Search results for: Molecular Modeling

Authors: Abul Bashar

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The recent surge in the adoption of cloud computing systems by various organizations has brought forth the challenge of evaluating their performance. One of the major issues faced by the cloud service providers and customers is to assess the ability of cloud computing systems to provide the desired services in accordance to the QoS and SLA constraints. To this end, an opportunity exists to develop means to ensure that the desired performance levels of such systems are met under simulated environments. This will eventually minimize the service disruptions and performance degradation issues during the commissioning and operational phase of cloud computing infrastructure. However, it is observed that several simulators and modelers are available for simulating the cloud computing systems. Therefore, this paper presents a critical evaluation of the state-of-the-art modeling and simulation frameworks applicable to cloud computing systems. It compares the prominent simulation frameworks in terms of the API features, programming flexibility, operating system requirements, supported services, licensing needs and popularity. Subsequently, it provides recommendations regarding the choice of the most appropriate framework for researchers, administrators and managers of cloud computing systems.

Keywords: cloud computing, modeling framework, performance evaluation, simulation tools

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

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

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

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Authors: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

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Low-molecular-weight organogelators form gels by self-assembly into the crystalline network which immobilizes the organic solvent. For single bisamide organogelator systems, the effect of the molecular structure on the molecular interaction and their self-assembly behavior has been explored. The spatial arrangement of bisamide molecules in the gel-state is driven by a combination of hydrogen bonding and Van der Waals interactions. The hydrogen-bonding pattern between the amide groups of bisamide molecules is regulated by the number of methylene spacers; the even number of methylene spacers between two amide groups, in even-spaced bisamides, leads to the antiparallel position of amide groups within a molecule. An even-spaced bisamide molecule with antiparallel amide groups can make two pairs of hydrogen bonding with the molecules on the same plane. The odd-spaced bisamide with a parallel directionality of amide groups can form four independent hydrogen bonds with four other bisamide molecules on different planes. The arrangement of bisamide molecules in the crystalline state and the interaction of these molecules depends on the molecular structure, particularly the parity of the spacer length between the amide groups in the bisamide molecule. In this study, the directionality of amide groups has been exploited as a structural characteristic to affect the arrangement of molecules in the crystalline state and produce different binary bisamide gelators with different degrees of crystallinities. Single odd- and even-spaced single bisamides were synthesized and blended to produce binary bisamide organogelators to be characterized in order to understand the effect of the different directionality of amide groups on the molecular interaction in the crystalline state. The pattern of molecular interactions between these blended molecules, mixing or phase separation, has been monitored via differential scanning calorimetry (DSC) and crystallography techniques; X-ray powder diffraction (XRD) and Small-angle X-ray scattering (SAXS). The formation of lamellar structures for odd- and even-spaced bisamide gelators was confirmed by using SAXS and XRD techniques. DSC results have shown that binary bisamide organogelators with different parity of methylene spacers (odd-even binary blends) have a higher tendency for phase separation compared to the binary bisamides with the same parity (odd-odd or even-even binary blends). Phase separation in binary odd-even bisamides was confirmed by the presence of individual (100) reflections of odd and even lamellar structures. The structural characteristic of bisamide organogelators, the parity of spacer length in binary systems, is a promising tool to control the arrangement of molecules and their crystalline structure.

Keywords: binary bisamide organogelators, crystalline structure, phase separation, self-assembly behavior

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Authors: Gia Surguladze, Nino Topuria, Lily Petriashvili, Giorgi Surguladze

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Modeling of building processes of a multimodal freight transportation support information system is discussed based on modern CASE technologies. Functional efficiencies of ports in the eastern part of the Black Sea are analyzed taking into account their ecological, seasonal, resource usage parameters. By resources, we mean capacities of berths, cranes, automotive transport, as well as work crews and neighbouring airports. For the purpose of designing database of computer support system for Managerial (Logistics) function, using Object-Role Modeling (ORM) tool (NORMA – Natural ORM Architecture) is proposed, after which Entity Relationship Model (ERM) is generated in automated process. The software is developed based on Process-Oriented and Service-Oriented architecture, in Visual Studio.NET environment.

Keywords: seaport resources, business-processes, multimodal transportation, CASE technology, object-role model, entity relationship model, SOA

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Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

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FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

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

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

Keywords: 5α-reductase inhibitor, benign prostatic hyperplasia, ligands, molecular docking, QSAR

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Authors: W. Sriwattanapongse, S. Prasitwattanaseree, S. Wongtrangan

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The transportation accidents mortality is a major problem that leads to loss of human lives, and economic. The objective was to identify patterns of statistical modeling for estimating mortality rates due to transportation accidents in Thailand by using data from 2000 to 2009. The data was taken from the death certificate, vital registration database. The number of deaths and mortality rates were computed classifying by gender, age, year and region. There were 114,790 cases of transportation accidents deaths. The highest average age-specific transport accident mortality rate is 3.11 per 100,000 per year in males, Southern region and the lowest average age-specific transport accident mortality rate is 1.79 per 100,000 per year in females, North-East region. Linear, poisson and negative binomial models were chosen for fitting statistical model. Among the models fitted, the best was chosen based on the analysis of deviance and AIC. The negative binomial model was clearly appropriate fitted.

