Search results for: molecular characterization

Authors: Kaining Zhang, Lang Chen, Danyang Liu, Jianying Lu, Kun Yang, Junying Wu

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In order to solve the problem of a large amount of simulation and limited simulation scale in the first-principle molecular dynamics simulation of energetic material detonation reaction, we established an artificial intelligence model for analyzing and predicting the detonation reaction mechanism of CL-20 based on the first-principle molecular dynamics simulation of the multiscale shock technique (MSST). We employed principal component analysis to identify the dominant charge features governing molecular reactions. We adopted the K-means clustering algorithm to cluster the reaction paths and screen out the key reactions. We introduced the neural network algorithm to construct the mapping relationship between the charge characteristics of the molecular structure and the key reaction characteristics so as to establish a calculation method for predicting detonation reactions based on the charge characteristics of CL-20 and realize the rapid analysis of the reaction mechanism of energetic materials.

Keywords: energetic material detonation reaction, first-principle molecular dynamics simulation of multiscale shock technique, neural network, CL-20

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Authors: Abishek Rajkumar

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Antibiotic resistance can occur naturally given the selective pressure placed on antibiotics. Within a large population of bacteria, there is a significant chance that some of those bacteria can develop resistance via mutations or genetic recombination. However, a growing public health concern has arisen over the fact that antibiotic resistance has increased significantly over the past few decades. This is because humans have been over-consuming and producing antibiotics, which has ultimately accelerated the antibiotic resistance seen in these bacteria. The product of all of this is an ongoing race between scientists and the bacteria as bacteria continue to develop resistance, which creates even more demand for an antibiotic that can still terminate the newly resistant strain of bacteria. This paper will focus on a myriad of aspects of antibiotic resistance in bacteria starting with how it occurs on a molecular level and then focusing on the antibiotic concentrations and how they affect the resistance and fitness seen in bacteria.

Keywords: antibiotic, molecular, mutation, resistance

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Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

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The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

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Authors: M. A. Islam, P. J. Hazell, J. P. Escobedo, M. Saadatfar

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Quasistatic compression and micro structural characterization of closed cell aluminium foams of different pore size and cell distributions has been carried out. Metallic foams have good potential for lightweight structures for impact and blast mitigation and therefore it is important to find out the optimized foam structure (i.e. cell size, shape, relative density, and distribution) to maximize energy absorption. In this paper, we present results for two different aluminium metal foams of density 0.5 g/cc and 0.7 g/cc respectively that have been tested in quasi-static compression. The influence of cell geometry and cell topology on quasistatic compression behavior has been investigated using computed tomography (micro-CT) analysis. The compression behavior and micro structural characterization will be presented.

Keywords: metal foams, micro-CT, cell topology, quasistatic compression

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Authors: Guanlin Wu, Jiajia Yao, Fang Liu, Junshuai Xue, Jincheng Zhang, Yue Hao

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Owing to the excellent thermal conductivity and ultra-wide bandgap, Aluminum nitride (AlN)/Gallium nitride (GaN) is a highly promising material to achieve high breakdown voltage and output power devices among III-nitrides. In this study, we explore the growth and characterization of polarization-induced AlN/GaN heterostructures using plasma-assisted molecular beam epitaxy (PA-MBE) on AlN-on-sapphire templates. To improve the crystal quality and demonstrate the effectiveness of the PA-MBE approach, a thick AlN buffer of 180 nm was first grown on the AlN-on sapphire template. This buffer acts as a back-barrier to enhance the breakdown characteristic and isolate leakage paths that exist in the interface between the AlN epilayer and the AlN template. A root-mean-square roughness of 0.2 nm over a scanned area of 2×2 µm2 was measured by atomic force microscopy (AFM), and the full-width at half-maximum of (002) and (102) planes on the X-ray rocking curve was 101 and 206 arcsec, respectively, using by high-resolution X-ray diffraction (HR-XRD). The electron mobility of 443 cm2/Vs with a carrier concentration of 2.50×1013 cm-2 at room temperature was achieved in the AlN/GaN heterostructures by using a polarization-induced GaN channel. The low depletion capacitance of 15 pF is resolved by the capacitance-voltage. These results indicate that the polarization-induced AlN/GaN heterostructures have great potential for next-generation high-temperature, high-frequency, and high-power electronics.

