Search results for: molecular docking and simulation

Authors: W. Soufi, F. Boukli Hacene, S. Ghalem

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Alzheimer's disease (AD) is a neurodegenerative disease that leads to a progressive and permanent deterioration of nerve cells. This disease is progressively accompanied by an intellectual deterioration leading to psychological manifestations and behavioral disorders that lead to a loss of autonomy. It is the most frequent of degenerative dementia. Alzheimer's disease (AD), which affects a growing number of people, has become a major public health problem in a few years. In the context of the study of the mechanisms governing the evolution of AD disease, we have found that natural flavonoids are good acetylcholinesterase inhibitors that reduce the rate of ßA secretion in neurons. This work is to study the inhibition of acetylcholinesterase (AChE) which is an enzyme involved in Alzheimer's disease, by methods of molecular modeling. These results will probably help in the development of an effective therapeutic tool in the fight against the development of Alzheimer's disease. Our goal of the research is to study the inhibition of acetylcholinesterase (AChE) by molecular modeling methods.

Keywords: Alzheimer's disease, acetylcholinesterase, flavonoids, molecular modeling

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Authors: Aliyu Adamu, Fahrul Huyop, Roswanira Abdul Wahab, Mohd Shahir Shamsir

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Halogenated organic compounds occur in huge amount in biosphere. This is attributable to the diverse use of halogen-based compounds in the synthesis of various industrially important products. Halogenated compound is toxic and may persist in the environment, thereby causing serious health and environmental pollution problems. L-2-haloacid dehalogenases (EC 3.8.1.2) catalyse the specific cleavage of carbon-halogen bond in L-isomers of halogenated compounds, which consequently reverse the effects of environmental halogen-associated pollution. To enhance the efficiency and utility of these enzymes, this study investigates the catalytic amino acid residues and the molecular functional mechanism of DehL, by classical molecular dynamic simulations, MM-PBSA and ab initio fragments molecular orbital (FMO) calculations. The results of the study will serve as the basis for the molecular engineering of the enzyme.

Keywords: DehL, Functional mechanism, Catalytic residues, L-2-haloacid dehalogenase

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Authors: F. Boukli Hacene, W. Soufi, S. Ghalem

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Glaucoma disease is a progressive degenerative optic neuropathy, with irreversible visual field deficits and high eye pressure being one of the risk factors. Sulfonamides are carbonic anhydrase-II inhibitors that aim to decrease the secretion of aqueous humor by direct inhibition of this enzyme at the level of the ciliary processes. These drugs present undesirable effects that are difficult to accept by the patient. In our study, we are interested in the inhibition of carbonic anhydrase-II by different natural ligands (curcumin analogues) using molecular modeling methods using molecular operating environment (MOE) software to predict their interaction with this enzyme.

Keywords: carbonic anhydrase-II, curcumin analogues, drug research, molecular modeling

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Authors: P. Haldar, P. Ghosh, S. Ghoshdastidar, K. Kargupta

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In polymer electrolyte membrane fuel cells (PEMFC), the membrane electrode assembly (MEA) is consisting of two platinum coated carbon electrodes, sandwiched with one proton conducting phosphoric acid doped polymeric membrane. Due to low mechanical stability, flooding and fuel cell crossover, application of phosphoric acid in polymeric membrane is very critical. Phosphorous and silica based 3D inorganic gel gains the attention in the field of supercapacitors, fuel cells and metal hydrate batteries due to its thermally stable highly proton conductive behavior. Also as a large amount of water molecule and phosphoric acid can easily get trapped in Si-O-Si network cavities, it causes a prevention in the leaching out. In this study, we have performed molecular dynamics (MD) simulation and first principle calculations to understand the structural, electronics and electrochemical and morphological behavior of this inorganic gel at various P to Si ratios. We have used dipole-dipole interactions, H bonding, and van der Waals forces to study the main interactions between the molecules. A 'structure property-performance' mapping is initiated to determine optimum P to Si ratio for best proton conductivity. We have performed the MD simulations at various temperature to understand the temperature dependency on proton conductivity. The observed results will propose a model which fits well with experimental data and other literature values. We have also studied the mechanism behind proton conductivity. And finally we have proposed a structure for the gel paste with optimum P to Si ratio.

