Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1655

Search results for: molecular topology

1445 Effect of Polymer Molecular Structures on Properties of Dental Cement Restoratives

Authors: Dong Xie, Jun Zhao, Yiming Weng

Abstract:

One of the challenges in dental cement biomaterials is how to make a restorative with mechanical strengths and wear resistance that are comparable to contemporary dental resin composites. Currently none of the dental cement restoratives has been used in high stress-bearing sites due to their low mechanical strengths and poor wear-resistance. The objective of this study was to synthesize and characterize the poly(alkenoic acid)s with different molecular structures, use these polymers to formulate a dental cement restorative, and study the effect of molecular structures on reaction kinetics, viscosity, and mechanical strengths of the formed polymers and cement restoratives. In this study, poly(alkenoic acid)s with different molecular structures were synthesized. The purified polymers were formulated with commercial Fuji II LC glass fillers to form the experimental cement restoratives. The reaction kinetics was studied via 1HNMR spectroscopy. The formed restoratives were evaluated using compressive strength, diametral tensile strength, flexural strength, hardness and wear-resistance tests. Specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. Fuji II LC restorative was used as control. The results show that the higher the arm number and initiator concentration, the faster the reaction was. It was also found that the higher the arm number and branching that the polymer had, the lower the viscosity of the polymer in water and the lower the mechanical strengths of the formed restorative. The experimental restoratives were 31-53% in compressive strength, 37-55% in compressive modulus, 80-126% in diametral tensile strength, 76-94% in flexural strength, 4-21% in fracture toughness and 53-96% in hardness higher than Fuji II LC. For wear test, the experimental restoratives were only 5.4-13% of abrasive and 6.4-12% of attritional wear depths of Fuji II LC in each wear cycle. The aging study also showed that all the experimental restoratives increased their strength continuously during 30 days, unlike Fuji II LC. It is concluded that polymer molecular structures have significant and positive impact on mechanical properties of dental cement restoratives.

Keywords: Biomaterials, Polymers, Dental Materials, Strength

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1444 Analysis of Expert Possibilities While Identifying Human Teeth

Authors: Saule Mussabekova

Abstract:

Forensic investigation of human teeth plays an important role in detection of crime, particularly in cases of personal identification of dead bodies changed by putrefactive processes or skeletonized bodies as well as when finding bodies of unknown persons. 152 teeth have been investigated; 85 of them belonged to men and 67 belonged to women taken from alive people of different age. Teeth have been investigated after extraction. Two types of teeth have been investigated: teeth without integrity violation of dental crown and teeth with different degrees of its violation. Additionally, 517 teeth have been investigated that were collected from dead bodies, 252 of which belonged to women and 265 belonged to men, whatever the cause of death with death limitation from 1 month to 20 years. Isohemagglutinating serums and Coliclons of different series have been used for the research of tooth-group specificity by serological methods according to the AB0 system. Standard protocols of different techniques have been used for DNA purification from teeth (by reagent Chelex 100 produced by Bio-Rad using reagent kit 'DNA IQTM System' produced by Promega company (USA) and using columns 'QIAamp DNA Investigator Kit' produced by Qiagen company). Results of comparative forensic investigation of human teeth using serological and molecular genetic methods have shown that use of serological methods for forensic identification is sensible only in cases of preselection prior to the next molecular genetic investigation as well as in cases of impossibility of corresponding genetic investigation for different objective reasons. A number of advantages of methods of molecular genetics in the dental investigation have been marked, particularly in putrefactive changes, in personal identification. Key moments of modern condition of personal identification have been reflected according to dental state. Prospective directions of advance preparation of material have been emphasized for identification of teeth in forensic practice.

