Search results for: molecular switches

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

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The subject of this paper is to correlate antibacterial behavior of benzimidazole derivatives with their molecular characteristics using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on the inhibitory activity of benzimidazole derivatives against Staphylococcus aureus. The data were processed by linear least squares (LLS) and artificial neural network (ANN) procedures. The LLS mathematical models have been developed as a calibration models for prediction of the inhibitory activity. The quality of the models was validated by leave one out (LOO) technique and by using external data set. High agreement between experimental and predicted inhibitory acivities indicated the good quality of the derived models. These results are part of the CMST COST Action No. CM1306 "Understanding Movement and Mechanism in Molecular Machines".

Keywords: Antibacterial, benzimidazoles, chemometric, QSAR.

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Authors: Babak Safaei, A. M. Fattahi

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Polymer/carbon nanotube nanocomposites have a wide range of promising applications Due to their enhanced properties. In this work, free vibration analysis of single-walled carbon nanotube-reinforced composite plates is conducted in which carbon nanotubes are embedded in an amorphous polyethylene. The rule of mixture based on various types of plate model namely classical plate theory (CLPT), first-order shear deformation theory (FSDT), and higher-order shear deformation theory (HSDT) was employed to obtain fundamental frequencies of the nanocomposite plates. Generalized differential quadrature (GDQ) method was used to discretize the governing differential equations along with the simply supported and clamped boundary conditions. The material properties of the nanocomposite plates were evaluated using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites. Then the results obtained directly from MD simulations were fitted with those calculated by the rule of mixture to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results are presented to address the influences of nanotube volume fraction and edge supports on the value of fundamental frequency of carbon nanotube-reinforced composite plates corresponding to both long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, free vibration, generalized, differential quadrature (GDQ) method

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Kamel Laidi, Khelifa Benmansour, Ouahid Bouchhida

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Neural networks-based approach for 2-cells serial converter has been developed and implemented. The approach is based on a behavioural description of the different operating modes of the converter. Each operating mode represents a well-defined configuration, and for which is matched an operating zone satisfying given invariance conditions, depending on the capacitors' voltages and the load current of the converter. For each mode, a control vector whose components are the control signals to be applied to the converter switches has been associated. Therefore, the problem is reduced to a classification task of the different operating modes of the converter. The artificial neural nets-based approach, which constitutes a powerful tool for this kind of task, has been adopted and implemented. The application to a 2-cells chopper has allowed ensuring efficient and robust control of the load current and a high capacitors voltages balancing.

Keywords: neural nets, control, multicellular converters, 2-cells chopper

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Authors: S. Chandrasekaran, S. Nandita, M. Shivathmika, Srikrishnan Shivakumar

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The objective of the research work is to analyze the computational chemical-composition of carbohydrates in the context of healthcare informatics. The computation involves the representation of complex chemical molecular structure of carbohydrate using graph theory and in a deployable Chemical Markup Language (CML). The parallel molecular structure of the chemical molecules with or without other adulterants for the sake of business profit can be analyzed in terms of robustness and derivatization measures. The rural healthcare program should create awareness in malnutrition to reduce ill-effect of decomposition and help the consumers to know the level of such energy storage mixtures in a quantitative way. The earlier works were based on the empirical and wet data which can vary from time to time but cannot be made to reuse the results of mining. The work is carried out on the quantitative computational chemistry on carbohydrates to provide a safe and secure right to food act and its regulations.

Keywords: carbohydrates, chemical-composition, chemical markup, robustness, food safety

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Authors: S. Dargouthi, S. Boughdiri, B. Tangour

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This work invoked two complementary parts. In the first, we performed a theoretical study of various dimers of molecular of titanium dioxide. Five structures were examined. Three among them, the (T), (C) and (T/P) isomers, may be considered as stable compounds because they represent absolute minima on their potential energy surfaces. (T) and (C) may coexist because they are separted by only 6.5 kcal mol-1 but (T/P) dimer is in a metastable state from an energetic point of view. Non bonded dimer (P) transforms into its homologue (O) which has been considered as transitory specie with low lifetime which evolves to (T) structure. In the second part, we highlight the possible stabilization of (T), (C) and (P) dimers by encapsulation in carbon nanotubes. This indicates the probable role that plays this transitory specie the polymerization process of molecular TiO2. Confinement is suitable to control the fast evolution process and could towards the synthesis of new titanium dioxide nanostructured materials. An alternative description of TiO2 polymorphs (Rutie, anatase et Brookite) is proposed from (T), (C) and (T/P) dimmers motifs.

Keywords: titanium dioxide, carbon nanotube, confinement. encapsulation, transitory specie

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Authors: Hiroyuki Aoki

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The glass transition phenomenon has been extensively studied for a long time. The glass transition of polymer materials is assigned to the transition of the dynamics of the chain backbone segment. However, the detailed mechanism of the transition behavior of the segmental motion is still unclear. In the current work, the single molecule detection technique was employed to reveal the trajectory of the molecular motion of the single polymer chain. The center segment of poly(butyl methacrylate) chain was labeled by a perylenediimide dye molecule and observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was analyzed near the glass transition temperature. The direct observation of the individual polymer chains revealed the intermittent behavior of the segmental motion, indicating the spatial inhomogeneity.