Keywords: transportation accidents, mortality, modeling, analysis of deviance

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Authors: Y. Z. Gad

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Disorders of Sex Development (DSD) are defined as congenital conditions in which development of chromosomal, gonadal or anatomical sex is atypical. The DSD are relatively prevalent in Egypt. In spite of that, the relative rarity of the individual disease types or their molecular pathologies frequently resulted in reporting on single or few cases. This augmented the challenging nature of phenotype-genotype correlation in this disease group and its utilization in the management of such medical emergency. Through critical assessment of the published DSD reports, the current review aims at analyzing the clinical characteristics of the various DSD forms in relation to the underlying molecular pathologies. A systematic literature search was done in Pubmed, using relevant keywords (Egypt versus DSD, genital ambiguity or ambiguous genitalia, the old terms of 'intersex, hermaphroditism and pseudohermaphroditism', and a list of the DSD entities and their related genes). The search yielded 24 reports of molecular data in Egyptian patients presenting with ambiguous genitalia. However, only 21 publications fulfilled the criteria of inclusion of detailed clinical descriptions and definitive molecular diagnoses of individual patients. Curation of the data yielded a total of 53 cases that were ascertained from 40 families. Fifty-one patients present with ambiguous genitalia only while 2 had multiple congenital anomalies. Parental consanguinity was noted in 60% of cases. Sex of rearing at initial presentation was female in 75% and 60% in 46,XY and 46,XX DSD cases, respectively. The external genital phenotype in 2/3 of the 46,XY DSD cases showed moderate undermasculinization [Quigley scores 3 & 4] and 1/3 had severe presentations [scores 5 & 6]. For 46,XX subjects, 1 had severe virilization of the external genitalia while 8 had moderate phenotype. Hormonal data were inconclusive or contradictory to final diagnosis in a forth of cases. Collectively, 31 families [31/40, 77.5%] with 46,XY DSD had molecular defects in the genes, 5 alpha reductase 2 (SRD5A2) [12/31], 17 beta-hydroxysteroid dehydrogenase 3 [8/31], androgen receptor [7/31], Steroidogenic factor 1 [2/31], luteinizing hormone receptor [1/31], and fibroblast growth factor receptor 1 [1/31]. In a multiethnic study, 9 families afflicted with 46,XX DSD due to 11 beta hydroxylase (CYP11B1) deficiency were documented. Two recurrent mutations, G34R and N160D, in SRD5A2 were present, respectively, in 42 and 17% of cases. Similarly, 4 recurrent mutations resulted in 89% of the CYP11B1 presentations. In conclusion, this analysis highlights the importance of autosomal recessive inheritance and inbreeding among DSD presentations, the importance of founder effect in at least 2 disorders, the difficulties in relating the genotype with the indeterminate genital phenotype, the under-reporting of some DSD subtypes, and the notion that the reported mutational profiles among Egyptian DSD cases are relatively different from those reported in other ethnic groups.

Keywords: disorders of sex development, genital ambiguity, mutation, molecular diagnosis, Egypt

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Authors: Chunyang Miao, Bingxin Li, Shanglong Ning, Christopher J. B. Ford