Keywords: teeth, dental state, forensic identification, molecular genetic analysis

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1443 Viscoelastic Response of the Human Corneal Stroma Induced by Riboflavin/UVA Cross-Linking

Authors: C. Labate, M. P. De Santo, G. Lombardo, R. Barberi, M. Lombardo, N. M. Ziebarth

Abstract:

In the past decades, the importance of corneal biomechanics in the normal and pathological functions of the eye has gained its credibility. In fact, the mechanical properties of biological tissues are essential to their physiological function. We are convinced that an improved understanding of the nanomechanics of corneal tissue is important to understand the basic molecular interactions between collagen fibrils. Ultimately, this information will help in the development of new techniques to cure ocular diseases and in the development of biomimetic materials. Therefore, nanotechnology techniques are powerful tools and, in particular, Atomic Force Microscopy has demonstrated its ability to reliably characterize the biomechanics of biological tissues either at the micro- or nano-level. In the last years, we have investigated the mechanical anisotropy of the human corneal stroma at both the tissue and molecular levels. In particular, we have focused on corneal cross-linking, an established procedure aimed at slowing down or halting the progression of the disease known as keratoconus. We have obtained the first evidence that riboflavin/UV-A corneal cross-linking induces both an increase of the elastic response and a decrease of the viscous response of the most anterior stroma at the scale of stromal molecular interactions.

Keywords: Atomic Force Spectroscopy, Viscoelasticity, cross-linking, corneal stroma

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1442 Investigation of Ignition Delay for Low Molecular Hydrocarbon Fuel and Oxygen Mixture behind the Reflected Shock

Authors: Aldin Justin Sundararaj, A. N. Subash, K. R. Guna, B. C. Pillai

Abstract:

A systematic study has been made for ignition delay times measurement behind a reflected shock wave for the low molecular weight hydrocarbon fuel in argon simulated gas mixtures. The low molecular hydrocarbon fuel–oxygen was diluted with argon for desired concentration is taken for the study. The suitability of the shock tube for measuring the ignition delay time is demonstrated by measuring the ignition delay for the liquefied petroleum gas for equivalence ratios (ф=0.5 & 1) in the temperature range 1150-1650 K. The pressure range was fixed from 5-15 bar. The ignition delay was measured by recording the ignition-induced pressure jump and emission from CH radical simultaneously. From conducting experiments, it was found that the ignition delay time for liquefied petroleum gas reduces with increase in temperature. The shock tube was calibrated for ethane-oxygen gas mixture and the results obtained from this study is compared with the earlier reported values and found to be comparably well suited for the measurement of ignition delay times. The above work was carried out using the shock tube facility at propulsion and high enthalpy laboratory, Karunya University.

Keywords: ignition delay, shock wave, LPG, reflected shock

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1441 Preliminary Analysis of a Phylogeography Study of Dendropsophus minutus in the Guiana Shield

Authors: Mera-Martínez Daniela

Abstract:

Dendropsophus minutus, is a species distributed in South America including the slopes of the Andes, the Amazon basin, forests of southeastern Brazil and in Guyana where tropical forests are characteristic. The relationship of amphibians found in this locality is evidenced by molecular markers, with the objective of analyzing if the geographic distance is influencing the structure of the populations of D. minutus in Guyana; we analyzed 65 sequences from the 3 localities of Guyana where haplotype networks, Mantel Test and phylogeny were realized to know the influence. It was evidenced that there is a haplotypic difference in the locality of Guyana compared to Suriname and French Guyana, but this does not have a correlation with the geographic distance, but this one can be influenced by the conditions of the places.

Keywords: Phylogeography, Molecular markers, Dendropsophus, geographic distance

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1440 Poly (N-Isopropyl Acrylamide-Co-Acrylic Acid)-Graft-Polyaspartate Coated Magnetic Nanoparticles for Molecular Imaging and Therapy

Authors: Van Tran Thi Thuy, Dukjoon Kim

Abstract:

A series of pH- and thermosensitive poly(N-isopropyl acrylamide-co-acrylic acid) were synthesized by radical polymerization and grafted on poly succinimide backbones. The poly succinimide derivatives synthesized were coated on iron oxide magnetic nanoparticles for potential applications in drug delivery systems with theranostic and molecular imaging. The structure of polymer shell was confirmed by FT-IR, H-NMR spectroscopies. Its thermal behavior was tested by UV-Vis spectroscopy. The particle size and its distribution are measured by dynamic light scattering (DLS) and transmission electron microscope (TEM). The mean diameter of the core-shell structure is from 20 to 80 nm.