Keywords: AlN, GaN, MBE, heterostructures

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Authors: Nithin Krisshna Gunasekaran, Prathima Prabhu Tumkur, Nicole Nazario Bayon, Krishnan Prabhakaran, Joseph C. Hall, Govindarajan T. Ramesh

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Cerium oxide and turmeric have antioxidant properties, which have gained interest among researchers to study their applications in the field of biomedicine, such asanti-inflammatory, anticancer, and antimicrobial applications. In this study, the turmeric extract was prepared and mixed with cerium nitrate hexahydrate, stirred continuously to obtain a homogeneous solution and then heated on a hot plate to get the supernatant evaporated, then calcinated at 600°C to obtain the cerium oxide nanoparticles. Characterization of synthesized cerium oxide nanoparticles through Scanning Electron Microscopy determined the particle size to be in the range of 70 nm to 250 nm. Energy Dispersive X-Ray Spectroscopy determined the elemental composition of cerium and oxygen. Individual particles were identified through the characterization of cerium oxide nanoparticles using Field Emission Scanning Electron Microscopy, in which the particles were determined to be spherical and in the size of around 70 nm. The presence of cerium oxide was assured by analyzing the spectrum obtained through the characterization of cerium oxide nanoparticles by Fourier Transform Infrared Spectroscopy. The crystal structure of cerium oxide nanoparticles was determined to be face-centered cubic by analyzing the peaks obtained through theX-Ray Diffraction method. The crystal size of cerium oxide nanoparticles was determined to be around 13 nm by using the Debye Scherer equation. This study confirmed the synthesis of cerium oxide nanoparticles using turmeric extract.

Keywords: antioxidant, characterization, cerium oxide, synthesis, turmeric

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Authors: Ling Dai

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Surface-sensing devices such as atomic force microscope have been widely used to characterize the surface structure and properties of nanoscale polymer films. However, using molecular dynamics simulations, we show that there is intrinsic and unavoidable inelastic deformation at polymer surfaces induced by the sensing tip. For linear chain polymers like perfluoropolyether, such tip-induced deformation derives from the differences in the atomic interactions which are atomic specie-based Van der Waals interactions, and resulting in atomic shuffling and causing inelastic alternation in both molecular structures and mechanical properties at the regions of the polymer surface. For those aromatic chain polymers like epoxy, the intrinsic deformation is depicted as the intra-chain rotation of aromatic rings and kinking of linear atomic connections. The present work highlights the need to reinterpret the data obtained from surface-sensing tests by considering this intrinsic inelastic deformation occurring at polymer surfaces.

Keywords: polymer, surface, nano, molecular dynamics

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Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić

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Prion is a protein substance whose certain form is considered as infectious agent. It is presumed to be the cause of the transmissible spongiform encephalopathies (TSEs). The protein it is composed of, called PrP, can fold in structurally distinct ways. At least one of those 3D structures is transmissible to other prion proteins. Prions can be found in brain tissue of healthy people and have certain biological role. The structure of prions naturally occurring in healthy organisms is marked as PrPc, and the structure of infectious prion is labeled as PrPSc. PrPc may play a role in synaptic plasticity and neuronal development. Also, it may be required for neuronal myelin sheath maintenance, including a role in iron uptake and iron homeostasis. PrPSc can be considered as an environmental pollutant. The main aim of this study was to carry out the molecular modeling and calculation of molecular descriptors (lipophilicity, physico-chemical and topological descriptors) of structurally diverse compounds which can be considered as anti-prion agents. Molecular modeling was conducted applying ChemBio3D Ultra version 12.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The Austin Model 1 (AM-1) was used for full geometry optimization of all structures. The obtained set of molecular descriptors is applied in analysis of similarities and dissimilarities among the tested compounds. This study is an important step in further development of quantitative structure-activity relationship (QSAR) models, which can be used for prediction of anti-prion activity of newly synthesized compounds.