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While it is challenging to fabricate electronic devices close to atomic dimensions in conventional top-down lithography, molecular electronics is promising to help maintain the exponential increase in component densities via using molecular building blocks to fabricate electronic components from the bottom up. It offers smaller, faster, and more energy-efficient electronic and photonic systems. A self-assembled monolayer (SAM) of molecules is a layer of molecules that self-assembles on a substrate. They are mechanically flexible, optically transparent, low-cost, and easy to fabricate. A large-area multi-layer structure has been designed and investigated by the team, where a SAM of designed molecules is sandwiched between graphene and gold electrodes. Each molecule can act as a quantum dot, with all molecules conducting in parallel. When a source-drain bias is applied, significant current flows only if a molecular orbital (HOMO or LUMO) lies within the source-drain energy window. If electrons tunnel sequentially on and off the molecule, the charge on the molecule is well-defined and the finite charging energy causes Coulomb blockade of transport until the molecular orbital comes within the energy window. This produces ‘Coulomb diamonds’ in the conductance vs source-drain and gate voltages. For different tunnel barriers at either end of the molecule, it is harder for electrons to tunnel out of the dot than in (or vice versa), resulting in the accumulation of two or more charges and a ‘Coulomb staircase’ in the current vs voltage. This nanostructure exhibits highly reproducible Coulomb-staircase patterns, together with additional oscillations, which are believed to be attributed to molecular vibrations. Molecules are more isolated than semiconductor dots, and so have a discrete phonon spectrum. When tunnelling into or out of a molecule, one or more vibronic states can be excited in the molecule, providing additional transport channels and resulting in additional peaks in the conductance. For useful molecular electronic devices, achieving the optimum orbital alignment of molecules to the Fermi energy in the leads is essential. To explore it, a drop of ionic liquid is employed on top of the graphene to establish an electric field at the graphene, which screens poorly, gating the molecules underneath. Results for various molecules with different alignments of Fermi energy to HOMO have shown highly reproducible Coulomb-diamond patterns, which agree reasonably with DFT calculations. In summary, this large-area SAM molecular junction is a promising candidate for future electronic circuits. (1) The small size (1-10nm) of the molecules and good flexibility of the SAM lead to the scalable assembly of ultra-high densities of functional molecules, with advantages in cost, efficiency, and power dissipation. (2) The contacting technique using graphene enables mass fabrication. (3) Its well-observed Coulomb blockade behaviour, narrow molecular resonances, and well-resolved vibronic states offer good tuneability for various functionalities, such as switches, thermoelectric generators, and memristors, etc.

Keywords: molecular electronics, Coulomb blokade, electron-phonon coupling, self-assembled monolayer

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Authors: Elisa Y. M. Ang, Teng Yong Ng, Jingjie Yeo, Rongming Lin, Zishun Liu, K. R. Geethalakshmi

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By stacking carbon nanotubes (CNT) one on top of another, single layer CNT arrays can perform water-salt separation with ultra-high permeability and selectivity. Such outer-wall CNT slit membrane is named as the transverse flow CNT membrane. By adjusting the slit size between neighboring CNTs, the membrane can be configured to sieve out different solutes, right down to the separation of monovalent salt ions from water. Molecular dynamics (MD) simulation results show that the permeability of transverse flow CNT membrane is more than two times that of conventional axial-flow CNT membranes, and orders of magnitude higher than current reverse osmosis membrane. In addition, by carrying out MD simulations with different CNT size, it was observed that the variance in desalination performance with CNT size is small. This insensitivity of the transverse flow CNT membrane’s performance to CNT size is a distinct advantage over axial flow CNT membrane designs. Not only does the membrane operate well under constant pressure desalination operation, but MD simulations further indicate that oscillatory operation can further enhance the membrane’s desalination performance, making it suitable for operation such as electrodialysis reversal. While there are still challenges that need to be overcome, particularly on the physical fabrication of such membrane, it is hope that this versatile membrane design can bring the idea of using low dimensional structures for desalination closer to reality.

Keywords: carbon nanotubes, membrane desalination, transverse flow carbon nanotube membrane, molecular dynamics

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Authors: Huda Qari, I. A. Hassan

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The brown alga Padina boryanawas was used for bioassay of polycyclic aromatic hydrocarbons (PAHs) accumulation at the seashore of Jeddah city. PAHs were determined in the coastal water and algal tissues by GC-MS. Acenaphthene (Ace) and dibenzo (a,h) anthracene (dB(a,h)An) were the main PAHs in seawater (50.02 and 46.18) and algal tissues (64.67 and 72.45), respectively. The ratios of low molecular weight/high molecular weight hydrocarbons (1.76 – 1.44), fluoranthene/pyrene (1.57 – 1.52) and phenanthrene/anthracene (0.86 – 0.67) in seawater and algal tissues, respectively, indicated the origin of the PAHs to be mainly petrogenic. This study has demonstrated the utility of using Padina boryanawas as a biomonitor of PAH contamination and bioavailability in the coastal waters.

Keywords: polycyclic aromatic hydrocarbons, Padina boryanawas, bioaccumulation, waste water

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Authors: S. Zolghadri, M. Mousavi-Daramoroudi, H. Yousefnia, F. Abbasi-Davani

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In this study, the absorbed dose of human organs after injection of ¹⁷⁷Lu-DOTATOC was studied based on the biodistribution of the complex in adenocarcinoma breast cancer bearing mice. For this purpose, the biodistribution of the radiolabelled complex was studied and compartmental modeling was applied to calculate the absorbed dose with high precision. As expected, ¹⁷⁷Lu-DOTATOC illustrated a notable specific uptake in tumor and pancreas, organs with high level of somatostatin receptor on their surface and the effectiveness of the radio-conjugate for targeting of the breast adenocarcinoma tumors was indicated. The elicited results of modeling were the exponential equations, and those are utilized for obtaining the cumulated activity data by taking their integral. The results also exemplified that non-target absorbed-doses such as the liver, spleen and pancreas were approximately 0.008, 0.004, and 0.039, respectively. While these values were so much lower than target (tumor) absorbed-dose, it seems due to this low toxicity, this complex is a good agent for therapy.

