Search results for: molecular docking and simulation

Authors: Alok Shiomurti Tripathi, Ajay Kumar Timiri, Papiya Mitra Mazumder, Anil Chandewar

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The present study evaluates the possible drug interaction between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ) induced in diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction by molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg/kg, ip) and confirms it by assessing the blood and urine biochemical parameters on 28th day of its induction. Selected DN animals were used for the drug interaction between GLIM (0.5mg/kg, p.o.) and SIL (2.5 mg/kg, p.o.) after 29th and 70th day of protocol. Drug interaction were assessed by evaluating the plasma drug concentration using HPLC-UV and also determine the change in the biochemical parameter in blood and urine. Mechanism of the interaction was postulated by molecular modeling study using Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in the blood and urine biochemical parameter in STZ treated groups. The concentration of SIL increased significantly (p<0.001) in rat plasma when co administered with GLIM after 70th day of protocol. Molecular modelling study revealed few important interactions with rat serum albumin and CYP2C9.GLIM has strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL. Whereas, for CYP2C9, GLIM has strong hydrogen bond with polar contacts and hydrophobic interactions than SIL. Present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals and mechanism has been supported by molecular modeling studies.

Keywords: diabetic nephropathy, glimepiride, sildenafil citrate, pharmacokinetics, homology modeling, schrodinger

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Authors: Youngjae Jin, Daeshik Kim

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This paper describes a cycle accurate simulation results of weight values learned by an auto-encoder behavior model in terms of pre-route simulation. Given the results we visualized the first layer representations with natural images. Many common deep learning threads have focused on learning high-level abstraction of unlabeled raw data by unsupervised feature learning. However, in the process of handling such a huge amount of data, the learning method’s computation complexity and time limited advanced research. These limitations came from the fact these algorithms were computed by using only single core CPUs. For this reason, parallel-based hardware, FPGAs, was seen as a possible solution to overcome these limitations. We adopted and simulated the ready-made auto-encoder to design a behavior model in Verilog HDL before designing hardware. With the auto-encoder behavior model pre-route simulation, we obtained the cycle accurate results of the parameter of each hidden layer by using MODELSIM. The cycle accurate results are very important factor in designing a parallel-based digital hardware. Finally this paper shows an appropriate operation of behavior model based pre-route simulation. Moreover, we visualized learning latent representations of the first hidden layer with Kyoto natural image dataset.

Keywords: auto-encoder, behavior model simulation, digital hardware design, pre-route simulation, Unsupervised feature learning

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Authors: Arunas Burinskas, Manuela Tvaronavičienė

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Although the new trade theories, unlike the theories of an industrial organisation, see the structure of the market and competition between enterprises through their heterogeneity according to various parameters, they do not pay any particular attention to the analysis of the market structure and its development. In this article, although we relied mainly on models developed by the scholars of new trade theory, we proposed a different approach. In our simulation model, we model market demand according to normal distribution function, while on the supply side (as it is in the new trade theory models), productivity is modeled with the Pareto distribution function. The results of the simulation show that companies with higher productivity (lower marginal costs) do not pass on all the benefits of such economies to buyers. However, even with higher marginal costs, firms can choose to offer higher value-added goods to stay in the market. In general, the structure of the market is formed quickly enough and depends on the skills available to firms.

Keywords: market, structure, simulation, heterogenous firms

Procedia PDF Downloads 123

Authors: Hossein Keshtkar, Ali Nasiri Toosi

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With the growing concerns about gasoline environmental pollution and also the need for a more widely available fuel source, natural gas is finding its way to the automotive engines. But before this could happen industrially, simulations of natural gas direct injection need to take place to maximize and optimize power output. KIVA is one of the most powerful tools when it comes to engine simulation. Widely accepted by both researchers and the industry, KIVA an open-source code, offers great in-depth simulation and analyzation. KIVA can compute complex phenomena’s which can occur inside the chamber before, whilst and after ignition. One downside to KIVA, is its in-capability of simulating gaseous injections, making it useful for only liquidized fuel. In this study, we developed a numerical code, to enable the simulation of gaseous injection within the KIVA code. By introducing our code as a subroutine, we modified the original KIVA program. To ensure the correct application of gaseous fuel injection using our modified KIVA code, we simulated two different cases and compared them with their experimental data. We concluded our modified version of KIVA’s simulation results came in very close to those measured experimentally.