Keywords: first principle calculation, molecular dynamics simulation, phosphorous and silica based 3D inorganic gel, polymer electrolyte membrane fuel cells, proton conductivity

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Authors: Nicola G. G. Cecca

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In Italian IPSSEOAs, high schools that give a vocational education to students that will work in the field of Enogastronomy and Hotel Management, the course of Food Science allows the students to start and see food as a mixture of substances that they will transform during their profession. These substances are characterized not only by a chemical composition but also by a molecular structure that makes them nutritionally active. But the increasing number of new products proposed by Food Industry, the modern techniques of production and transformation, the innovative preparations required by customers have made many information reported in the most wide spread Food Science textbooks not up-to-date or too poor for the people who will work in catering sector. Often Authors offer information aged to Bohr’s Atomic Model and to the ‘Octet Rule’ proposed by G.N. Lewis to describe the Chemical Bond, without giving any reference to new as Orbital Atomic Model and Molecular Orbital Theory that, in the meantime, start to be old themselves. Furthermore, this antiquated information precludes an easy understanding of a wide range of properties of nutritive substances and many reactions in which the food constituents are involved. In this paper, our attention is pointed out to use GEOMAG™ to represent the dynamics with which the chemical bond is formed during the synthesis of the molecules. GEOMAG™ is a toy, produced by the Swiss Company Geomagword S.A., pointed to stimulate in children, aged between 6-10 years, their fantasy and their handling ability and constituted by metallic spheres and metallic magnetic bars coated by coloured plastic materials. The simulation carried out with GEOMAG™ is based on the similitude existing between the Coulomb’s force and the magnetic attraction’s force and in particular between the formulae with which they are calculated. The electrostatic force (F in Newton) that allows the formation of the chemical bond can be calculated by mean Fc = kc q1 q2/d2 where: q1 e q2 are the charge of particles [in Coulomb], d is the distance between the particles [in meters] and kc is the Coulomb’s constant. It is surprising to observe that the attraction’s force (Fm) acting between the magnetic extremities of GEOMAG™ used to simulate the chemical bond can be calculated in the same way by using the formula Fm = km m1 m2/d2 where: m1 e m2 represent the strength of the poles [A•m], d is the distance between the particles [m], km = μ/4π in which μ is the magnetic permeability of medium [N•A-2]. The magnetic attraction can be tested by students by trying to keep the magnetic elements of GEOMAG™ separate by hands or trying to measure by mean an appropriate dynamometric system. Furthermore, by using a dynamometric system to measure the magnetic attraction between the GEOMAG™ elements is possible draw a graphic F=f(d) to verify that the curve obtained during the simulation is very similar to that one hypnotized, around the 1920’s by Linus Pauling to describe the formation of H2+ in according with Molecular Orbital Theory.

Keywords: chemical bond, molecular orbital theory, magnetic attraction force, GEOMAG™

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Authors: Ainoa Guinart, Maria Korpidou, Daniel Doellerer, Cornelia Palivan, Ben L. Feringa

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Stimuli responsive systems arise from the need to meet unsolved needs of current molecular drugs. Our study presents the design of a delivery system with high spatiotemporal control and tuneable release profiles. We study the incorporation of a hydrophobic synthetic molecular motor into PDMS-b-PMOXA block copolymer vesicles to create a self-assembled system. We prove their successful incorporation and selective activation by low powered visible light (λ 430 nm, 6.9 mW). We trigger the release of a fluorescent dye with high release efficiencies over sequential cycles (up to 75%) with the ability to turn on and off the release behaviour on demand by light irradiation. Low concentrations of photo-responsive units are proven to trigger release down to 1 mol% of molecular motor. Finally, we test our system in relevant physiological conditions using a lung cancer cell line and the encapsulation of an approved drug. Similar levels of cell viability are observed compared to the free-given drugshowing the potential of our platform to deliver functional drugs on demand with the same efficiency and lower toxicity.