Keywords: ¹⁷⁷Lu, breast cancer, compartmental modeling, dosimetry

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Authors: A. I. Khalafalla, K. A. Al-Busada, I. M. El-Sabagh

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Pox and pox-like diseases of camels are a group of exanthematous skin conditions that have become increasingly important economically. They may be caused by three distinct viruses: camelpox virus (CMPV), camel contagious ecthyma virus (CCEV) and camel papillomavirus (CAPV). These diseases are difficult to differentiate based on clinical presentation in disease outbreaks. Molecular methods such as PCR targeting species-specific genes have been developed and used to identify CMPV and CCEV, but not simultaneously in a single tube. Recently, multiplex PCR has gained reputation as a convenient diagnostic method with cost- and time–saving benefits. In the present communication, we describe the development, optimization and validation a multiplex PCR assays able to detect simultaneously the genome of the three viruses in one single test allowing for rapid and efficient molecular diagnosis. The assay was developed based on the evaluation and combination of published and new primer sets, and was applied to the detection of 110 tissue samples. The method showed high sensitivity, and the specificity was confirmed by PCR-product sequencing. In conclusion, this rapid, sensitive and specific assay is considered a useful method for identifying three important viruses in specimens from camels and as part of a molecular diagnostic regime.

Keywords: multiplex PCR, diagnosis, pox and pox-like diseases, camels

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Authors: Gizaw Mamo Gebeyehu, Marianna Pap, Geza Makkai, Tibor Z. Janosi, Shima Rashidian, Tibor A. Rauch

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Sepsis poses a significant global health threat, necessitating extensive exploration of indicators tied to its pathological mechanisms and multi-organ dysfunction. While murine studies have shed light on sepsis, the intricate cellular and molecular landscape in human sepsis remains enigmatic. Exploring the influence of activated monocyte-derived exosomes in sepsis sheds light on a promising pathway for understanding the intricate cellular and molecular mechanisms involved in this condition in humans. In sepsis, exosome-borne mRNA and miRNA orchestrate immune response gene expression in recipient cells. Yet, the specifics of exosome-mediated cell-to-cell communication, especially how mRNA cargoes modulate gene expression in recipient cells, remain poorly understood. This study aims to elucidate the precise molecular pathways through which exosomal mRNA cargo, particularly MAFB, contributes to the developing sepsis-induced molecular aberrations in liver tissues, employing rigorously defined cell culture conditions. THP-1 cells were treated with LPS to induce changes in exosomal RNA profiles. Exosomes were isolated and characterized using microscopy and mass spectrometry. RNA was extracted from exosomes and sequenced. The most abundant exosomal mRNAs were subjected to GO analysis for functional annotation analysis and KEGG database analysis to identify the involved enriched pathways. PCR (Polymerase Chain Reaction), RNA sequencing, and Western blotting were involved to analyze changes in gene expression, protein levels, and signaling pathways within the liver cells( HepG2) after exposure to exosomal MAFB. This study pinpoints exosomal MAFB as a potential key regulator linked to liver cell damage during sepsis, along with associated genes (miR155HG, H3F3A, and possibly JARD2) forming a crucial molecular pathway contributing to liver cell injury, Together, these elements indicate a vital molecular pathway that plays a significant role in the emergence of liver cell injury during sepsis.. These findings suggest the importance of further research on these components for potential therapeutic interventions in managing acute liver damage in sepsis.

Keywords: sepsis, exososome, exosomal MAFB, LPS-induced THP-1 cells, RNA profiles, sepsis-triggered liver injury

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Authors: Neslihan Demirci, Serdar Durdağı