Keywords: gaseous injections, KIVA, natural gas direct injection, numerical code, simulation

Procedia PDF Downloads 263

Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

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Authors: Young June Yoon

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We will present four different topics in estimating the mechanical properties of biological tissues. First we elucidate the viscoelastic behavior of collagen molecules whose diameter is a couple of nanometers. By using the molecular dynamics simulation, we observed the viscoelastic behavior in different pulling velocity. Second, the protein layer, so called ‘sheath’ in enamel microstructure reduces the stress concentration in enamel minerals. We examined the result by using the finite element methods. Third, the anisotropic elastic constants of dentin are estimated by micromechanical analysis and estimated results are close to the experimentally measured data. Last, new formulation between the fabric tensor and the wave velocity is established for calcaneus by employing the poroelasticity. This formulation can be simply used for future experiments.

Keywords: tissues, mechanics, mechanical properties, wave propagation

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Authors: Parimalah Velo, Ahmad Zakaria

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Introduction: Monte Carlo simulations of preclinical imaging systems allow opportunity to enable new research that could range from designing hardware up to discovery of new imaging application. The simulation system which could accurately model an imaging modality provides a platform for imaging developments that might be inconvenient in physical experiment systems due to the expense, unnecessary radiation exposures and technological difficulties. The aim of present study is to validate the Monte Carlo simulation of thyroid phantom imaging using Geant4-GATE for Siemen’s e-cam single head gamma camera. Upon the validation of the gamma camera simulation model by comparing physical characteristic such as energy resolution, spatial resolution, sensitivity, and dead time, the GATE simulation of thyroid phantom imaging is carried out. Methods: A thyroid phantom is defined geometrically which comprises of 2 lobes with 80mm in diameter, 1 hot spot, and 3 cold spots. This geometry accurately resembling the actual dimensions of thyroid phantom. A planar image of 500k counts with 128x128 matrix size was acquired using simulation model and in actual experimental setup. Upon image acquisition, quantitative image analysis was performed by investigating the total number of counts in image, the contrast of the image, radioactivity distributions on image and the dimension of hot spot. Algorithm for each quantification is described in detail. The difference in estimated and actual values for both simulation and experimental setup is analyzed for radioactivity distribution and dimension of hot spot. Results: The results show that the difference between contrast level of simulation image and experimental image is within 2%. The difference in the total count between simulation and actual study is 0.4%. The results of activity estimation show that the relative difference between estimated and actual activity for experimental and simulation is 4.62% and 3.03% respectively. The deviation in estimated diameter of hot spot for both simulation and experimental study are similar which is 0.5 pixel. In conclusion, the comparisons show good agreement between the simulation and experimental data.

Keywords: gamma camera, Geant4 application of tomographic emission (GATE), Monte Carlo, thyroid imaging

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Authors: Yanyan Yu, Haiping Ding, Pengjun Chen, Yiou Sun

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Fault depth is an important parameter to be determined in ground motion simulation, and peak ground velocity (PGV) demonstrates good application prospect. Using numerical simulation method, the variations of distribution and peak value of near-fault PGV with different fault depth were studied in detail, and the reason of some phenomena were discussed. The simulation results show that the distribution characteristics of PGV of fault-parallel (FP) component and fault-normal (FN) component are distinctly different; the value of PGV FN component is much larger than that of FP component. With the increase of fault depth, the distribution region of the FN component strong PGV moves forward along the rupture direction, while the strong PGV zone of FP component becomes gradually far away from the fault trace along the direction perpendicular to the strike. However, no matter FN component or FP component, the strong PGV distribution area and its value are both quickly reduced with increased fault depth. The results above suggest that the fault depth have significant effect on both FN component and FP component of near-fault PGV.