Keywords: molecular motor, polymer, drug delivery, light-responsive, cancer, selfassembly

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Authors: Menna Ewida, Dalal Abou El-Ella, Dina Lasheen, Huessin El-Subbagh

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Introduction: Vascular Endothelial Growth Factor receptor (VEGF) is a signal protein produced by cells that stimulates vasculogenesis to create new blood vessels. VEGF family binds to three trans-membrane tyrosine kinase receptors,Dihydrofolate reductase (DHFR) is an enzyme of crucial importance in medicinal chemistry. DHFR catalyzes the reduction 7,8 dihydro-folate to tetrahydrofolate and intimately couples with thymidylate synthase which is a pivotal enzyme that catalysis the reductive methylation of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP) utilizing N5,N10-methylene tetrahydrofolate as a cofactor which functions as the source of the methyl group. Purpose: Novel substituted Thiazole agents were designed as DHFR and VEGF-TK inhibitors with increased synergistic activity and decreased side effects. Methods: Five series of compounds were designed with a rational that mimic the pharmacophoric features present in the reported active compounds that target DHFR & VEGFR. These molecules were docked against Methotrexate & Sorafenib as controls. An in silico ADMET study was also performed to validate the bioavailability of the newly designed compounds. The in silico molecular docking & ADMET study were also applied to the non-classical antifolates for comparison. The interaction energy comparable to that of MTX for DHFRI and Sorafenib for VEGF-TKI activity were recorded. Results: Compound 5 exhibited the highest interaction energy when docked against Sorafenib, While Compound 9 showed the highest interaction energy when docked against MTX with the perfect binding mode. Comparable results were also obtained for the ADMET study. Most of the compounds showed absorption within (95-99) zone which varies according to the type of substituents. Conclusions: The Substituted Thiazole Analogues could be a suitable template for antitumor drugs that possess enhanced bioavailability and act as DHFR and VEGF-TK inhibitors.

Keywords: anti-tumor agents, DHFR, drug design, molecular modeling, VEGFR-TKIs

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Authors: Kai Jin, Hua Li, Qing Song

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Homeland security and border safety is an issue for any country. This paper takes the border security of US as an example to discuss the usage and efficiency of simulation tools in the homeland security application. In this study, available resources and different illegal infiltration parameters are defined, including their individual behavior and objective, in order to develop a model that describes border patrol system. A simulation model is created in Arena. This simulation model is used to study the dynamic activities in the border security. Possible factors that may affect the effectiveness of the border patrol system are proposed. Individual and factorial analysis of these factors is conducted and some suggestions are made.

Keywords: resource optimization, simulation, modeling, border security

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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: 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: Ziraguen O. Williams, Shield B. Lin, Fouad N. Matari, Leslie J. Quiocho

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In a task to assist NASA in analyzing the dynamic forces caused by operational countermeasures of an astronaut’s exercise platform impacting the spacecraft, feedback delay, and signal noise were added to a simulation model of an active-controlled vibration isolation system to regulate the movement of the exercise platform. Previous simulation work was conducted primarily via MATLAB/Simulink. Two additional simulation tools used in this study were Trick and MBDyn, NASA co-developed software simulation environments. Simulation results obtained from these three tools were very similar. All simulation results support the hypothesis that an active-controlled vibration isolation system outperforms a passive-controlled system even with the addition of feedback delay and signal noise to the active-controlled system. In this paper, squat exercise was used in creating excited force to the simulation model. The exciter force from a squat exercise was calculated from the motion capture of an exerciser. The simulation results demonstrate much greater transmitted force reduction in the active-controlled system than the passive-controlled system.

Keywords: control, counterweight, isolation, vibration

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Authors: Joseph E. Estevez, Mahdi Ghazizadeh, James G. Ryan, Ajit D. Kelkar

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Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B10’s large neutron capture cross section. The B10 has an effective neutron capture cross section suitable for low energy neutrons ranging from 10-5 to 104 eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm3. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.

Keywords: boron nitride nanotube, radiation shielding, young modulus, atomistic modeling

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Authors: Tsai-Pei Liu, Zhi-Rou Zheng, Tzu-Tzu Wen

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Innovative logistics system simulation teaching is to extract the characteristics of the system through simulation methodology. The system has randomness and interaction problems in the execution time. Therefore, the simulation model can usually deal with more complex logistics process problems, giving students different learning modes. Students have more autonomy in learning time and learning progress. System simulation has become a new educational tool, but it still needs to accept many tests to use it in the teaching field. Although many business management departments in Taiwan have started to promote, this kind of simulation system teaching is still not popular, and the prerequisite for popularization is to be supported by students. This research uses an extension of Integration Unified Theory of Acceptance and Use of Technology (UTAUT2) to explore the acceptance of students in universities of science and technology to use system simulation as a learning tool. At the same time, it is hoped that this innovation can explore the effectiveness of the logistics system simulation after the introduction of teaching. The results indicated the significant influence of performance expectancy, social influence and learning value on students’ intention towards confirmed the influence of facilitating conditions and behavioral intention. The extended UTAUT2 framework helps in understanding students’ perceived value in the innovative logistics system teaching context.

