, fifth generation, 5G, handover, mobility, unmanned aerial vehicle, UAV, urban environments.

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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

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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: Farzana Yasmeen, Md. Nurul Huda, Md. Enamul Haque, Michihiro Aoki, Shigeki Yamada

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Delay-Tolerant Networks (DTNs) are sparse, wireless networks where disconnections are common due to host mobility and low node density. The Message Ferrying (MF) scheme is a mobilityassisted paradigm to improve connectivity in DTN-like networks. A ferry or message ferry is a special node in the network which has a per-determined route in the deployed area and relays messages between mobile hosts (MHs) which are intermittently connected. Increased contact opportunities among mobile hosts and the ferry improve the performance of the network, both in terms of message delivery ratio and average end-end delay. However, due to the inherent mobility of mobile hosts and pre-determined periodicity of the message ferry, mobile hosts may often -miss- contact opportunities with a ferry. In this paper, we propose the combination of stationary ferry access points (FAPs) with MF routing to increase contact opportunities between mobile hosts and the MF and consequently improve the performance of the DTN. We also propose several placement models for deploying FAPs on MF routes. We evaluate the performance of the FAP placement models through comprehensive simulation. Our findings show that FAPs do improve the performance of MF-assisted DTNs and symmetric placement of FAPs outperforms other placement strategies.

Keywords: Service infrastructure, delay-tolerant network, messageferry routing, placement models.

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Authors: Zhiyuan Du, Baisravan Hom Chaudhuri, Pierluigi Pisu

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In connected vehicle systems where wireless communication is available among the involved vehicles and intersection controllers, it is possible to design an intersection coordination strategy that leads the connected and automated vehicles (CAVs) travel through the road intersections without the conventional traffic light control. In this paper, we present a distributed coordination strategy for the CAVs at multiple interconnected intersections that aims at improving system fuel efficiency and system mobility. We present a distributed control solution where in the higher level, the intersection controllers calculate the road desired average velocity and optimally assign reference velocities of each vehicle. In the lower level, every vehicle is considered to use model predictive control (MPC) to track their reference velocity obtained from the higher level controller. The proposed method has been implemented on a simulation-based case with two-interconnected intersection network. Additionally, the effects of mixed vehicle types on the coordination strategy has been explored. Simulation results indicate the improvement on vehicle fuel efficiency and traffic mobility of the proposed method.

Keywords: Connected vehicles, automated vehicles, intersection coordination systems, multiple interconnected intersections, model predictive control.

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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: Dhiraj Dolai, Rupayan Bhattacharya

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In this study, a comparison of Range Of Motion (ROM) of middle and long-distance runners and swimmers has been made. The mobility of the various joints is essential for the quick movement of any sportsman. Knowledge of a ROM helps in preventing injuries, in repeating the movement, and in generating speed and power. ROM varies among individuals, and it is influenced by factors such as gender, age, and whether the motion is performed actively or passively. ROM for running and swimming, both performed with due consideration on speed, plays an important role. The time of generation of speed and mobility of the particular joints are very important for both kinds of athletes. The difficulties that happen during running and swimming in the direction of motion is changed. In this study, data were collected for a total of 102 subjects divided into three groups: control group (22), middle and long-distance runners (40), and swimmers (40), and their ages are between 12 to 18 years. The swimmers have higher ROM in shoulder joint flexion, extension, abduction, and adduction movement. Middle and long-distance runners have significantly greater ROM from Control Group in the left shoulder joint flexion with a 5.82 mean difference. Swimmers have significantly higher ROM from the Control Group in the left shoulder joint flexion with 24.84 mean difference and swimmers have significantly higher ROM from the Middle and Long distance runners in left shoulder flexion with 19.02 mean difference. The picture will be clear after a more detailed investigation.

Keywords: Range of motion, runners, swimmers, significance.

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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: Ali Jahanfar, Brajesh Dubey, Bahram Gharabaghi, Saber Bayat Movahed

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Ever increasing population growth of major urban centers and environmental challenges in siting new landfills have resulted in a growing trend in design of mega-landfills some with extraordinary heights and dangerously steep slopes. Landfill failure mobility risk analysis is one of the most uncertain types of dynamic rheology models due to very large inherent variabilities in the heterogeneous solid waste material shear strength properties. The waste flow of three historic dumpsite and two landfill failures were back-analyzed using run-out modeling with DAN-W model. The travel distances of the waste flow during landfill failures were calculated approach by taking into account variability in material shear strength properties. The probability distribution function for shear strength properties of the waste material were grouped into four major classed based on waste material compaction (landfills versus dumpsites) and composition (high versus low quantity) of high shear strength waste materials such as wood, metal, plastic, paper and cardboard in the waste. This paper presents a probabilistic method for estimation of the spatial extent of waste avalanches, after a potential landfill failure, to create maps of vulnerability scores to inform property owners and residents of the level of the risk.