Keywords: chemometrics, molecular modeling, molecular descriptors, prions, QSAR

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Authors: M. Ravindiran, P. Shankar

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This paper deals with the comparison of two synthesis methods, namely, sol-gel, and combustion to prepare Fe doped ZnO nano material. Characterization results for structural, optical and magnetic properties were analyzed for the sol gel and combustion synthesis derived materials. Magnetic studies of the prepared compounds reveal that the combustion synthesis derived material has good magnetization of 50 emu/gm with a better hysteresis loop curve.

Keywords: DMS, combustion, ferromagnetic, synthesis methods

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Authors: Abdulmannan Fadel

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Arabinoxylan is a non-starch polysaccharide (NSP), which is one of the most important polysaccharides contained within cereal grains. Wheat endosperm pentosan and rice bran contain a significant amount of arabinoxylan (7% in rice bran and 10-12% in wheat endosperm pentosan). Several methods have been used for arabinoxylan extraction with varying degrees of success e.g. enzymatic and alkaline treatment. Yet, the use of extrusion alone as a pre-treatment to increase the yield and reduce the molecular weight in wheat endosperm pentosan and rice bran has not been investigated. The samples (wheat pentosan and rice bran) were extruded using a Twin-screw extruder at a range of screw speeds (80 and 160 rpm) and barrel temperatures range (80 to 140°C) with a throughput of 30 Kg hr-1 and moisture content of 25%. Arabinoxylans were extracted with water and the extraction yield and molecular weight was determined using size exclusion high-pressure liquid chromatography system. It was found that increasing screw speed from 80 rpm to 160 rpm, did not effect the extraction yield (p < 0.05) of arabinoxylan from either the wheat endosperm pentosan or the rice bran. However, the molecular weight of the extracted arabinoxylans from pentosan was found to decrease with increasing screw speed in wheat endosperm pentosan. These low molecular weight arabinoxylans have been suggested as immunomodulators.

Keywords: arabinoxylans, extrusion, wheat endosperm pentosan, rice bran

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Authors: Hafiz Md. HasanBabu, Khandaker Mohammad Mohi Uddin, Md. IstiakJaman Ami, Rahat Hossain Faisal

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Computing in biomolecular programming performs through the different types of reactions. Proteins and nucleic acids are used to store the information generated by biomolecular programming. DNA (Deoxyribose Nucleic Acid) can be used to build a molecular computing system and operating system for its predictable molecular behavior property. The DNA device has clear advantages over conventional devices when applied to problems that can be divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in memory and conduct multiple operations at once, thus solving decomposable problems much faster. Programmable Logic Array, abbreviated as PLA is a programmable device having programmable AND operations and OR operations. In this paper, a DNA PLA is designed by different molecular operations using DNA molecules with the proposed algorithms. The molecular PLA could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism, and extraordinary energy efficiency.

Keywords: biological systems, DNA computing, parallel computing, programmable logic array, PLA, DNA