Keywords: UTAUT2, logistics system simulation, learning value, Taiwan

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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: Jiří Barta, Josef Krahulec, Jiří F. Urbánek

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Education and practical training crisis management members are a topical issue nowadays. The paper deals with the perspectives and possibilities of ‘smart solutions’ to education for crisis management staff. Currently, there are a large number of simulation tools, which notes that they are suitable for practical training of crisis management staff. The first part of the paper is focused on the introduction of the technology simulation tools. The simulators aim is to create a realistic environment for the practical training of extending units of crisis staff. The second part of the paper concerns the possibilities of using the simulation technology to the education process. The aim of this section is to introduce the practical capabilities and potential of the simulation programs for practical training of crisis management staff.

Keywords: crisis management staff, computer simulation, software, technological education

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Authors: Shuofeng Yuan, Bojian Zheng

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Assembly of the heterotrimeric polymerase complex of influenza virus from the individual subunits PB1, PA, and PB2 is a prerequisite for viral replication, in which the interaction between the N-terminal of PB1 (PB1N) and the C terminal of PA (PAC) may be a desired target for antiviral development. In this study, we first compared the feasibility of high throughput screening by enzyme-linked immunosorbent assay (ELISA) and fluorescence polarization (FP) assay. Among the two, ELISA was demonstrated to own broader dynamic range so that it was used for screening inhibitors, which blocked PA and PB1 interaction. Several binding inhibitors of PAC-PB1N were identified and subsequently tested for the antiviral efficacy. Apparently, 3-(2-chlorophenyl)-6-ethyl-7-methyl[1,2,4]triazolo[4,3-a]pyrimidin-5-ol, designated ANA-1, was found to be a strong inhibitor of PAC-PB1N interaction and act as a potent antiviral agent against the infections of multiple subtypes of influenza A virus, including H1N1, H3N2, H5N1, H7N7, H7N9 and H9N2 subtypes, in cell cultures. Intranasal administration of ANA-1 protected mice from lethal challenge and reduced lung viral loads in H1N1 virus infected BALB/c mice. Docking analyses predicted that ANA-1 bound to an allosteric site of PAC, which would cause conformational changes thereby disrupting the PAC-PB1N interaction. Overall, our study has identified a novel compound with potential to be developed as an anti-influenza drug.

Keywords: influenza, antiviral, viral polymerase, compounds

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Authors: A. M. Naraghi, V. Gonzalez, M. O'Sullivan, C. G. Walker, M. Poshdar, F. Ying, M. Abdelmegid

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Discrete Event Simulation (DES) and Agent Based Simulation (ABS) are two simulation approaches that have been proposed to support decision-making in the construction industry. Despite the wide use of these simulation approaches in the construction field, their applications for production and material planning is still limited. This is largely due to the dynamic and complex nature of construction material supply chain systems. Moreover, managing the flow of construction material is not well integrated with site logistics in traditional construction planning methods. This paper presents a hybrid of DES and ABS to simulate on-site and off-site material supply processes. DES is applied to determine the best production scenarios with information of on-site production systems, while ABS is used to optimize the supply chain network. A case study of a construction piling project in New Zealand is presented illustrating the potential benefits of using the proposed hybrid simulation model in construction material flow planning. The hybrid model presented can be used to evaluate the impact of different decisions on construction supply chain management.