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Mycobacterium tuberculosis is still a worldwide disease-causing agent that, according to WHO, led to the death of 1.5 million people from tuberculosis (TB) in 2020. The bacteria reside in macrophages located specifically in the lung. There is a known quadruple drug therapy regimen for TB consisting of isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB). Over the past 60 years, there have been great contributions to treatment options, such as recently approved delamanid (OPC67683) and bedaquiline (TMC207/R207910), targeting mycolic acid and ATP synthesis, respectively. Also, there are natural compounds that can block the tryptophanyl-tRNA synthetase (TrpRS) enzyme, chuangxinmycin, and indolmycin. Yet, already the drug resistance is reported for those agents. In this study, the newly released TrpRS enzyme structure is investigated for potential inhibitor drugs from already synthesized molecules to help the treatment of resistant cases and to propose an alternative drug for the quadruple drug therapy of tuberculosis. Maestro, Schrodinger is used for docking and molecular dynamic simulations. In-house library containing ~8000 compounds among FDA-approved indole-containing compounds, a total of 57 obtained from the ChemBL were used for both ATP and tryptophan binding pocket docking. Best of indole-containing 57 compounds were subjected to hit expansion and compared later with virtual screening workflow (VSW) results. After docking, VSW was done. Glide-XP docking algorithm was chosen. When compared, VSW alone performed better than the hit expansion module. Best scored compounds were kept for ten ns molecular dynamic simulations by Desmond. Further, 100 ns molecular dynamic simulation was performed for elected molecules according to Z-score. The top three MMGBSA-scored compounds were subjected to steered molecular dynamic (SMD) simulations by Gromacs. While SMD simulations are still being conducted, ponesimod (for multiple sclerosis), vilanterol (β₂ adrenoreceptor agonist), and silodosin (for benign prostatic hyperplasia) were found to have a significant affinity for tuberculosis TrpRS, which is the propulsive force for the urge to expand the research with in vitro studies. Interestingly, top-scored ponesimod has been reported to have a side effect that makes the patient prone to upper respiratory tract infections.

Keywords: drug repurposing, molecular dynamics, tryptophanyl-tRNA synthetase, tuberculosis

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Authors: Phumelele Kubheka, Pius Owolawi, Gbolahan Aiyetoro

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Twitter is one of the most popular social media platforms where users can share their opinions on different subjects. As of 2010, The Twitter platform generates more than 12 Terabytes of data daily, ~ 4.3 petabytes in a single year. For this reason, Twitter is a great source for big mining data. Many industries such as Telecommunication companies can leverage the availability of Twitter data to better understand their markets and make an appropriate business decision. This study performs topic modeling on Twitter data using Latent Dirichlet Allocation (LDA). The obtained results are benchmarked with another topic modeling technique, Latent Semantic Indexing (LSI). The study aims to retrieve topics on a Twitter dataset containing user tweets on South African Telcos. Results from this study show that LSI is much faster than LDA. However, LDA yields better results with higher topic coherence by 8% for the best-performing model represented in Table 1. A higher topic coherence score indicates better performance of the model.

Keywords: big data, latent Dirichlet allocation, latent semantic indexing, telco, topic modeling, twitter

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Authors: Catherine Felce, Lior Pachter

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Current methods for building phylogenetic trees from gene expression data consider mean expression levels. With single-cell technologies, we can leverage more information about cell dynamics by considering the entire distribution of gene expression across cells. Using biophysical modeling, we propose a method for constructing phylogenetic trees from scRNA-seq data, building on Felsenstein's method of continuous characters. This method can highlight genes whose level of expression may be unchanged between species, but whose rates of transcription/decay may have evolved over time.

Keywords: phylogenetics, single-cell, biophysical modeling, transcription

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Authors: Mehrnaz Farzingohar, Mehran Yasemi, Ahmad Savari

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The oil products are imported and exported via Rajaee’s tanker terminal. Within loading and discharging in several cases the oil is released into the berths and made oil spills. The spills are distributed within short time and seriously affected Rajaee port’s environment and even extended areas. The trajectory and fate of oil spills investigated by modeling and parted by three risk levels base on the modeling results. First GNOME (General NOAA Operational Modeling Environment) applied to trajectory the liquid oil. Second, ALOHA (Areal Location Of Hazardous Atmosphere) air quality model, is integrated to predict the oil evaporation path within the air. Base on the identified zones the high risk areas are signed by colored dots which their densities calculated and clarified on a map which displayed the harm places. Wind and water circulation moved the pollution to the East of Rajaee Port that accumulated about 12 km of coastline. Approximately 20 km of north east of Qeshm Island shore is covered by the three levels of risky areas. Since the main wind direction is SSW the pollution pushed to the east and the highest risk zones formed on the crests edges hence the low risk appeared on the concavities. This assessment help the management and emergency systems to monitor the exposure places base on the priority factors and find the best approaches to protect the environment.