Keywords: Magnetic, Nano, PNIPAM, polysuccinimide

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1439 A First-Principles Investigation of Magnesium-Hydrogen System: From Bulk to Nano

Authors: Paramita Banerjee, K. R. S. Chandrakumar, G. P. Das

Abstract:

Bulk MgH2 has drawn much attention for the purpose of hydrogen storage because of its high hydrogen storage capacity (~7.7 wt %) as well as low cost and abundant availability. However, its practical usage has been hindered because of its high hydrogen desorption enthalpy (~0.8 eV/H2 molecule), which results in an undesirable desorption temperature of 3000C at 1 bar H2 pressure. To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, a detailed first-principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12), as well as their interaction with molecular hydrogen (H2), is reported here. It has been found that due to the absence of d-electrons within the Mg atoms, hydrogen remained in molecular form even after its interaction with neutral and charged Mg nanoclusters. Interestingly, the H2 molecules do not enter into the interstitial positions of the nanoclusters. Rather, they remain on the surface by ornamenting these nanoclusters and forming new structures with a gravimetric density higher than 15 wt %. Our observation is that the inclusion of Grimme’s DFT-D3 dispersion correction in this weakly interacting system has a significant effect on binding of the H2 molecules with these nanoclusters. The dispersion corrected interaction energy (IE) values (0.1-0.14 eV/H2 molecule) fall in the right energy window, that is ideal for hydrogen storage. These IE values are further verified by using high-level coupled-cluster calculations with non-iterative triples corrections i.e. CCSD(T), (which has been considered to be a highly accurate quantum chemical method) and thereby confirming the accuracy of our ‘dispersion correction’ incorporated DFT calculations. The significance of the polarization and dispersion energy in binding of the H2 molecules are confirmed by performing energy decomposition analysis (EDA). A total of 16, 24, 32 and 36 H2 molecules can be attached to the neutral and charged nanoclusters of size m = 2, 4, 8 and 12 respectively. Ab-initio molecular dynamics (AIMD) simulation shows that the outermost H2 molecules are desorbed at a rather low temperature viz. 150 K (-1230C) which is expected. However, complete dehydrogenation of these nanoclusters occur at around 1000C. Most importantly, the host nanoclusters remain stable up to ~500 K (2270C). All these results on the adsorption and desorption of molecular hydrogen with neutral and charged Mg nanocluster systems indicate towards the possibility of reducing the dehydrogenation temperature of bulk MgH2 by designing new Mg-based nano materials which will be able to adsorb molecular hydrogen via this weak Mg-H2 interaction, rather than the strong Mg-H bonding. Notwithstanding the fact that in practical applications, these interactions will be further complicated by the effect of substrates as well as interactions with other clusters, the present study has implications on our fundamental understanding to this problem.

Keywords: Molecular Dynamics, Hydrogen Storage, physisorption, Density Functional Theory, dft, Nanoclusters, molecular hydrogen adsorption

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1438 Molecular Detection and Isolation of Benzimidazole Resistant Haemonchus contortus from Pakistan

Authors: M. Younus, I. Khan, K. Ali, M. F. Qamar, M. A. Zaman, S. Ehtisham-ul-Haque, R. Tamkeen, M. I. Rashid, Q. Ali

Abstract:

This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region.

Keywords: Haemonchus contortus, Benzimidazole resistant, β-tubulin-1 gene, abattoirs

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1437 Applying Computer Simulation Methods to a Molecular Understanding of Flaviviruses Proteins towards Differential Serological Diagnostics and Therapeutic Intervention

Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

Abstract:

The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: Biomolecular Interactions, Molecular mechanisms, Zika, electrostatic interactions

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1436 Synthesis, Molecular Docking, and Cytotoxic Activity of Novel Triazolopyridazine Derivatives

Authors: Azza T. Tahera, Eman M. Ahmeda, Nadia A. Khalila, Yassin M. Nissanb

Abstract:

New 3-(pyridin-4-yl)-[1,2,4] triazolo [4,3-b] pyridazine derivatives 2a-i, 4a,b and 6a,b were designed, synthesized and evaluated as cytotoxic agents. All compounds were investigated for their in vitro cytotoxicity at a single dose 10-5M concentration towards 60 cancer cell lines according to USA NCI protocol. The preliminary screening results showed that the majority of tested compounds exhibited remarkable activity against SR (leukemia) cell panel. Molecular docking for all synthesized compounds was performed on the active site of c-Met kinase. The most active compounds, 2f and 4a were further evaluated at a seven dose level screening and their IC50 as a c-Met kinase inhibitors were determined in vitro.

Keywords: triazolopyridazines, pyridazines, cytotoxic activity, cell panel

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1435 A Study of Anthraquinone Dye Removal by Using Chitosan Nanoparticles

Authors: Sonal Gupta, Pyar S. Jassal, Neema Chand, Rajni Johar

Abstract:

In present study, Low molecular weight chitosan naoparticles (LMWCNP) were synthesized by using low molecular weight chitosan (LMWC) and sodium tripolyphosphate for the adsorption of anthraquinone dyes from waste water. The ionic-gel technique was used for this purpose. Size of nanoparticles was determined by “Scherrer equation”. The absorbance was carried out with UV-visible spectrophotometer for Acid Green 25 (AG25) and Reactive Blue 4 (RB4) dyes solutions at λmax 644 and λmax 598 nm respectively. The removal of dyes was dependent on the pH and the optimum adsorption was between pH 2 to 9. The extraction of dyes was linearly dependent on temperature. The equilibrium parameters, RL was calculated by using the Langmuir isotherm and shows that adsorption of dyes is favorable on the LMWCNP. The XRD images of LMWC show a crystalline nature whereas LMWCNP is amorphous one. The thermo gravimetric analysis (TGA) shows that LMWCNP thermally more stable than LMWC. As the contact time increases, percentage removal of Acid Green 25 and Reactive Blue 4 dyes also increases. TEM images reveal the size of the LMWCNP were in the range of 45-50 nm. The capacity of AG25 dye on LMWC was 5.23 mg/g, it compared with LMWCNP capacity which was 6.83 mg/g respectively. The capacity of RB4 dye on LMWC was 2.30 mg/g and 2.34 mg/g was on LMWCNP.

Keywords: adsorption isotherm, removal efficiency, low molecular weight chitosan nanoparticles, anthraquinone dye

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1434 Development of Calcium Carbonate Molecular Sheets via Wet Chemical Route

Authors: Sudhir Kumar Sharma, Ramesh Jagannathan

Abstract:

The interaction of organic and inorganic matrices of biological origin resulting in self-assembled structures with unique properties is well established. The development of such self-assembled nanostructures by synthetic and bio-inspired techniques is an established field of active research. Among bio-materials, nacre, a laminar stack of calcium carbonate nanosheets, which are interleaved with organic material, has long been focused research due to its unique mechanical properties. In this paper, we present the development of nacre-like lamellar structures made up of calcium carbonate via a wet chemical route. We used the binding affinity of carboxylate anions and calcium cations using poly (acrylic) acid (PAA) to lead CaCO₃ crystallization. In these experiments, we selected calcium acetate as the precursor molecule along with PAA (Mw ~ 8000 Da). We found that Ca⁺²/COO⁻ ratio provided a tunable control for the morphology and growth of CaCO₃ nanostructures. Drop casting one such formulation on a silicon substrate followed by calcination resulted in co-planner, molecular sheets of CaCO₃, separated by a spacer layer of carbon. The scope of our process could be expanded to produce unit cell thick molecular sheets of other important inorganic materials.

Keywords: Bio-Inspired Materials, calcium carbonate, self-assembled structures, wet chemical route

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1433 Study of Functional Relevant Conformational Mobility of β-2 Adrenoreceptor by Means of Molecular Dynamics Simulation

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

Abstract:

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 behaviour.