Keywords: construction supply-chain management, simulation modeling, decision-support tools, hybrid simulation

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Authors: Ki Hyun Park, Hye Min Park, Jeong Ho Kim, Chan Jong Park, Koan Sik Joo

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In the modern days, the use of radioactive substances is on the rise in the areas like chemical weaponry, industrial usage, and power plants. Although there are various technologies available to detect and monitor radioactive substances in the air, the technologies to detect underwater radioactive substances are scarce. In this study, computer simulation of the underwater detection system measuring beta-ray, a radioactive substance, has been done through MCNP. CaF₂, YAP(Ce) and YAG(Ce) have been used in the computer simulation to detect beta-ray as scintillator. Also, the source used in the computer simulation is Sr-90 and Y-90, both of them emitting only pure beta-ray. The distance between the source and the detector was shifted from 1mm to 10mm by 1 mm in the computer simulation. The result indicated that Sr-90 was impossible to measure below 1 mm since its emission energy is low while Y-90 was able to be measured up to 10mm underwater. In addition, the detector designed with CaF₂ had the highest efficiency among 3 scintillators used in the computer simulation. Since it was possible to verify the detectable range and the detection efficiency according to modeling through MCNP simulation, it is expected that such result will reduce the time and cost in building the actual beta-ray detector and evaluating its performances, thereby contributing the research and development.

Keywords: Beta-ray, CaF₂, detector, MCNP simulation, scintillator

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Authors: Nikolaos Simantiris, Markos Avlonitis

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This work builds a simulation platform, modeling the spatial diffusion of the invasive species Callinectes sapidus (blue crab) as a random walk, incorporating also generation, fatality, and fishing rates modeling the time evolution of its population. Antinioti lagoon in West Greece was used as a testbed for applying the simulation model. Field measurements from June 2020 to June 2021 on the lagoon’s setting, bathymetry, and blue crab juveniles provided the initial population simulation of blue crabs, as well as biological parameters from the current literature were used to calibrate simulation parameters. The scope of this study is to render the authors able to predict the evolution of the blue crab population in confined environments of the Ionian Islands region in West Greece. The first result of the simulation experiments shows the possibility for a robust prediction for blue crab population evolution in the Antinioti lagoon.

Keywords: antinioti lagoon, blue crab, stochastic simulation, random walk

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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: Jeong-Hwan Choi, Hyo-Sang Park, Tae-Hyung Lee

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The transmission tower is one of the crucial lifeline structures in a modern society, and it needs to be protected against extreme loading conditions. However, the transmission tower is a very complex structure and, therefore, it is very difficult to simulate the actual damage and the collapse behavior of the tower structure. In this study, the actual collapse behavior of the transmission tower due to lateral loading conditions such as wind load is evaluated through the computational simulation. For that, a progressive collapse procedure is applied to the simulation. In this procedure, after running the simulation, if a member of the tower structure fails, the failed member is removed and the simulation run again. The 154kV transmission tower is selected for this study. The simulation is performed by nonlinear static analysis procedure, namely pushover analysis, using OpenSEES, an earthquake simulation platform. Three-dimensional finite element models of those towers are developed.

Keywords: transmission tower, OpenSEES, pushover, progressive collapse

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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: 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: Justine Kiiza, Xu Jiafang

Abstract:

The world’s demand for energy is increasing rapidly due to population growth and a reduction in shallow conventional oil and gas reservoirs, resorting to deeper and mostly unconventional reserves like shale oil and gas. Most shale formations contain a large amount of expansive sodium montmorillonite (Na-Mnt), due to high water adsorption, hydration, and when the drilling fluid filtrate enters the formation with high Mnt content, the wellbore wall can be unstable due to hydration and swelling, resulting to shrinkage, sticking, balling, time wasting etc., and well collapse in extreme cases causing complex downhole accidents and high well costs. Recently, polyamines like 1, 6 – hexane diamine (HEDA) have been used as typical drilling fluid shale inhibitors to minimize and/or cab clay mineral swelling and maintain the wellbore stability. However, their application is limited to shallow drilling due to their sensitivity to elevated temperature and pressure. Inorganic potassium salts i.e., KCl, have long been applied for restriction of shale formation hydration expansion in deep wells, but their use is limited due to toxicity. Understanding the adsorption behaviour of HEDA on Na-Mnt surfaces in present of organo-salts, organic K-salts e.g., HCO₂K - main component of organo-salt drilling fluid, is of great significance in explaining the inhibitory performance of polyamine inhibitors. Molecular dynamic simulations (MD) were applied to investigate the influence of HCO₂K and KCl on the adsorption mechanism of HEDA on the Na-Mnt surface. Simulation results showed that adsorption configurations of HEDA are mainly by terminal amine groups with a flat-lying alkyl hydrophobic chain. Its interaction with the clay surface decreased the H-bond number between H₂O-clay and neutralized the negative charge of the Mnt surface, thus weakening the surface hydration ability of Na-Mnt. The introduction of HCO₂K greatly improved inhibition ability, coordination of interlayer ions with H₂O as they were replaced by K+, and H₂O-HCOO- coordination reduced H₂O-Mnt interactions, mobility and transport capability of H₂O molecules were more decreased. While KCl showed little ability and also caused more hydration with time, HCO₂K can be used as an alternative for offshore drilling instead of toxic KCl, with a maximum concentration noted in this study as 1.65 wt%. This study provides a theoretical elucidation for the inhibition mechanism and adsorption characteristics of HEDA inhibitor on Na-Mnt surfaces in the presence of K+-salts and may provide more insight into the evaluation, selection, and molecular design of new clay-swelling high-performance WBDF systems used in oil and gas complex offshore drilling well sections.