Keywords: oil spill, modeling, pollution, risk assessment

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Authors: Qin Ou, Yanghui Xu, Xintu Wang, Kim Maren Lompe, Gang Liu, Jan Peter Van Der Hoek

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Microplastics (MPs) can undergo the photooxidation process under ultraviolet (UV) exposure, which determines their transformation and fate in environments. The presence of dissolved organic matter (DOM) can interact with MPs and take participate in the photo-degradation of MPs. As an important DOM component, dissolved black carbon (DBC), widely distributed in aquatic environments, can accelerate or inhibit the sunlight-driven photo-transformation of environmental pollutants. However, the role and underlying mechanism of DBC in the photooxidation of MPs are not clear. Herein, the DBC (< 0.45 µm) was extracted from wood biochar and fractionated by molecular weight (i.e., <3 KDa, 3 KDa−30 KDa, 30 KDa−0.45 µm). The effects of DBC chemical composition (i.e., molecular weight and chemical structure) in DBC-mediated photo-transformation of polystyrene (PS) MPs were investigated. The results showed that DBC initially inhibited the photo-degradation of MPs due to light shielding. Under UV exposure for 6−24 h, the presence of 5 mg/L DBC decreased the carbonyl index of MPs compared to the control. This inhibitory effect of DBC was found to decrease with increasing irradiation time. Notably, DBC initially decreased but then increased the hydroxyl index with aging time, suggesting that the role of DBC may shift from inhibition to acceleration. In terms of the different DBC fractions, the results showed that the smallest fraction of DBC (<3 KDa) significantly accelerated the photooxidation of PS MPs since it acted as reactive oxygen species (ROS) generators, especially in promoting the production of ¹O₂ and ³DBC* and •OH. With the increase in molecular weight, the acceleration effect of DBC on the degradation of MPs was decreased due to the increase of light shielding and possible decrease of photosensitization ability. This study thoroughly investigated the critical role of DBC chemical composition in the photooxidation process, which helps to assess the duration of aging and transformation of MPs during long-term weathering in natural waters.

Keywords: microplastics, photo-degradation, dissolved black carbon, molecular weight, photosensitization

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Authors: Rim Bouhaouel, Naoufel Kraïem, Zuhoor Al Khanjari

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Unified Modeling Language (UML) is considered as one of the widespread modeling language standardized by the Object Management Group (OMG). Therefore, the model driving engineering (MDE) community attempts to provide reuse of UML diagrams, and do not construct it from scratch. The UML model appears according to a specific software development process. The existing method generation models focused on the different techniques of transformation without considering the development process. Our work aims to construct an UML component from fragments of UML diagram basing on an agile method. We define UML fragment as a portion of a UML diagram, which express a business target. To guide the generation of fragments of UML models using an agile process, we need a flexible approach, which adapts to the agile changes and covers all its activities. We use the software product line (SPL) to derive a fragment of process agile method. This paper explains our approach, named RECUP, to generate UML fragments following an agile process, and overviews the different aspects. In this paper, we present the approach and we define the different phases and artifacts.

Keywords: UML, component, fragment, agile, SPL

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Authors: Arpan Dwivedi, Yogesh Pahariya

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In this paper, optimal design of hybrid standalone power supply system (SAPS) is done for off grid applications in remote areas where transmission of power is difficult. The hybrid SAPS system uses two primary energy sources, wind and solar, and in addition to these diesel generator is also connected to meet the load demand in case of failure of wind and solar system. This paper presents mathematical modeling of 1.4 MW hybrid SAPS system for rural electrification. This paper firstly focuses on mathematical modeling of PV module connected in a string, secondly focuses on modeling of permanent magnet wind turbine generator (PMWTG). The hybrid controller is also designed for selection of power from the source available as per the load demand. The power output of hybrid SAPS system is analyzed for meeting load demands at urban as well as for rural areas.

Keywords: SAPS, DG, PMWTG, rural area, off-grid, PV module

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Authors: Aibek Kukpayev, Dhawal Shah

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Combustion of sour fuels containing high amount of sulfur leads to the formation of sulfur oxides, which adversely harm the environment and has a negative impact on human health. Considering this, several legislations have been imposed to bring down the sulfur content in fuel to less than 10 ppm. In recent years, novel deep eutectic solvents (DESs) have been developed to achieve deep desulfurization, particularly to extract thiophenic compounds from liquid fuels. These novel DESs, considered as analogous to ionic liquids are green, eco-friendly, inexpensive, and sustainable. We herein, using molecular dynamic simulation, analyze the interactions of metal-based DESs with model oil consisting of thiophenic compounds. The DES used consists of polyethylene glycol (PEG-200) as a hydrogen bond donor, choline chloride (ChCl) or tetrabutyl ammonium chloride (TBAC) as a hydrogen bond acceptor, and cobalt chloride (CoCl₂) as metal salt. In particular, the combination of ChCl: PEG-200:CoCl₂ at a ratio 1:2:1 and the combination of TBAC:PEG-200:CoCl₂ at a ratio 1:2:0.25 were simulated, separately, with model oil consisting of octane and thiophenes at 25ᵒC and 1 bar. The results of molecular dynamics simulations were analyzed in terms of interaction energies between different components. The simulations revealed a stronger interaction between DESs/thiophenes as compared with octane/thiophenes, suggestive of an efficient desulfurization process. In addition, our analysis suggests that the choice of hydrogen bond acceptor strongly influences the efficiency of the desulfurization process. Taken together, the results also show the importance of the metal ion, although present in small amount, in the process, and the role of the polymer in desulfurization of the model fuel.