Keywords: Landfill failure, waste flow, Voellmy rheology, friction coefficient, waste compaction and type.

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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

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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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Authors: Kholoud A. Al-Shammery , Badr El-Sabah A. Fetoh, Ahmed M. Alshammari

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Protein and Esterase electrophoresis were used to genetically identify two Saudi tick species. Engorged females of the camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks collected from infested camels and cattle in the animals resting house at Hail region in KSA were used. The results showed that there are a variation in both of protein and esterase activity levels and a high polymorphism within and between the genera and species of Hyalomma and Boophilus . In conclusion, the protein and esterase electrophoretic analysis used in the present study could successfully distinguish among tick species, commonly found in Saudi Arabia.

Keywords: Molecular biology, The camel tick Hyalomma dromedarii, The cattle tick Boophilus annulatus , Ticks.

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Authors: S. Kulsri, M. Jaroensutasinee, K. Jaroensutasinee

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We developed a new method based on quasimolecular modeling to simulate the cavity flow in three cavity shapes: rectangular, half-circular and bucket beer in cgs units. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. When a cavity flow was simulated, the instantaneous velocity vector fields were obtained by using an inverse distance weighted interpolation method. In all three cavity shapes, fluid motion was rotated counter-clockwise. The velocity vector fields of the three cavity shapes showed a primary vortex located near the upstream corners at time t ~ 0.500 s, t ~ 0.450 s and t ~ 0.350 s, respectively. The configurational kinetic energy of the cavities increased as time increased until the kinetic energy reached a maximum at time t ~ 0.02 s and, then, the kinetic energy decreased as time increased. The rectangular cavity system showed the lowest kinetic energy, while the half-circular cavity system showed the highest kinetic energy. The kinetic energy of rectangular, beer bucket and half-circular cavities fluctuated about stable average values 35.62 x 103, 38.04 x 103 and 40.80 x 103 ergs/particle, respectively. This indicated that the half-circular shapes were the most suitable shape for a shrimp pond because the water in shrimp pond flows best when we compared with rectangular and beer bucket shape.

Keywords: Quasi-molecular modelling, particle modelling, lid driven cavity flow.

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Authors: Safyeh Soufian, Hoosein Naderi-Manesh, Abdoali Alizadeh, Mohammad Nabi Sarbolouki

Abstract:

Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.

Keywords: Antimicrobial peptides, retro, molecular dynamic, circular dichroism.

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Authors: Amr A. El Hanafy, Yasir Anwar, Saleh A. Mohamed, Saleh Mohamed Saleh Al-Garni, Jamal S. M. Sabir, Osama A. H. Abu Zinadah, Mohamed Morsi Ahmed

Abstract:

In the vicinity of red sea about 15 fungi species were isolated from oil contaminated sites. On the basis of aptitude to degrade the crude oil and DCPIP assay, two fungal isolates were selected amongst 15 oil degrading strains. Analysis of ITS-1, ITS-2 and amplicon pyrosequencing studies of fungal diversity revealed that these strains belong to Penicillium and Aspergillus species. Two strains that proved to be the most efficient in degrading crude oil was Aspergillus niger (54%) and Penicillium commune (48%) Subsequent to two weeks of cultivation in BHS medium the degradation rate were recorded by using spectrophotometer and GC-MS. Hence, it is cleared that these fungal strains has capability of degradation and can be utilize for cleaning the Saudi Arabian environment.

Keywords: Fungal strains, hydrocarbon contaminants, molecular identification, biodegradation, GC-MS.

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Authors: B. Juhasova, I. Halenar, M. Juhas

Abstract:

The wireless communication is one of the widely used methods of data transfer at the present days. The benefit of this communication method is the partial independence of the infrastructure and the possibility of mobility. In some special applications it is the only way how to connect. This paper presents some problems in the implementation of a sensor network connection for measuring environmental parameters in the area of manufacturing plants.

Keywords: Network, communication, reliability, sensors.

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