Keywords: shale, hydration, inhibition, polyamines, organo-salts, simulation

Procedia PDF Downloads 37

Authors: Juraj Camaj, Anna Dolinayova, Jana Lalinska, Miroslav Bariak

Abstract:

Planning of infrastructure and processes in logistic center within the frame of various kinds of logistic hubs and technological activities in them represent quite complex problem. The main goal is to design appropriate layout, which enables to realize expected operation on the desired levels. The simulation software represents progressive contemporary experimental technique, which can support complex processes of infrastructure planning and all of activities on it. It means that simulation experiments, reflecting various planned infrastructure variants, investigate and verify their eligibilities in relation with corresponding expected operation. The inducted approach enables to make qualified decisions about infrastructure investments or measures, which derive benefit from simulation-based verifications. The paper represents simulation software for simulation infrastructural layout and technological activities in marshalling yard, intermodal terminal, warehouse and combination between them as the parts of logistic center.

Keywords: marshalling yard, intermodal terminal, warehouse, transport technology, simulation

Procedia PDF Downloads 511

Authors: Prasanthi Malapati, R. Reshma, Vijay Soni, Perumal Yogeeswari, Dharmarajan Sriram

Abstract:

In the present study, we attempted to develop Mycobacterium tuberculosis (Mtb) inhibitors by exploring the pharmaceutically underexploited enzyme targets which are majorly involved in cell wall biosynthesis of mycobacteria. For this purpose, glutamate racemase (coded by MurI gene) was selected. This enzyme racemize L-glutamate to D-glutamate required for the construction of peptidoglycan in the bacterial cell wall synthesis process. Furthermore this enzyme is neither expressed nor its product, D-glutamate is normally found in mammals, and hence designing inhibitors against this enzyme will not affect the host system as well act as potential antitubercular drugs. A library of BITS in house compounds were screened against Mtb MurI enzyme. Based on docking score, interactions and synthetic feasibility one hit lead was identified. Further optimization of lead was attempted and its derivatives were synthesized. Forty eight derivatives of 2-phenylbenzo[d]oxazole and 2-phenylbenzo[d]thiazole were synthesized and evaluated for Mtb MurI inhibition study, in vitro activities against Mtb, cytotoxicity against RAW 264.7 cell line. Chemical derivatization of the lead resulted in compounds NR-1213 AND NR-1124 as the potent M. tuberculosis glutamate racemase inhibitors with IC50 of 4-5µM which are remarkable and were found to be non-cytotoxic. Molecular dynamics, dormant models and cardiotoxicity studies of the most active molecules are in process.

Keywords: cell wall biosynthesis, dormancy, glutamate racemase, tuberculosis

Procedia PDF Downloads 265

Authors: N. Massoum, B. Bouazza

Abstract:

In this paper, we have developed a numerical simulation model to describe the electrical properties of GaInP MESFET with submicron gate (Lg = 0.5 µm). This model takes into account the three-dimensional (3D) distribution of the load in the short channel and the law effect of mobility as a function of electric field. Simulation software based on a stochastic method such as Monte Carlo has been established. The results are discussed and compared with those of the experiment. The result suggests experimentally that, in a very small gate length in our devices (smaller than 40 nm), short-channel tunneling explains the degradation of transistor performance, which was previously enhanced by velocity overshoot.

Keywords: Monte Carlo simulation, transient electron transport, MESFET device, simulation software

Procedia PDF Downloads 506

Authors: T. Rajamäki

Abstract:

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

Procedia PDF Downloads 274