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Authors: Vigen Barkhudaryan

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The influence of external effects (γ-, UV–radiations, high temperature) in presence of air oxygen on structural transformations of low-density polyethylene (LDPE) have been investigated dependent on the polymers’ thickness, the intensity and the dose of external actions. The methods of viscosimetry, light scattering, turbidimetry and gelation measuring were used for this purpose. The comparison of influence of external effects on LDPE shows, that the destruction and cross-linking processes of macromolecules proceed simultaneously with all kinds of external effects. A remarkable growth of average molecular mass of LDPE along with the irradiation doses and heat treatment exposure growth was established. It was linear for the mass average molecular mass and at the initial doses is mainly the result of the increase of the macromolecular branching. As a result, the macromolecular hydrodynamic volumes have been changed, and therefore the dependence of viscosity average molecular mass on the doses was going through the minimum at initial doses. A significant change of molecular mass, sizes and shape of macromolecules of LDPE occurs under the influence of external effects. The influence is limited only by diffusion of oxygen during -irradiation and heat treatment. At UV–irradiation the influence is limited both by diffusion of oxygen and penetration of radiation. Consequently, the molecular transformations are deeper and evident in case of -irradiation, as soon as the polymer is transformed in a whole volume. It was also established, that the mechanism of molecular transformations in polymers from the surface layer distinctly differs from those of the sample deeper layer. A comparison of the results of these investigations allows us to conclude, that the mechanisms of influence of investigated external effects on polyethylene are similar.

Keywords: cross-linking, destruction, high temperature, LDPE, γ-radiations, UV-radiations

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Authors: Asho Ali

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Tuberculosis is a disease of grave concern which infects one-third of the global population. The high incidence of tuberculosis is further compounded by the increasing emergence of drug resistant strains including multi drug resistant (MDR). Global incidence MDR-TB is ~4%. Molecular epidemiological studies, based on the assumption that patients infected with clustered strains are epidemiologically linked, have helped understand the transmission dynamics of disease. It has also helped to investigate the basis of variation in Mycobacterium tuberculosis (MTB) strains, differences in transmission, and severity of disease or drug resistance mechanisms from across the globe. This has helped in developing strategies for the treatment and prevention of the disease including MDR.

Keywords: Mycobcaterium tuberculosis, molecular epidemiology, drug resistance, disease

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Authors: J. Subbalakshmi, G. Dhruvasamhith, S. M. Hussain

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Polyaniline (PANI) is one of the most extensively studied material among the conducting polymers due to its simple synthesis by chemical and electrochemical routes. PANIs have advantages of chemical stability and high conductivity making their commercial applications quite attractive. However, to our knowledge, very little work has been reported on the tensile strength properties of templated PANIs processed with polyvinyl alcohol and also, detailed study has not been carried out. We have investigated the effect of small molecule and polymers as templates on PANI. Stable aqueous colloidal suspensions of trisodium citrate (TSC), poly(ethylenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS), and polyethylene glycol (PEG) templated PANIs were prepared through chemical synthesis, processed with polyvinyl alcohol (PVA) and were fabricated into films by solution casting. Absorption and infra-red spectra were studied to gain insight into the possible molecular interactions. Surface morphology was studied through scanning electron microscope and optical microscope. Interestingly, tensile testing studies revealed least strain for pure PVA when compared to the blends of templated PANI. Furthermore, among the blends, TSC templated PANI possessed maximum elasticity. The ultimate tensile strength for PVA processed, PEG-templated PANI was found to be five times more than other blends considered in this study. We establish structure–property correlation with morphology, spectral characterization and tensile testing studies.

Keywords: surface morphology, processed films, polyvinyl alcohol, templated polyanilines, tensile testing

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Authors: Salem El-Tohami Ashoor

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A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Said Belaaouad

