Search results for: molecular junction

Authors: Mohamed Ahmed Khali

Abstract:

Numbers of deep well anode ground beds (GBs) have been retrieved due to un operated anode chains. New identical magnetite anode chains(MAC) have been installed at Raslanuf complex impressed current Cathodic protection(ICCP) system, distributed at different plants(Utility, ethylene and polyethylene). All problems associated with retrieving and installation of MACs have been discussed, rectified and presented. All GB associated severely corroded wellhead casings were well maintained and/ or replaced by new fabricated and modified ones. The main cause of wellhead casings internal corrosion was discussed, and the conducted remedy action to overcome future corrosion problem is presented. All GB connected anode junction boxes (AJBs) and shunts were closely inspected, maintained, and necessary replacement/and or modification were carried out on shunts. All damaged GB concrete foundations (CF) have been inspected and completely replaced. All GB associated Transformer-Rectifiers units (TRUs) were subjected to through inspection, and necessary maintenance has been performed on each individual TRU. After completion of all MACs and TRU maintenance activities, each cathodic protection station (CPS) has been re-operated. An alternative current (AC), direct current (DC), voltage and structure to soil potential (S/P) measurements have been conducted, recorded, and all obtained test results are presented. DC current outputs has been adjusted, and DC current outputs of each MAC has been recorded for each GB AJB.

Keywords: magnatite anode, deep well, ground bed, cathodic protection, transformer rectifies, impreced current, junction box

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Authors: Said Belaaouad

Abstract:

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

Procedia PDF Downloads 100

Authors: Adam Abate, Elham Rasti, Philip Romero

Abstract:

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

Abstract:

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: 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 287

Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

Abstract:

The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

Procedia PDF Downloads 527

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

Abstract:

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

Procedia PDF Downloads 490

Authors: Mohamed Ahmed Khalil

Abstract:

The number of deep well anode ground beds (GBs) have been retrieved due to unoperated anode chains. New identical magnetite anode chains (MAC) have been installed at Raslanuf complex impressed current Cathodic protection (ICCP) system, distributed at different plants (Utility, ethylene and polyethylene). All problems associated with retrieving and installation of MACs have been discussed, rectified and presented. All GB-associated severely corroded wellhead casings were well maintained and/or replaced by new fabricated and modified ones. The main cause of the wellhead casing's severe internal corrosion was discussed and the conducted remedy action to overcome future corrosion problems is presented. All GB-connected anode junction boxes (AJBs) and shunts were closely inspected, maintained and necessary replacement and/or modifications were carried out on shunts. All damaged GB concrete foundations (CF) have been inspected and completely replaced. All GB-associated Transformer-Rectifiers Units (TRU) were subjected to thorough inspection and necessary maintenance was performed on each individual TRU. After completion of all MACs and TRU maintenance activities, each cathodic protection station (CPS) has been re-operated, alternative current (AC), direct current (DC), voltage and structure to soil potential (S/P) measurements have been conducted, recorded and all obtained test results are presented. DC current outputs have been adjusted and DC current outputs of each MAC have been recorded for each GB AJB.

Keywords: magnetite anodes, deep well, ground beds, cathodic protection, transformer rectifier, impressed current, junction boxes

Procedia PDF Downloads 125

Authors: Son Nguyen, Thanh Van, Ly Le

Abstract:

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: 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

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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 479

Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

Abstract:

Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

Procedia PDF Downloads 349

Authors: Mahmoud A. Abdulhamid

Abstract:

Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

Procedia PDF Downloads 98

Authors: Lise P. Labéjof, Ivna Mororó, Raquel G. Bastos, Maria Isabel G. Severo, Arno H. de Oliveira

Abstract:

This work presents an alternative mode of intestine mucosa renewal that may allow to better understand the total loss of villi after irradiation. It was tested a morphological method of 3d reconstruction using micrographs of serial sections of rat duodenum. We used hundreds of sections of each specimen of duodenum placed on glass slides and examined under a light microscope. Those containing the detachment, approximately a dozen, were chosen for observation under a transmission electron microscope (TEM). Each of these sections was glued on a block of epon resin and recut into a hundred of 60 nm-thick sections. Ribbons of these ultrathin sections were distributed on a series of copper grids in the same order of appearance than during the process of microstomia. They were then stained by solutions of uranyl and lead salts and observed under a TEM. The sections were pictured and the electron micrographs showing signs of cells detachment were transferred into two softwares, ImageJ to align the cellular structures and Reconstruct to realize the 3d reconstruction. It has been detected epithelial cells that exhibited all signs of programmed cell death and localized at the villus-crypt junction. Their nucleus was irregular in shape with a condensed chromatin in clumps. Their cytoplasm was darker than that of neighboring cells, containing many swollen mitochondria. In some places of the sections, we could see intercellular spaces enlarged by the presence of shrunk cells which displayed a plasma membrane with an irregular shape in thermowell as if the cell interdigitations would distant from each other. The three-dimensional reconstruction of the crypts has allowed observe gradual loss of intercellular contacts of crypt cells in the longitudinal plan of the duodenal mucosa. In the transverse direction, there was a gradual increase of the intercellular space as if these cells moved away from one another. This observation allows assume that the gradual remoteness of the cells at the villus-crypt junction is the beginning of the mucosa detachment. Thus, the shrinking of cells due to apoptosis is the way that they detach from the mucosa and progressively the villi also. These results are in agreement with our initial hypothesis and thus have demonstrated that the villi become detached from the mucosa at the villus-crypt junction by the programmed cell death process. This type of loss of entire villus helps explain the rapid denudation of the intestinal mucosa in case of irradiation.

Keywords: 3dr, transmission electron microscopy, ionizing radiations, rat small intestine, apoptosis

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

Abstract:

As the production process of self-standing GaN substrates evolves, the commercialization of low dislocation density, large-scale, semi-insulating self-standing GaN substrates is gradually becoming a reality. This advancement has given rise to increased interest in GaN materials' homoepitaxial technology. However, at the homoepitaxial interface, there are considerable concentrations of impurity elements, including C, Si, and O, which generate parasitic leakage channels at the re-growth junction. This phenomenon results in leaked HEMTs that prove difficult to switch off, rendering them effectively non-functional. The emergence of leakage channels can also degrade the high-frequency properties and lower the power devices' breakdown voltage. In this study, the uniform epitaxy of AlGaN/GaN heterojunction with high electron mobility was accomplished through the surface treatment of the GaN substrates prior to growth and the design of the AlN isolation layer structure. By employing a procedure combining gallium atom in-situ cleaning and plasma nitridation, the C and O impurity concentrations at the homoepitaxial interface were diminished to the scale of 10¹⁷ cm-³. Additionally, the 1.5 nm nitrogen-rich AlN isolation layer successfully prevented the diffusion of Si impurities into the GaN channel layer. The result was an AlGaN/GaN heterojunction with an electron mobility of 1552 cm²/Vs and an electron density of 1.1 × 10¹³ cm-² at room temperature, obtained on a Fe-doped semi-insulating GaN substrate.

Keywords: MBE, AlGaN/GaN, homogenerous epitaxy, HEMT

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

Abstract:

Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

Abstract:

Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Nikhil Agrawal, Adam A. Skelton

Abstract:

Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

Procedia PDF Downloads 348

Authors: Micheale Yifter Weldemichael

Abstract:

Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

Procedia PDF Downloads 47

Authors: M. Ghali, M. Elnimr, G. F. Ali, A. M. Eissa, H. Talaat

Abstract:

CuIn₃Se₅ material is indexed as ordered vacancy compounds having excellent matching properties with CuInGaSe (CIGS) solar absorber layer. For example, the valence band offset of CuIn₃Se₅ with CIGS is nearly 0.3 eV, and the lattice mismatch is less than 1%, besides the absence of discontinuity in their conduction bands. Thus, CuIn₃Se₅ can work as a passivation layer for repelling holes from CIGS/CdS interface and hence to reduce the interface carriers recombination and consequently enhancing the efficiency of CIGS/CdS solar cells. Theoretically, it was reported earlier that an improvement in the efficiency of p-CIGS-based solar cell with a thin ~100 nm of n-CuIn₃Se₅ layer is expected. Recently, a reported experiment demonstrated significant improvement in the efficiency of Molecular Beam Epitaxy (MBE) grown CIGS solar cells from 13.4 to 14.5% via inserting a thin layer of MBE-grown Cu(In,Ga)₃Se₅ layer at the CdS/CIGS interface. It should be mentioned that CuIn₃Se₅ material in either bulk or thin film form, are usually fabricated by high vacuum physical vapor deposition techniques (e.g., three-source co-evaporation, RF sputtering, flash evaporation, and molecular beam epitaxy). In addition, achieving photosensitive films of n-CuIn₃Se₅ material is important for new hybrid organic/inorganic structures, where inorganic photo-absorber layer, with n-type conductivity, can form n–p junction with organic p-type material (e.g., conductive polymers). A detailed study of the physical properties of CuIn₃Se₅ is still necessary for better understanding of device operation and further improvement of solar cells performance. Here, we report on the low-cost synthesis of CuIn₃Se₅ material in nano-scale size, with an average diameter ~10nm, using simple solution-based colloidal chemistry. In contrast to traditionally grown bulk tetragonal CuIn₃Se₅ crystals using high Vacuum-based technology, our colloidal CuIn₃Se₅ nanocrystals show cubic crystal structure with a shape of nanoparticles and band gap ~1.33 eV. Ink-coated thin films prepared from these nanocrystals colloids; display n-type character, 1.26 eV band gap and strong photo-responsive behavior with incident white light. This suggests the potential use of colloidal CuIn₃Se₅ as an active layer in all-solution-processed thin film solar cells.

Keywords: nanocrystals, CuInSe, thin film, optical properties

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Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

Abstract:

This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

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Authors: Salah Belaidi

Abstract:

We have carried out extensive and in-depth research to search for bioactive compounds based on Algerian plants. A selection of 50 ligands from Algerian medicinal plants. Several compounds used in herbal medicine have been drawn using Marvin Sketch software. We determined the three-dimensional structures of the ligands with the MMFF94 force field in order to prepare these ligands for molecular docking. The 3D protein structure of the SARS-CoV-2 main protease was taken from the Protein Data Bank. We used AutoDockVina software to apply molecular docking. The hydrogen atoms were added during the molecular docking process, and all the twist bonds of the ligands were added using the (ligand) module in the AutoDock software. The COVID-19 main protease (Mpro) is a key enzyme that plays a vital role in viral transcription and mediating replication, so it is a very attractive drug target for SARS-CoV-2. In this work, an evaluation was carried out on the biologically active compounds present in these selected medicinal plants as effective inhibitors of the protease enzyme of COVID-19, with an in-depth computational calculation of the molecular docking using the Autodock Vina software. The top 7 ligands: Phloroglucinol, Afzelin, Myricetin-3-O- rutinosidTricin 7-neohesperidoside, Silybin, Silychristinthat and Kaempferol are selected among the 50 molecules studied which are Algerian medicinal plants, whose selection is based on the best binding energy which is relatively low compared to the reference molecule with binding affinities of -9.3, -9.3, -9, -8.9, -8 .5, 8.3 and -8.3 kcal mol-1 respectively. Then, we analyzed the ADME properties of the best7 ligands using the web server SwissADME. Two ligands (Silybin, Silychristin) were found to be potential candidates for the discovery and design of novel drug inhibitors of the protease enzyme of SARS-CoV-2. The stability of the two ligands in complexing with the Mpro protease was validated by molecular dynamics simulation; they revealed a stable trajectory in both techniques, RMSD and RMSF, by showing molecular properties with coherent interactions in molecular dynamics simulations. Finally, we conclude that the Silybin ligand forms a more stable complex with the Mpro protease compared to the Silychristin ligand.

Keywords: COVID-19, medicinal plants, molecular docking, ADME properties, molecular dynamics

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Authors: Ambrish Singh

Abstract:

The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

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Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

Abstract:

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

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Authors: Mohammad Najmol Haque, Takeshi Maki, Jun Sasaki

Abstract:

Headed stud shear connections are widely used in the junction or embedded zone of hybrid girder to achieve whole composite action with continuity that can sustain steel-concrete interfacial tensile and shear forces. In Japan, Japan Road Association (JRA) specifications are used for hybrid girder design that utilizes very low level of stud capacity than those of American Institute of Steel Construction (AISC) specifications, Japan Society of Civil Engineers (JSCE) specifications and EURO code. As low design shear strength is considered in design of connections, the time dependent shear behavior due to sustained external loading is not considered, even not fully studied. In this study, a finite element approach was used to evaluate the time dependent shear behavior for headed studs used as connections at the junction. This study clarified, how the sustained loading distinctively impacted on changing the interfacial shear of connections with time which was sensitive to lodging history, positions of flanges, neighboring studs, position of prestress bar and reinforcing bar, concrete strength, etc. and also identified a shear influence area. Stud strength was also confirmed through pushout tests. The outcome obtained from the study may provide an important basis and reference data in designing connections of hybrid girders with enhanced stud capacity with due consideration of their long-term shear behavior.