Keywords: Principal Component Analysis, X-Ray Crystallography, seven-transmembrane receptors, constitutive activity, activation, molecular dynamics simulation

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1432 Molecular Dynamics Simulation for Buckling Analysis at Nanocomposite Beams

Authors: Babak Safaei, A. M. Fattahi

Abstract:

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, generalized differential quadrature (GDQ), axial buckling

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1431 Molecular Insights into the Genetic Integrity of Long-Term Micropropagated Clones Using Start Codon Targeted (SCoT) Markers: A Case Study with Ansellia africana, an Endangered, Medicinal Orchid

Authors: Vijay Kumar, Johannes Van Staden, Paromik Bhattacharyya

Abstract:

Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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1430 A Survey of Novel Opportunistic Routing Protocols in Mobile Ad Hoc Networks

Authors: R. Poonkuzhali, M. Y. Sanavullah, M. R. Gurupriya

Abstract:

Opportunistic routing is used, where the network has the features like dynamic topology changes and intermittent network connectivity. In Delay Tolerant network or Disruption tolerant network opportunistic forwarding technique is widely used. The key idea of opportunistic routing is selecting forwarding nodes to forward data and coordination among these nodes to avoid duplicate transmissions. This paper gives the analysis of pros and cons of various opportunistic routing techniques used in MANET.

Keywords: throughput, ETX, opportunistic routing, PSR

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1429 Molecular Characterization and Phylogenetic Analysis of Influenza a(H3N2) Virus Circulating during the 2010-2011 in Riyadh, Saudi Arabia

Authors: Ghazanfar Ali, Fahad N Almajhdi

Abstract:

This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: Saudi Arabia, RT-PCR, influenza A (H3N2), genetic characterization, viral isolation

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1428 Prediction of Phonon Thermal Conductivity of F.C.C. Al by Molecular Dynamics Simulation

Authors: Tanvir Ahmed, Leila Momenzadeh, Alexander V. Evteev, Elena V. Levchenko, Irina Belova, Graeme Murch

Abstract:

In this work, the phonon thermal conductivity of f.c.c. Al is investigated in detail in the temperature range 100 – 900 K within the framework of equilibrium molecular dynamics simulations making use of the Green-Kubo formalism and one of the most reliable embedded-atom method potentials. It is found that the heat current auto-correlation function of the f.c.c. Al model demonstrates a two-stage temporal decay similar to the previously observed for f.c.c Cu model. After the first stage of decay, the heat current auto-correlation function of the f.c.c. Al model demonstrates a peak in the temperature range 100-800 K. The intensity of the peak decreases as the temperature increases. At 900 K, it transforms to a shoulder. To describe the observed two-stage decay of the heat current auto-correlation function of the f.c.c. Al model, we employ decomposition model recently developed for phonon-mediated thermal transport in a monoatomic lattice. We found that the electronic contribution to the total thermal conductivity of f.c.c. Al dominates over the whole studied temperature range. However, the phonon contribution to the total thermal conductivity of f.c.c. Al increases as temperature decreases. It is about 1.05% at 900 K and about 12.5% at 100 K.

Keywords: Molecular Dynamics, Aluminum, gGreen-Kubo formalism, phonon thermal conductivity

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1427 Characterization of Organic Matter in Spodosol Amazonian by Fluorescence Spectroscopy

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

Abstract:

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: Characterization, Humic Acid , Fluorescence, lifetime, Amazonian soil

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1426 Molecular Biomonitoring of Bacterial Pathogens in Wastewater

Authors: Sahar Zaki, Desouky Abd El Haleem

Abstract:

This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp, bacterial pathogens

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1425 Phase Transition of Aqueous Ternary (THF + Polyvinylpyrrolidone + H2O) System as Revealed by Terahertz Time-Domain Spectroscopy

Authors: Yun-Ho Ahn, Hyery Kang, Dong-Yeun Koh, Huen Lee

Abstract:

Determination of the behavior of clathrate hydrate with inhibitor in the THz region will provide useful information about hydrate plug control in the upstream of the oil and gas industry. In this study, terahertz time-domain spectroscopy (THz-TDS) revealed the inhibition of the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different molecular weights. Distinct footprints of phase transition in the THz region (0.4–2.2 THz) were analyzed and absorption coefficients and real part of refractive indices are obtained in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: Terahertz spectroscopy, tetrahydrofuran, clathrate hydrate, inhibitor

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1424 Probabilistic Graphical Model for the Web

Authors: M. Nekri, A. Khelladi

Abstract:

The world wide web network is a network with a complex topology, the main properties of which are the distribution of degrees in power law, A low clustering coefficient and a weak average distance. Modeling the web as a graph allows locating the information in little time and consequently offering a help in the construction of the research engine. Here, we present a model based on the already existing probabilistic graphs with all the aforesaid characteristics. This work will consist in studying the web in order to know its structuring thus it will enable us to modelize it more easily and propose a possible algorithm for its exploration.

Keywords: clustering coefficient, preferential attachment, small world, web community

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1423 A Machine Learning-Based Model to Screen Antituberculosis Compound Targeted against LprG Lipoprotein of Mycobacterium tuberculosis

Authors: Syed Asif Hassan, Syed Atif Hassan

Abstract:

Multidrug-resistant Tuberculosis (MDR-TB) is an infection caused by the resistant strains of Mycobacterium tuberculosis that do not respond either to isoniazid or rifampicin, which are the most important anti-TB drugs. The increase in the occurrence of a drug-resistance strain of MTB calls for an intensive search of novel target-based therapeutics. In this context LprG (Rv1411c) a lipoprotein from MTB plays a pivotal role in the immune evasion of Mtb leading to survival and propagation of the bacterium within the host cell. Therefore, a machine learning method will be developed for generating a computational model that could predict for a potential anti LprG activity of the novel antituberculosis compound. The present study will utilize dataset from PubChem database maintained by National Center for Biotechnology Information (NCBI). The dataset involves compounds screened against MTB were categorized as active and inactive based upon PubChem activity score. PowerMV, a molecular descriptor generator, and visualization tool will be used to generate the 2D molecular descriptors for the actives and inactive compounds present in the dataset. The 2D molecular descriptors generated from PowerMV will be used as features. We feed these features into three different classifiers, namely, random forest, a deep neural network, and a recurring neural network, to build separate predictive models and choosing the best performing model based on the accuracy of predicting novel antituberculosis compound with an anti LprG activity. Additionally, the efficacy of predicted active compounds will be screened using SMARTS filter to choose molecule with drug-like features.

Keywords: Machine Learning, prediction, classifier, molecular descriptors, antituberculosis drug

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1422 Performance of Non-Deterministic Structural Optimization Algorithms Applied to a Steel Truss Structure

Authors: Ersilio Tushaj

Abstract:

The efficient solution that satisfies the optimal condition is an important issue in the structural engineering design problem. The new codes of structural design consist in design methodology that looks after the exploitation of the total resources of the construction material. In recent years some non-deterministic or meta-heuristic structural optimization algorithms have been developed widely in the research community. These methods search the optimum condition starting from the simulation of a natural phenomenon, such as survival of the fittest, the immune system, swarm intelligence or the cooling process of molten metal through annealing. Among these techniques the most known are: the genetic algorithms, simulated annealing, evolution strategies, particle swarm optimization, tabu search, ant colony optimization, harmony search and big bang crunch optimization. In this study, five of these algorithms are applied for the optimum weight design of a steel truss structure with variable geometry but fixed topology. The design process selects optimum distances and size sections from a set of commercial steel profiles. In the formulation of the design problem are considered deflection limitations, buckling and allowable stress constraints. The approach is repeated starting from different initial populations. The design problem topology is taken from an existing steel structure. The optimization process helps the engineer to achieve good final solutions, avoiding the repetitive evaluation of alternative designs in a time consuming process. The algorithms used for the application, the results of the optimal solutions, the number of iterations and the minimal weight designs, will be reported in the paper. Based on these results, it would be estimated, the amount of the steel that could be saved by applying structural analysis combined with non-deterministic optimization methods.