Keywords: deep eutectic solvents, desulfurization, molecular dynamics simulations, thiophenes

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Authors: Maha Bakkari, Fatiha Lemmeni, Rachid Tadili

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In this work, we present some characteristics of the furnace studied, its operating principle and the experimental measurements of the evolutions of the temperatures inside and outside the walls of the This work deals with the problem of energy consumption of pottery kilns whose energy consumption is relatively too high. In this work, we determined the sources of energy loss by studying the heat transfer of a pottery furnace, we proposed a recovery system to reduce energy consumption, and then we developed a numerical model modeling the transfers through the walls of the furnace and to optimize the insulation (reduce heat losses) by testing multiple insulators. The recovery and reuse of energy recovered by the recovery system will present a significant gain in energy consumption of the oven and cooking time. This research is one of the solutions that helps reduce the greenhouse effect of the planet earth, a problem that worries the world.

Keywords: recovery lost energy, energy efficiency, modeling, heat transfer

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Authors: Abhishikta Ghosh Roy

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Breast cancer is the most common malignancy among women globally, including India. Human breast cancer results from the genetic and environmental interaction. The present study attempts to understand the molecular heterogeneity of BRCA1 and BRCA2 genes, as well as to understand the association of various lifestyle and reproductive variables for the Breast Cancer risk. The study was conducted amongst 110 patients and 128 controls with total DNA sequencing of flanking and coding regions of BRCA1 BRCA2 genes that revealed ten Single Nucleotide Polymorphisms (SNPs) (6 novels). The controls selected for the study were age, sex and ethnic group matched. After written and informed consent biological samples were collected from the subjects. After detailed molecular analysis, significant (p < 0.005) molecular heterogeneity is revealed in terms of SNPs in BRCA1 (4 Exonic & 1 Intronic) and BRCA2 (2exonic and 3 Intronic) genes. The augmentation study investigated significant (p < 0.05) association with positive family history, early age at menarche, irregular menstrual periods, menopause, prolong contraceptive use, nulliparity, history of abortions, consumption of alcohol and smoking for breast cancer risk. To the best of authors knowledge, this study is the first of its kind, envisaged that the identification of the SNPs and modification of the lifestyle factors might aid to minimize the risk among the Bengalee Hindu females.

Keywords: breast cancer, BRCA, lifestyle, India

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Authors: Anna Avramenko, Heikki Haario

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This paper reports the development and application of a 2D depth-averaged model. The main goal of this contribution is to apply the depth averaged equations to a wind park model in which the treatment of the geometry, introduced on the mathematical model by the mass and momentum source terms. The depth-averaged model will be used in future to find the optimal position of wind turbines in the wind park. K-E and 2D LES turbulence models were consider in this article. 2D CFD simulations for one hill was done to check the depth-averaged model in practise.

Keywords: depth-averaged equations, numerical modeling, CFD, wind park model

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Authors: Elham Rezaee, Sayyed Abbas Tabatabai

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Dual inhibition of COX-2 and sEH enzymes represents one of the distinct pharmaceutical approaches for the treatment of inflammation, pain, cancers, and other diseases. The discovery of these inhibitors for treatment is a great deal of attention because of some advantages such as increased efficacy, a promising safety profile, ease of formulation, and better target engagement. In this research, based on the structure-activity relationship of COX-2 and sEH inhibitors, some amide derivatives with oxadiazole and dihydropyrimidinone rings against sEH and COX-2 enzymes were developed. The designed compounds showed high affinity to the active site of both enzymes in docking studies and were synthesized in good yield and characterized by IR, Mass, 1HNMR, and 13CNMR. All of the novel compounds exhibited considerable in-vitro sEH and COX-2 inhibitory activities in comparison with 12-(3-Adamantan-1-yl-ureido)- dodecanoic acid and celecoxib (a potent urea-based sEH inhibitor and selective nonsteroidal anti-inflammatory drug, respectively). Ethyl 6-methyl-4-(4-(4-(methylsulfonyl)benzamido)phenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate was found to be the most selective COX-2 inhibitor (COX-2/COX-1 ratio: 683) with IC50 value of 2.1 nM targeting sEH enzyme.