Keywords: fault depth, near-fault, PGV, numerical simulation

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Authors: Suyeb Ahmed Khan, Mahmood Mian

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Simulation plays an important role during all phases of the design and engineering of communications systems, from early stages of conceptual design through the various stages of implementation, testing, and fielding of the system. In the present paper, a simulation model has been constructed for the WCDMA system in order to evaluate the performance. This model describes multiusers effects and calculation of BER (Bit Error Rate) in 3G mobile systems using Simulink MATLAB 7.1. Gaussian Approximation defines the multi-user effect on system performance. BER has been analyzed with comparison between transmitting data and receiving data.

Keywords: WCDMA, simulations, BER, MATLAB

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Authors: Kiyoumars Roushangar, Shabnam Mirheidarian

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This study proposes metamodel approaches as a new intelligent technique for the explicit formulation of friction factors of water conveyance structures. For this purpose, experimental data of a movable bed flume with dune bed form were used. Analyzing the result clears the high capability of metamodel approaches (MNE= 0.05, R= 0.92) as a powerful tool for optimizing and explicit simulation of Manning's roughness coefficients of water conveyance structures compared to other nonlinear approaches.

Keywords: intelligent techniques, explicit simulation, roughness coefficient, water conveyance structure

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Authors: Zdravko Eškinja, Lovre Miljanić, Ognjen Kuljača

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This paper is an overview of simulation tools used to model specific thermal dynamics that occurs while controlling double skin façade. Research has been conducted on simplified construction with single zone where one side is glazed. Heat flow and temperature responses are simulated in three different simulation tools: IDA-ICE, EnergyPlus and HAMBASE. The excitation of observed system, used in all simulations, was a temperature step of exterior environment. Air infiltration, insulation and other disturbances are excluded from this research. Although such isolated behaviour is not possible in reality, experiments are carried out to gain novel information about heat flow transients which are not observable under regular conditions. Results revealed new possibilities for adapting the parameters of the neural network regulator. Along numerical simulations, the same set-up has been also tested in a real-time experiment with a 1:18 scaled model and thermal chamber. The comparison analysis brings out interesting conclusion about simulation accuracy in this particular case.

Keywords: double skin façade, experimental tests, heat control, heat flow, simulated tests, simulation tools

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Authors: Marzieh Jafarzadeh, Fatemeh Rezaee

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Introduction: The effect of ionizing radiation on human health can be effective for genomic integrity and cell viability. It also increases the risk of cancer and malignancy. Therefore, X-ray behavior and absorption dose calculation are considered. One of the applicable tools for calculating and evaluating the absorption dose in human tissues is Monte Carlo simulation. Monte Carlo offers a straightforward way to simulate and integrate, and because it is simple and straightforward, Monte Carlo is easy to use. The Monte Carlo BEAMnrc code is one of the most common diagnostic X-ray simulation codes used in this study. Method: In one of the understudy hospitals, a certain number of CT scan images of patients who had previously been imaged were extracted from the hospital database. BEAMnrc software was used for simulation. The simulation of the head of the device with the energy of 0.09 MeV with 500 million particles was performed, and the output data obtained from the simulation was applied for phantom construction using CT CREATE software. The percentage of depth dose (PDD) was calculated using STATE DOSE was then compared with international standard values. Results and Discussion: The ratio of surface dose to depth dose (D/Ds) in the measured energy was estimated to be about 4% to 8% for bone and 3% to 7% for bone marrow. Conclusion: MC simulation is an efficient and accurate method for simulating bone marrow and calculating the absorbed dose.