Keywords: Structural Optimization, non-deterministic methods, truss structures, steel truss

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1421 Probability-Based Damage Detection of Structures Using Kriging Surrogates and Enhanced Ideal Gas Molecular Movement Algorithm

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

Abstract:

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: Artificial Intelligence, Uncertainty quantification, kriging, enhanced ideal gas molecular movement (EIGMM), probability-based damage detection (PBDD), surrogate modeling

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1420 Enhanced Stability of Piezoelectric Crystalline Phase of Poly(Vinylidene Fluoride) (PVDF) and Its Copolymer upon Epitaxial Relationships

Authors: Devi Eka Septiyani Arifin, Jrjeng Ruan

Abstract:

As an approach to manipulate the performance of polymer thin film, epitaxy crystallization within polymer blends of poly(vinylidene fluoride) (PVDF) and its copolymer poly(vinylidene fluoride-trifluoroethylene) P(VDF-TrFE) was studied in this research, which involves the competition between phase separation and crystal growth of constitutive semicrystalline polymers. The unique piezoelectric feature of poly(vinylidene fluoride) crystalline phase is derived from the packing of molecular chains in all-trans conformation, which spatially arranges all the substituted fluorene atoms on one side of the molecular chain and hydrogen atoms on the other side. Therefore, the net dipole moment is induced across the lateral packing of molecular chains. Nevertheless, due to the mutual repulsion among fluorene atoms, this all-trans molecular conformation is not stable, and ready to change above curie temperature, where thermal energy is sufficient to cause segmental rotation. This research attempts to explore whether the epitaxial interactions between piezoelectric crystals and crystal lattice of hexamethylbenzene (HMB) crystalline platelet is able to stabilize this metastable all-trans molecular conformation or not. As an aromatic crystalline compound, the melt of HMB was surprisingly found able to dissolve the poly(vinylidene fluoride), resulting in homogeneous eutectic solution. Thus, after quenching this binary eutectic mixture to room temperature, subsequent heating or annealing processes were designed to explore the involve phase separation and crystallization behavior. The phase transition behaviors were observed in-situ by X-ray diffraction and differential scanning calorimetry (DSC). The molecular packing was observed via transmission electron microscope (TEM) and the principles of electron diffraction were brought to study the internal crystal structure epitaxially developed within thin films. Obtained results clearly indicated the occurrence of heteroepitaxy of PVDF/PVDF-TrFE on HMB crystalline platelet. Both the concentration of poly(vinylidene fluoride) and the mixing ratios of these two constitutive polymers have been adopted as the influential factors for studying the competition between the epitaxial crystallization of PVDF and P(VDF-TrFE) on HMB crystalline. Furthermore, the involved epitaxial relationship is to be deciphered and studied as a potential factor capable of guiding the wide spread of piezoelectric crystalline form.

Keywords: Crystallization, Epitaxy, crystalline platelet, thin film and mixing ratio

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1419 Kinetic Monte Carlo Simulation of ZnSe Homoepitaxial Growth and Characterization

Authors: Hamid Khachab, Yamani Abdelkafi, Mouna Barhmi

Abstract:

The epitaxial growth has great important in the fabricate of the new semi-conductors devices and upgrading many factors, such as the quality of crystallization and efficiency with their deferent types and the most effective epitaxial technique is the molecular beam epitaxial. The MBE growth modeling allows to confirm the experiments results out by atomic beam and to analyze the microscopic phenomena. In of our work, we determined the growth processes specially the ZnSe epitaxial technique by Kinetic Monte Carlo method and we also give observations that are made in real time at the growth temperature using reflection high energy electron diffraction (RHEED) and photoemission current.