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This study aimed to explore the quantitative structure-activity relationship (QSAR) of 1,2,4-Triazine-3(2H)-one derivative as a potential anticancer agent against breast cancer. The electronic descriptors were obtained using the Density Functional Theory (DFT) method, and a multiple linear regression techniques was employed to construct the QSAR model. The model exhibited favorable statistical parameters, including R2=0.849, R2adj=0.656, MSE=0.056, R2test=0.710, and Q2cv=0.542, indicating its reliability. Among the descriptors analyzed, absolute electronegativity (χ), total energy (TE), number of hydrogen bond donors (NHD), water solubility (LogS), and shape coefficient (I) were identified as influential factors. Furthermore, leveraging the validated QSAR model, new derivatives of 1,2,4-Triazine-3(2H)-one were designed, and their activity and pharmacokinetic properties were estimated. Subsequently, molecular docking (MD) and molecular dynamics (MD) simulations were employed to assess the binding affinity of the designed molecules. The Tubulin colchicine binding site, which plays a crucial role in cancer treatment, was chosen as the target protein. Through the simulation trajectory spanning 100 ns, the binding affinity was calculated using the MMPBSA script. As a result, fourteen novel Tubulin-colchicine inhibitors with promising pharmacokinetic characteristics were identified. Overall, this study provides valuable insights into the QSAR of 1,2,4-Triazine-3(2H)-one derivative as potential anticancer agent, along with the design of new compounds and their assessment through molecular docking and dynamics simulations targeting the Tubulin-colchicine binding site.

Keywords: QSAR, molecular docking, ADMET, 1, 2, 4-triazin-3(2H)-ones, breast cancer, anticancer, molecular dynamic simulations, MMPBSA calculation

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Authors: John Vergara, Giuseppe Palmese

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Fundamental studies aimed at elucidating the key contributions to corrosion performance are needed to make progress toward effective and environmentally compliant corrosion control. Epoxy/amine systems are typically employed as barrier coatings for corrosion control. However, the hardening agents used for coating applications can be very complex, making fundamental studies of water and oxygen permeability challenging to carry out. Creating model building blocks for epoxy/amine coatings is the first step in carrying out these studies. We will demonstrate the synthesis and characterization of model amine building blocks from saturated fatty acids and simple amines such as diethylenetriamine (DETA) and Bis(3-aminopropyl)amine. The structure-property relationship of thermosets made from these model amines and Diglycidyl ether of bisphenol A (DGBEA) will be discussed.

Keywords: building block, amine, synthesis, characterization

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Authors: Adam Abate, Elham Rasti, Philip Romero

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Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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Authors: Eunae Lee, Oh-Kuen Kwon, Ki-Sub Kim, Jeong Won Kang

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We investigated the dynamic properties of graphene-nanoribbon (GNR) memory encapsulating graphene-nanoflake (GNF) shuttle in the potential to be applicable as a non-volatile random access memory via molecular dynamics simulations. This work explicitly demonstrates that the GNR encapsulating the GNF shuttle can be applied to nonvolatile memory. The potential well was originated by the increase of the attractive vdW energy between the GNRs when the GNF approached the edges of the GNRs. So the bistable positions were located near the edges of the GNRs. Such a nanoelectromechanical non-volatile memory based on graphene is also applicable to the development of switches, sensors, and quantum computing.

Keywords: graphene nanoribbon, graphene nanoflake, shuttle memory, molecular dynamics

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Authors: Ogunniran Kehinde Olurotimi, Adekoya Joseph, Ehi-Eromosele Cyril, Mehdi Shihab, Mesubi Adediran, Tadigoppula Narender

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Nicotinic acid hydrazide and 2,4-dihydoxylbenzaldehyde were condensed at 20°C to form an acylhydrazone (H3L) with ONO coordination pattern. The structure of the acylhydrazone was elucidated by using CHN analyzer, ESI mass spectrometry, IR, 1H NMR, 13C NMR and 2D NMR such as COSY and HSQC. Thereafter, five novel metal complexes [Mn(II), Fe(II), Pt(II) Zn(II) and Pd(II)] of the hydrazone ligand were synthesized and their structural characterization were achieved by several physicochemical methods, namely elemental analysis, electronic spectra, infrared, EPR, molar conductivity and powder X-ray diffraction studies. Structural geometries of some of the compounds were supported by using Hyper Chem-8 program for the molecular mechanics and semi-empirical calculations. The stability energy (E) and electron potentials (eV) for the frontier molecules were calculated by using PM3 method. An octahedral geometry was suggested for both Pd(II) and Zn(II) complexes while both Mn(II) and Fe(II) complexes conformed with tetrahedral pyramidal. However, Pt(II) complex agreed with tetrahedral geometry. In vitro antitubercular activity study of the ligand and the metal complexes were evaluated against Mycobacterium tuberculosis, H37Rv, by using micro-diluted method. The results obtained revealed that (PtL1) (MIC = 0.56 µg/mL), (ZnL1) (MIC = 0.61 µg/mL), (MnL1) (MIC = 0.71 µg/mL) and (FeL1) (MIC = 0.82 µg/mL), exhibited a significant activity when compared with first line drugs such as isoniazid (INH) (MIC = 0.9 µg/mL). H3L1 exhibited lesser antitubercular activity with MIC value of 1.02 µg/mL. However, the metal complexes displayed higher cytoxicity but were found to be non-significant different (P ˂ 0.05) to isoniazid drug.