Keywords: Monte Carlo, absorption dose, BEAMnrc, bone marrow

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: Kunj Parikh, S. Bhattacharya, V. Natarajan

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TCAD numerical simulation is one of the most tried and tested powerful tools for designing devices in semiconductor foundries worldwide. It has also been used to explain conduction in organic thin films where the processing temperature is often enough to make homogeneous samples (often imperfect, but homogeneously imperfect). In this report, we have presented the results of TCAD simulation in multi-grain thin films. The work has addressed the inhomogeneity in one dimension, but can easily be extended to two and three dimensions. The effect of grain boundaries has mainly been approximated as barriers located at the junction between two adjacent grains. The effect of the value of grain boundary barrier, the bulk traps, and the measurement temperature have been investigated.

Keywords: polycrystalline thin films, space charge limited conduction, Technology Computer-Aided Design (TCAD) simulation, traps

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Ahmad Kavousi, Ali Delaviz

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In this project, the landing process is simulated by using of multi-body dynamics commercial software. Various factors, including landing situations, aircraft structures and climate are used in this simulation. The purpose of this project is to determine the forces exerted on the aircraft landing gears in landing process in various landing conditions. For this purpose, the ADAMS multi-body dynamics software is used. Different scenarios based on FAR-25, including level landing, tail-down landing, crab landing are simulated. Results of dynamic simulation software with landing load factor obtained from the analytical solution are compared. The effect of fuselage elasticity on the landing load is studied. For this purpose, both of elastic and rigid body assumptions are used in the simulation process, and the results are compared and some conclusions are made.

Keywords: landing gear, landing process, aircraft, multi-body dynamics

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Authors: Ewelina Nowak, Anna Wisla-Swider, Gohar Khachatryan, Krzysztof Danel

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Complexes of ionic liquids with different heterocyclic-rings were synthesized by ion exchange reactions with pure salmon DNA. Ionic liquids (ILs) like 1-hexyl-3-methylimidazolium chloride, 1-butyl-4-methylpyridinium chloride and 1-ethyl-1-methylpyrrolidinium bromide were used. The ILs were built into helical state and confirmed by IR spectrometric techniques. Patterns of UV-Vis, photoluminescence, IR, and CD spectra indicated inclusion of small molecules into DNA structure. Molecular weight and radii of gyrations values of ILs-DNA complexes chains were established by HPSEC–MALLS–RI method. Modification DNA with 1-ethyl-1-methylpyrrolidinium bromide gives more uniform material and leads to elimination of high molecular weight chains. Thus, the incorporation DNA double helical structure with both 1-hexyl-3-methylimidazolium chloride and 1-butyl-4-methylpyridinium chloride exhibited higher molecular weight values. Scanning electron microscopy images indicate formation of nanofibre structures in all DNA complexes. Fluorescence depends strongly on the environment in which the chromophores are inserted and simultaneously on the molecular interactions with the biopolymer matrix. The most intensive emission was observed for DNA-imidazole ring complex. Decrease in intensity UV-Vis peak absorption is a consequence of a reduction in the spatial order of polynucleotide strands and provides different π–π stacking structure. Changes in optical properties confirmed by spectroscopy methods make DNA-ILs complexes potential biosensor applications.

Keywords: biopolymers, biosensors, cationic surfactant, DNA, DNA-gels

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Authors: Hariti Rafika, Fekih Malika, Saighi Mohamed

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During the period storage of liquefied natural gas, stability is necessarily affected by natural convection along the walls of the tank with thermal insulation is not perfectly efficient. In this paper, we present the numerical simulation of heat transfert by natural convection double diffusion,in unsteady laminar regime in a storage tank. The storage tank contains a liquefied natural gas (LNG) in its gaseous phase. Fluent, a commercial CFD package, based on the numerical finite volume method, is used to simulate the flow. The gas is just on the surface of the liquid phase. This numerical simulation allowed us to determine the temperature profiles, the stream function, the velocity vectors and the variation of the heat flux density in the vapor phase in the LNG storage tank volume. The results obtained for a general configuration, by numerical simulation were compared to those found in the literature.