Keywords: Simulation, kinetic Monte Carlo, photoemission, molecular beam epitaxy, II-VI, morpholy, RHEED, ZnSe

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1418 Mechanical and Microstructural Study of Photo-Aged Low Density Polyethylene (LDPE) Films

Authors: Meryem Imane Babaghayou, Abdelhafidi Asma

Abstract:

This study deals with the ageing of Blown extruded films of low-density polyethylene (LDPE), used for greenhouse covering. The LDPE have been subjected to climatic ageing in a sub-Saharan facility at Laghouat (Algeria) with direct exposure to sun. The microstructural changes in the films were analyzed by IRFT for different states of ageing. The mechanical characterization was performed on a uniaxial tensile apparatus. The mechanical properties such as Young's modulus, strain at break, and stress at break have been followed for different states of exposure time (0 to 6 months). The Climatic ageing of LDPE films shows the effect of ageing on the microstructural Plan which leads to: i) To an oxidation of the molecular chains. ii) To the formation of cross-linkings and breaking chains, which both of them are responsible for the mechanical behavior’s modifications of the material. Cross-links are in favor of strengthening of the mechanical properties at break (the increase of σr and εr). In other side, the chains breaking leads to a decrease of these properties. The increase in the Young's modulus also seems to be related to those structural changes since the cross-links increase the average molecular weight. Branchings and tangles are favorable pairs for the ductile nature of the material. And in other side, the chains breaking reduces the average molecular weight and therefore promotes the stiffening (following to morphological changes) so the material becomes fragile. The post-mortem analysis of the samples shows that the mechanical stress has an effect on the molecular structure of the material. Although if quantitatively the concentrations of different chemical species exchanges, from a quantitative point of view only the unsaturations raises the polemics of a possible microstructural modification induced by mechanical stress applied during the tensile test. Also, we recommend a more rigorous analysis with other means of investigation.

Keywords: Ageing, Mechanical Properties, low-density polyethylene, IRTF

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1417 Morphological and Molecular Analysis of Selected Fast-Growing Blue Swimming Crab (Portunus pelagicus) in South of Sulawesi

Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

Abstract:

Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: Morphology, RAPD, crab, portunus pelagicus, Carapace

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1416 Molecular Insights into the 5α-Reductase Inhibitors: Quantitative Structure Activity Relationship, Pre-Absorption, Distribution, Metabolism, and Excretion and Docking Studies

Authors: Richa Dhingra, Monika, Manav Malhotra, Tilak Raj Bhardwaj, Neelima Dhingra

Abstract:

5-Alpha-reductases (5AR), a membrane bound, NADPH dependent enzyme and convert male hormone testosterone (T) into more potent androgen dihydrotestosterone (DHT). DHT is the required for the development and function of male sex organs, but its overproduction has been found to be associated with physiological conditions like Benign Prostatic Hyperplasia (BPH). Thus the inhibition of 5ARs could be a key target for the treatment of BPH. In present study, 2D and 3D Quantitative Structure Activity Relationship (QSAR) pharmacophore models have been generated for 5AR based on known inhibitory concentration (IC₅₀) values with extensive validations. The four featured 2D pharmacophore based PLS model correlated the topological interactions (–OH group connected with one single bond) (SsOHE-index); semi-empirical (Quadrupole2) and physicochemical descriptors (Mol. wt, Bromines Count, Chlorines Count) with 5AR inhibitory activity, and has the highest correlation coefficient (r² = 0.98, q² =0.84; F = 57.87, pred r² = 0.88). Internal and external validation was carried out using test and proposed set of compounds. The contribution plot of electrostatic field effects and steric interactions generated by 3D-QSAR showed interesting results in terms of internal and external predictability. The well validated 2D Partial Least Squares (PLS) and 3D k-nearest neighbour (kNN) models were used to search novel 5AR inhibitors with different chemical scaffold. To gain more insights into the molecular mechanism of action of these steroidal derivatives, molecular docking and in silico absorption, distribution, metabolism, and excretion (ADME) studies were also performed. Studies have revealed the hydrophobic and hydrogen bonding of the ligand with residues Alanine (ALA) 63A, Threonine (THR) 60A, and Arginine (ARG) 456A of 4AT0 protein at the hinge region. The results of QSAR, molecular docking, in silico ADME studies provide guideline and mechanistic scope for the identification of more potent 5-Alpha-reductase inhibitors (5ARI).

Keywords: Molecular Docking, ligands, QSAR, benign prostatic hyperplasia

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