Keywords: COX-2, dual inhibitors, sEH, synthesis

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Authors: Jian-Li Shao

Abstract:

Using Molecular Dynamic (MD) simulations, we simulated the microjet from the metal surface under decaying shock loading. The microjetting processes under release melting conditions are presented in detail, and some properties on the microjet mass and velocity are revealed. The phased increase of microjet mass with shock pressure is found. For all cases, the ratio of the maximal jetting velocity to the surface velocity approximately keeps a constant for liquid state. In addition, the temperature of the microjet can be always above the melting point. When introducing slow decaying profiles, the microjet mass begins to increase with the decay rate, which is dominated by the deformation of the bubble during pull-back. When the decay rate becomes fast enough, the microspall occurs as expected, meanwhile, the microjet appears to reduce because of the shock energy reduction.

Keywords: microjetting, shock, metal, molecular dynamics

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Authors: Salima Djehaichia, Rachid Lassoued

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Reinforced concrete structural walls are very efficient elements for protecting buildings against excessive early damage and against collapse under earthquake actions. It is therefore of interest to develop a numerical model which simulates the typical behavior of these units, this paper presents and describes different modeling techniques that have been used by researchers and their advantages and limitations mentioned. The earthquake of Boumerdes in 2003 has demonstrated the fragility of structures and total neglect of sismique design rules in the realization of old buildings. Significant damage and destruction of buildings caused by this earthquake are not due to the choice of type of material, but the design and the study does not congruent with seismic code requirements and bad quality of materials. For idealizing the failure of rules, a parametric study focuses on: low rate of reinforcements, type of reinforcement, resistance moderate of concrete. As an application the modeling strategy based on finite elements combined with a discretization of wall more solicited by successive thin layers. The estimated performance level achieved during a seismic action is obtained from capacity curves under incrementally increasing loads. Using a pushover analysis, a characteristic non linear force-displacement relationship can be determined. The results of numeric model are confronted with those of Algerian Para seismic Rules (RPA) in force have allowed the determination of profits in terms of displacement, shearing action, ductility.

Keywords: modeling, old building, pushover analysis, structural walls

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Authors: Abdela Bulbula

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Background: Marek’s disease virus is a devastating infection, causing high morbidity and mortality in chickens in Ethiopia. Methods: The current study was conducted from March to November, 2021 with the general objective of performing antemortem and postmortem, isolation, and molecular detection of Marek’s disease virus from outbreak cases in southwestern Ethiopia. Accordingly, based on outbreak information reported from the study sites namely, Bedelle, Yayo, and Bonga towns in southwestern Ethiopia, 50 sick chickens were sampled. The backyard and intensive farming systems of chickens were included in the sampling and priorities were given for chickens that showed clinical signs that are characteristics of Marek’s disease. Results: By clinical examinations, paralysis of legs and wings, gray eye, loss of weight, difficulty in breathing, and depression were recorded on all chickens sampled for this study and death of diseased chickens was observed. In addition, enlargement of the spleen and gross lesions of the liver and heart were recorded during postmortem examination. The death of infected chickens was observed in both vaccinated and non-vaccinated flocks. Out of 50 pooled feather follicle samples, Marek’s disease virus was isolated from 14/50 (28%) by cell culture method and out of six tissue samples, the virus was isolated from 5/6(83.30%). By Real time polymerization chain reaction technique, which was targeted to detect the Meq gene, Marek’s disease virus was detected from 18/50 feather follicles which accounts for 36% of sampled chickens. Conclusion: In general, the current study showed that the circulating Marek’s disease virus in southwestern Ethiopia was caused by the oncogenic Gallid herpesvirus-2 (Serotype-1). Further research on molecular characterization of revolving virus in current and other regions is recommended for effective control of the disease through vaccination.

Keywords: Ethioi, Marek's disease, isolation, molecular

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Authors: Juan Portoviejo Brito, Daniel Icaza Alvarez, Christian Castro Samaniego

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In this article, we present the modeling, simulations, and energy conversion analysis of the solar-wind system for the Quingeo Heritage Center in Ecuador. A numerical model was constructed based on the 19 equations, it was coded in MATLAB R2017a, and the results were compared with the experimental data of the site. The model is built with the purpose of using it as a computer development for the optimization of resources and designs of hybrid systems in the Parish of Quingeo and its surroundings. The model obtained a fairly similar pattern compared to the data and curves obtained in the field experimentally and detailed in manuscript. It is important to indicate that this analysis has been carried out so that in the near future one or two of these power generation systems can be exploited in a massive way according to the budget assigned by the Parish GAD of Quingeo or other national or international organizations with the purpose of preserving this unique colonial helmet in Ecuador.

Keywords: hybrid system, wind turbine, modeling, simulation, Smart Grid, Quingeo Azuay Ecuador

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