Keywords: numerical simulation, natural convection, heat gains, storage tank, liquefied natural gas

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Authors: A. R. Momeninezhad

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Erosion of Slurry Pumps in Related Industries, is one of the major costs in their production process. Many factories in extractive industries try to find ways to diminish this cost. In this paper, we consider the flow pattern modifications by geometric variations made of numerical simulation of flow inside pump casing, which is one of the most important parts analyzed for erosion. The mentioned pump is a cyclone centrifugal slurry pump, which is operating in Sarcheshmeh Copper Industries in Kerman-Iran, named and tagged as HM600 cyclone pump. Simulation shows many improvements in local wear information and situations for better and more qualified design of casing shape and impeller position, before and after geometric corrections. By theory of liquid-solid two-phase flow, the local wear defeats are analyzed and omitted.

Keywords: flow pattern, slurry pump, simulation, wear

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Authors: Igor B. Sivaev

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Design of molecular machines is an extraordinary growing and very important area of research that it was recognized by awarding Sauvage, Stoddart and Feringa the Nobel Prize in Chemistry in 2016 'for the design and synthesis of molecular machines'. Based on the type of motion being performed, molecular machines can be divided into two main types: molecular motors and molecular switches. Molecular switches are molecules or supramolecular complexes having bistability, i.e., the ability to exist in two or more stable forms, among which may be reversible transitions under external influence (heating, lighting, changing the medium acidity, the action of chemicals, exposure to magnetic or electric field). Molecular switches are the main structural element of any molecular electronics devices. Therefore, the design and the study of molecules and supramolecular systems capable of performing mechanical movement is an important and urgent problem of modern chemistry. There is growing interest in molecular switches and other devices of molecular electronics based on transition metal complexes; therefore choice of suitable stable organometallic unit is of great importance. An example of such unit is bis(dicarbollide) complexes of transition metals [3,3’-M(1,2-C₂B₉H₁₁)₂]ⁿ⁻. The control on the ligand rotation in such complexes can be reached by introducing substituents which could provide stabilization of certain rotamers due to specific interactions between the ligands, on the one hand, and which can participate as Lewis bases in complex formation with external metals resulting in a change in the rotation angle of the ligands, on the other hand. A series of isomeric methyl sulfide derivatives of cobalt bis(dicarbollide) complexes containing methyl sulfide substituents at boron atoms in different positions of the pentagonal face of the dicarbollide ligands [8,8’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻, rac-[4,4’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[4,7’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ were synthesized by the reaction of CoCl₂ with the corresponding methyl sulfide carborane derivatives [10-MeS-7,8-C₂B₉H₁₁)₂]⁻ and [10-MeS-7,8-C₂B₉H₁₁)₂]⁻. In the case of asymmetrically substituted cobalt bis(dicarbollide) complexes the corresponding rac- and meso-isomers were successfully separated by column chromatography as the tetrabutylammonium salts. The compounds obtained were studied by the methods of ¹H, ¹³C, and ¹¹B NMR spectroscopy, single crystal X-ray diffraction, cyclic voltammetry, controlled potential coulometry and quantum chemical calculations. It was found that in the solid state, the transoid- and gauche-conformations of the 8,8’- and 4,4’-isomers are stabilized by four intramolecular CH···S(Me)B hydrogen bonds each one (2.683-2.712 Å and 2.709-2.752 Å, respectively), whereas gauche-conformation of the 4,7’-isomer is stabilized by two intramolecular CH···S hydrogen bonds (2.699-2.711 Å). The existence of the intramolecular CH·S(Me)B hydrogen bonding in solutions was supported by the 1H NMR spectroscopy. These data are in a good agreement with results of the quantum chemical calculations. The corresponding iron and nickel complexes were synthesized as well. The reaction of the methyl sulfide derivatives of cobalt bis(dicarbollide) with various labile transition metal complexes results in rupture of intramolecular hydrogen bonds and complexation of the methyl sulfide groups with external metal. This results in stabilization of other rotational conformation of cobalt bis(dicarbollide) and can be used in design of molecular switches. This work was supported by the Russian Science Foundation (16-13-10331).