Keywords: hydrazones, electron spin resonance, thermogravimetric, powder X-ray diffraction, antitubercular agents

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Authors: Betim Bahtiri, B. Arash, R. Rolfes

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Epoxy-based materials are frequently exposed to high-humidity environments in many engineering applications. As a result, their material properties would be degraded by water absorption. A full characterization of the material properties under hygrothermal conditions requires time- and cost-consuming experimental tests. To gain insights into the physics of diffusion mechanisms, atomistic simulations have been shown to be effective tools. Concerning the diffusion of water in polymers, spatial trajectories of water molecules are obtained from molecular dynamics (MD) simulations allowing the interpretation of diffusion pathways at the nanoscale in a polymer network. Conventional MD simulations of water diffusion in amorphous polymers lead to discrepancies at low temperatures due to the short timescales of the simulations. In the proposed model, this issue is solved by using a combined scheme of autonomous basin climbing (ABC) with kinetic Monte Carlo and reactive MD simulations to investigate the diffusivity of water molecules in epoxy resins across a wide range of temperatures. It is shown that the proposed simulation framework estimates kinetic properties of water diffusion in epoxy resins that are consistent with experimental observations and provide a predictive tool for investigating the diffusion of small molecules in other amorphous polymers.

Keywords: epoxy resins, water diffusion, autonomous basin climbing, kinetic Monte Carlo, reactive molecular dynamics

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Authors: Valentina Alessandra Carvalho do Vale, Elmo Thiago Lins Cöuras Ford

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Increasingly telecommunications sectors are adopting optical technologies, due to its ability to transmit large amounts of data over long distances. However, as in all systems of data transmission, optical communication channels suffer from undesirable and non-deterministic effects, being essential to know the same. Thus, this research allows the assessment of these effects, as well as their characterization and beneficial uses of these effects.

Keywords: optical communication, optical fiber, non-deterministic effects, telecommunication

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Authors: T. Rajamäki

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In clean room environment molecular contamination in very small concentrations can cause significant harm for the components and processes. This is commonly referred as airborne molecular contamination (AMC). There is a shortage of high sensitivity continuous measurement data for existence and behavior of several of these contaminants. Accordingly, in most cases correlation between concentration of harmful molecules and their effect on processes is not known. In addition, the formation and distribution of contaminating molecules are unclear. In this work sensitive optical techniques are applied in clean room facilities for investigation of concentrations, forming mechanisms and effects of contaminating molecules. Special emphasis is on reactive acid and base gases ammonia (NH3) and hydrogen fluoride (HF). They are the key chemicals in several operations taking place in clean room processes.