Keywords: finite element, hybrid girder, shear connections, sustained loading, time dependent behavior

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Authors: Salma M. Wakil

Abstract:

Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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Authors: Sajjad Seifoori

Abstract:

Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: impact, molecular dynamic, graphene, spring mass

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Authors: Hassan Irshad Bhatti, Saravanan Yuvaraja, Xiaohang Li

Abstract:

GaN-based devices, such as high electron mobility transistors (HEMTs), offer superior characteristics for high-power, high-frequency, and high-temperature applications [1]. However, this exceptional electrical performance is compromised by undesirable self-heating effects under high-power applications [2, 3]. Some of the issues caused by self-heating are current collapse, thermal runway and performance degradation [4, 5]. Therefore, accurate and reliable methods for measuring the temperature of individual devices on a chip are needed to monitor and control the thermal behavior of GaN-based devices [6]. Temperature measurement at the micro/nanoscale is a challenging task that requires specialized techniques such as Infrared microscopy, Raman thermometry, and thermoreflectance. Recently, micro-thermocouples (MTCs) have attracted considerable attention due to their advantages of simplicity, low cost, high sensitivity, and compatibility with standard fabrication processes [7, 8]. A micro-thermocouple is a junction of two different metal thin films, which generates a Seebeck voltage related to the temperature difference between a hot and cold zone. Integrating MTC in a device allows local temperature to be measured with high sensitivity and accuracy [9]. This work involves the fabrication and integration of micro-thermocouples (MTCs) to measure the channel temperature of GaN HEMT. Our fabricated MTC (Platinum-Chromium junction) has shown a sensitivity of 16.98 µV/K and can measure device channel temperature with high precision and accuracy. The temperature information obtained using this sensor can help improve GaN-based devices and provide thermal engineers with useful insights for optimizing their designs.

Keywords: Electrical Engineering, Thermal engineering, Power Devices, Semiconuctors

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Authors: Afsheen Aman, Shah Ali Ul Qader

Abstract:

Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

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Authors: Maatouk Mohamed, Nouira Mariem

Abstract:

Background and aims: Healthcare-associated infections (HAI) represent a major public health problem worldwide. They represent one of the most serious adverse events in health care. The objectives of our study were to estimate the prevalence of HAI at the Charles Nicolle Hospital (CNH) and to identify the main associated factors as well as to estimate the frequency of antibiotic use. Methods: It was a cross sectional study at the CNH with a unique passage per department (OctoberDecember 2018). All patients present at the wards for more than 48 hours were included. All patients from outpatient consultations, emergency and dialysis departments were not included. The site definitions of infections proposed by the Centers for Disease Control and Prevention (CDC) were used. Only clinically and/or microbiologically confirmed active HAIs were included. Results: A total of 318 patients were included with a mean age of 52 years and a sex ratio (Female/Male) of 1.05. A total of 41 patients had one or more active HAIs, corresponding to a prevalence of 13.1% (95% CI: 9.3%-16.9%). The most frequent sites infections were urinary tract infections and pneumonia. Multivariate analysis among adult patients (>=18 years) (n=261), revealed that infection on admission (p=0.01), alcoholism (p=0.01), high blood pressure (p=0.008), having at least one invasive device inserted (p=0.004), and history of recent surgery (p=0.03), increased significantly the risk of HAIs. More than 1 of 3 patients (35.4%) were under antibiotics on the day of the survey, of which more than half (57.4%) were under 2 or more types of antibiotics. Conclusion: The prevalence of HAIs and antibiotic prescriptions at the CNH were considerably high. An infection prevention and control committee, as well as the development of an Antibiotic stewardship program with continuous monitoring using repeated prevalence surveys must be implemented to limit the frequency of these infections effectively.

Keywords: tumors, oesophagectomy, esophagogastric junction, systematic review

Procedia PDF Downloads 85