Keywords: molecular switches, NMR spectroscopy, single crystal X-ray diffraction, transition metal bis(dicarbollide) complexes, quantum chemical calculations

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Authors: Ali M. EL-Soll

Abstract:

Physical properties of Sarir waxy crude oil was investigated, pour-point was determined using ASTM D-79 procedure, paraffin content and carbon number distribution of the paraffin was determined using gas liquid Chromatography(GLC), polymeric additives were prepared and their structures were confirmed using IR spectrophotometer. The molecular weight and molecular weigh distribution of these additives were determined by gel permeation chromatography (GPC). the performance of the synthesized additives as pour-point depressants was evaluated, for the mentioned crude oil.

Keywords: sarir, waxy, crude, pour point, depressants

Procedia PDF Downloads 436

Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G(d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G(d,p) method show good agreement with experimental X-ray data. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide, polarizability

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Authors: A. Archibong-Eso, J. Shi, Y Baba, S. Alagbe, W. Yan, H. Yeung

Abstract:

This study presents over 100 experiments conducted in a 25.4 mm internal diameter (ID) horizontal pipeline. Oil viscosity ranging from 3.5 Pa.s–5.0 Pa.s are used with superficial velocities of oil and water ranging from 0.06 to 0.55 m/s and 0.01 m/s to 1.0 m/s, respectively. Pressure gradient measurements and flow pattern observations are discussed. Numerical simulation of some flow conditions is performed using the commercial CFD code ANSYS Fluent® and the simulation results are compared with experimental results. Results indicate that CFD numerical simulation performed moderately well in predicting the flow configurations observed in this study while discrepancies were observed in the pressure gradient predictions.

Keywords: flow patterns, plug, pressure gradient, rivulet

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Authors: M. F. Elzarei, A. M. Alseaf

Abstract:

Hundred uncorrelated animal and thirty six markers were used in this study to study the molecular characterization of Saudi native Ardi goat (BM18189, ILSTS030, INRA005, OarFCB48, BM2113, ILSTS033, INRA023, RM088, CSRD247, ILSTS034, INRA063, SRCRSP1, ILSTS002, ILSTS044, INRA172, SRCRSP5, ILSTS005, ILSTS049, MAF70, SRCRSP8, ILSTS011, ILSTS058, OarAE54, SRCRSP9, ILSTS019, ILSTS059, OARCP34, TGLA53, ILSTS022, ILSTS082, OARE129, TGLA73, ILSTS029, ILSTS087, OARE193, and RM004). Ardi goat showed high variability. The mean number of alleles per locus ranged from 5 in SRCRSP1 locus to 13.5 in CSRD247 locus. Gene diversities varied within a wide range, from 0.53 in ILSTS002 locus to 0.86 in RM088 locus. Hardy-Weinberg equilibrium was tested in order to evaluate the significance of inbreeding occurring in each locus in Ardi population. Only SRCRSP9, INRA005, ILSTS030 loci showed significance in this way.

Keywords: molecular characterization, microsatellite markers, Ardi goats, Hardy-Weinberg equilibrium

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Authors: Asma Ahmed Aljohani, Mohammed Orif

Abstract:

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

Keywords: bivalves, biomonitoring, hydrocarbons, PAHs

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Authors: Mohammad Ruhul Amin, Nusrat Jahan

Abstract:

Natural gas is a cleaner fuel compared to the others. But it needs some treatment before it is in a state to be used. So natural gas purification is an integral part of any process where natural gas is used as raw material or fuel. There are several impurities in natural gas that have to be removed before use. CO2 is one of the major contaminants. In this project we have removed CO2 by amine process by using MEA solution. We have built up the whole amine process for removing CO2 in Aspen Hysys and simulated the process. At the end of simulation we have got very satisfactory results by using MEA solution for the removal of CO2. Simulation result shows that amine absorption process enables to reduce CO2 content from NG by 58%. HYSYS optimizer allowed us to get a perfect optimized plant. After optimization the profit of existing plant is increased by 2.34 %.Simulation and optimization by Aspen-HYSYS simulator makes available us to enormous information which will help us to further research in future.