Keywords: AMC, clean room, concentration, reactive gas

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Mariana Gomez Gomez, Maria Elena Sanchez Vergara

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Many sustainable approaches to generate electric energy have emerged in the last few decades; one of them is through solar cells. Yet, this also has the disadvantage of highly polluting inorganic semiconductor manufacturing processes. Therefore, the use of molecular semiconductors must be considered. In this work, allene compounds C24H26O4 and C24H26O5 were used as dopants to manufacture semiconductors films based on PbPc by high-vacuum evaporation technique. IR spectroscopy was carried out to determine the phase and any significant chemical changes which may occur during the thermal evaporation. According to UV-visible spectroscopy and Tauc’s model, the deposition process generated thin films with an activation energy range of 1.47 to 1.55 eV for direct transitions and 1.29 to 1.33 eV for indirect transitions. These values place the manufactured films within the range of low bandgap semiconductors. The flexible devices were manufactured: polyethylene terephthalate (PET), Indium tin oxide (ITO)/organic semiconductor/ Cubic Close Packed (CCP). The characterization of the devices was carried out by evaluating electrical conductivity using the four-probe collinear method. I-V curves were obtained under different lighting conditions at room temperature. OS1 (PbPc/C24H26O4) showed an Ohmic behavior, while OS2 (PbPc/C24H26O5) reached higher current values ​​at lower voltages. The results obtained show that the semiconductors devices doped with allene compounds can be used in the manufacture of optoelectronic devices.

Keywords: electrical properties, optical gap, phthalocyanine, thin film.

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Maninderjeet K. Grewal, Sakshi Bhatnor, Renu Chadha

Abstract:

The composition of pharmaceutical entities and the molecular interactions can be altered to optimize drug properties such as solubility and bioavailability by the crystal engineering technique. The present work has emphasized on the preparation, characterization, and biopharmaceutical evaluation of co-crystal of BCS Class II anti-osteoarthritis drug, Oxaprozin (OXA) with aspartic acid (ASPA) as co-former. The co-crystals were prepared through the mechanochemical solvent drop grinding method. Characterization of the prepared co-crystal (OXA-ASPA) was done by using analytical tools such as differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction (PXRD). DSC thermogram of OXA-ASPA cocrystal showed a single sharp melting endotherm at 235 ºC, which was between the melting peaks of the drug and the counter molecules suggesting the formation of a new phase which is a co-crystal that was further confirmed by using other analytical techniques. FT-IR analysis of OXA-ASPA cocrystal showed a shift in a hydroxyl, carbonyl, and amine peaks as compared to pure drugs indicating all these functional groups are participating in cocrystal formation. The appearance of new peaks in the PXRD pattern of cocrystals in comparison to individual components showed that a new crystalline entity has been formed. The Crystal structure of cocrystal was determined using material studio software (Biovia) from PXRD. The equilibrium solubility study of OXA-ASPA showed improvement in solubility as compared to pure drug. Therefore, it was envisioned to prepare the co-crystal of oxaprozin with a suitable conformer to modulate its physiochemical properties and consequently, the biopharmaceutical parameters.

Keywords: cocrystals, coformer, oxaprozin, solubility

Procedia PDF Downloads 85

Authors: Fathi Soliman

Abstract:

With the ultimate goal of developing the separation of n-paraffin as phase change material (PCM) by means of molecular dynamic simulations, we attempt to predict the solubility of aromatic n-paraffin in two organic solvents: Butyl Acetate (BA) and Methyl Iso Butyl Ketone (MIBK). A simple model of aromatic paraffin: 2-hexadecylantharacene with amorphous molecular structure and periodic boundary conditions was constructed. The results showed that MIBK is the best solvent to separate ultra-pure phase change materials and this data was compatible with experimental data done to separate ultra-pure n-paraffin from waste petroleum aromatic paraffin wax, the separated n-paraffin was characterized by XRD, TGA, GC and DSC, moreover; data revealed that the n-paraffin separated by using MIBK is better as PCM than that separated using BA.

Keywords: molecular dynamics simulation, n-paraffin, organic solvents, phase change materials, solvent extraction

Procedia PDF Downloads 166

Authors: Muchun Yu, Xue Gao, Qian Chen

Abstract:

As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

Procedia PDF Downloads 441