Keywords: Aspen–Hysys, CO2 removal, flowsheet development, MEA solution, natural gas optimization

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Authors: A. Douka, S. Vouyiouka, L. M. Papaspyridi, D. Korres, C. Papaspyrides

Abstract:

A "green" process was studied for the preparation of partially renewable aliphatic polyesters based on 1,4-butanediol and 1,8-octanediol with various diacids and derivatives, namely diethyl succinate, adipic acid, sebacic acid, 1,12-dodecanedioic acid and 1,14-tetradecanedioic acid. A first step of enzymatic prepolymerization was carried out in the presence of two different solvents, toluene and diphenylether, applying molecular sieves and vacuum, respectively, to remove polycondensation by-products. Poly(octylene adipate) (PE 8.6), poly(octylene dodecanate)(PE 8.12) and poly(octylene tetradecanate) (PE 8.14) were firstly enzymatically produced in toluene using molecular sieves giving however, low-molecular-weight products. Thereafter, the synthesis of PE 8.12 and PE 8.14 was examined under optimized conditions using diphenylether as solvent and a more vigorous by-product removal step, such as application of vacuum. Apart from these polyesters, the optimized process was also implemented for the production of another long-chain polyester-poly(octylene sebacate) (PE 8.10) and a short-chain polyester-poly(butylene succinate) (PE 4.4). Subsequently, bulk post-polymerization in the melt or solid state was performed. SSP runs involved absence of biocatalyst and reaction temperatures (T) in the vicinity of the prepolymer melting point (Tm-T varied between 15.5 up to 4oC). Focusing on PE 4.4 and PE 8.12, SSP took place under vacuum or flowing nitrogen leading to increase of the molecular weight and improvement of the end product physical appearance and thermal properties.

Keywords: aliphatic polyester, enzymatic polymerization, solid state polymerization, Novozym 435

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Cristina Prandi, Piermichele Kobauri

Abstract:

The present study is based on molecular modeling of a series of twelve 5-(4-substituent-phenoxy)-3-methylfuran-2(5H)-one derivatives which have potential of strigolactones mimics toward Striga hermonthica. The first step of the analysis included the calculation of molecular descriptors which numerically describe the structures of the analyzed compounds. The descriptors ALOGP (lipophilicity), AClogS (water solubility) and BBB (blood-brain barrier penetration), served as the input variables in multiple linear regression (MLR) modeling of germination activity toward S. hermonthica. Two MLR models were obtained. The first MLR model contains ALOGP and AClogS descriptors, while the second one is based on these two descriptors plus BBB descriptor. Despite the braking Topliss-Costello rule in the second MLR model, it has much better statistical and cross-validation characteristics than the first one. The ALOGP and AClogS descriptors are often very suitable predictors of the biological activity of many compounds. They are very important descriptors of the biological behavior and availability of a compound in any biological system (i.e. the ability to pass through the cell membranes). BBB descriptor defines the ability of a molecule to pass through the blood-brain barrier. Besides the lipophilicity of a compound, this descriptor carries the information of the molecular bulkiness (its value strongly depends on molecular bulkiness). According to the obtained results of MLR modeling, these three descriptors are considered as very good predictors of germination activity of the analyzed compounds toward S. hermonthica seeds. This article is based upon work from COST Action (FA1206), supported by COST (European Cooperation in Science and Technology).

Keywords: chemometrics, germination activity, molecular modeling, QSAR analysis, strigolactones

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