Keywords: glass transition, molecular motion, polymer materials, single molecule

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Authors: Sahar Sohrabi

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The emergence of Cloud data centers has revolutionized the IT industry. Private Clouds in specific provide Cloud services for certain group of customers/businesses. In a real-time private Cloud each task that is given to the system has a deadline that desirably should not be violated. Scheduling tasks in a real-time private CLoud determine the way available resources in the system are shared among incoming tasks. The aim of the scheduling policy is to optimize the system outcome which for a real-time private Cloud can include: energy consumption, deadline violation, execution time and the number of host switches. Different scheduling policies can be used for scheduling. Each lead to a sub-optimal outcome in a certain settings of the system. A Bayesian Scheduling strategy is proposed for scheduling to further improve the system outcome. The Bayesian strategy showed to outperform all selected policies. It also has the flexibility in dealing with complex pattern of incoming task and has the ability to adapt.

Keywords: cloud computing, scheduling, real-time private cloud, bayesian

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Authors: Li Li, Lei Wang, Chenglin Du, Mengxin Ren, Xinzheng Zhang, Wei Cai, Jingjun Xu

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Strong coupling between excitons of quantum dots and plasmons in nanocavites can be realized at room temperature due to the strong confinement of the plasmon fields, which offers building blocks for quantum information systems or ultralow-power switches and lasers. In this work, by using cathodoluminescence, ultrastrong coupling with Rabi splitting above 1 eV between breathing plasmons in Aluminum metal-insulator-metal (MIM) cavity and excited state of CdZnS/ZnS quantum dots was reported in near-UV spectrum. Analytic analysis and full-wave electromagnetic simulations provide the evidence for the strong coupling and confirm the hybridization of the QDs exciton and LSP breathing mode. This study opens the way for new emerging applications based on strongly coupled light-matter states all over the visible region down to ultra-violet frequencies.

Keywords: breathing mode, plasmonics, quantum dot, strong coupling, ultraviolet

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Authors: Mary Josephine Rani

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Virtually all metals are toxic to aquatic organisms because of the devastating effect of these metals on humans; heavy metals are one of the most toxic forms of aquatic pollution. Metal concentrations in aquatic organisms appear to be of several magnitudes higher than concentrations present in the ecosystem. Mercury is one of the most toxic heavy metals in the environment. The principal sources of contamination in wastewater are chloralkali plants, battery factories, mercury switches, and medical wastes. Elevated levels of mercury in aquatic organisms specially fish represent both an ecological and human concern. Amino acid levels were estimated in five tissues (gills, liver, kidney, brain and muscle) of Clariasbatrachus after 28 days of chronic exposure to mercury. Free amino acids serve as precursor for energy production under stress and for the synthesis of required proteins to face the metal challenge.

Keywords: amino acids, fish, mercury, toxicity

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Authors: Albina V. Moskvicheva, Gevorg G. Kazarian, Anna R. Valeeva, Marina A. Efimova, Malik N. Mukminov, Eduard A. Shuralev, Rustam Kh. Ravilov, Kamil S. Khaertynov

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Improving the early diagnosis of tuberculosis and solving a number of problems associated with the differential diagnosis of Mycobacterium bovis infection, nonspecific tuberculin reactions caused by sensitization of the body by non-tuberculosis mycobacteria, is urgent. The filtrates and extracts of M. bovis cell surface components are promising antigens with diagnostic potential. The purpose of this study was to isolate and characterize antigenic proteins and determine the dominant M. bovis antigens recognized by the humoral immune system. The mycobacterial cells were homogenized on FastPrep-24. Gel-filtration chromatography was used to fractionate the lysates of cell surface component extracts and proteins isolated from M. bovis culture supernatant. The separated fractions were analyzed using two-dimensional gel electrophoresis followed by determination of antigen serological activity using immunoblot with specific hyperimmune rabbit blood serum. As a result of electrophoretic separation of components by molecular weight, 23 antigen fractions were obtained. Analysis of densitograms showed that the fractions contained two zones of antigens with pronounced serological activity, corresponding to molecular weights of 28 and 21 kDa. The high serological activity of the 28 kDa antigen was established by immunoblot using hyperimmune blood sera. Separated and characterized by M. bovis specific antigen with a molecular weight of 28 kDa was added to the collection of specific marker antigens for M. bovis.

Keywords: antigen, gel-filtration chromatography, immunoblot, Mycobacterium bovis

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Authors: Javier Varillas, Jorge Alcalá

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We investigate dislocation avalanche phenomena in face-centered cubic (FCC) and body-centered cubic (BCC) crystals using massive, large-scale molecular dynamics (MD) simulations. The analysis is focused on the intermittent development of dense dislocation arrangements subjected to uniaxial tensile straining under displacement control. We employ a novel computational scheme that allows us to inject an entangled dislocation structure in periodic MD domains. We assess the emission of plastic bursts (or dislocation avalanches) in terms of the sharp stress drops detected in the stress-strain curve. The plastic activity corresponds to the sporadic operation of specific dislocation glide processes exhibiting quiescent periods between successive avalanche events. We find that the plastic intermittences in our simulations do not overlap in time under sufficiently low strain rates as dissipation operates faster than driving, where the dense dislocation networks evolve through the emission of dislocation avalanche events whose carried slip adheres to self-organized power-law distributions. These findings enable the extension of the slip distributions obtained from strict displacement-controlled micropillar compression experiments towards smaller values of slip size. Our results furnish further understanding upon the development of entangled dislocation networks in metal plasticity, including specific mechanisms of dislocation propagation and annihilation, along with the evolution of specific dislocation populations through dislocation density analyses.

Keywords: dislocations, intermittent plasticity, molecular dynamics, slip distributions

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

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Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Siti Rafeah Md Rafei, Karen Wang Yanping, Park Mi Kyoung

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Tissue samples are precious supply for molecular studies or disease identification diagnosed using molecular assays, namely real-time PCR (qPCR). It is critical to establish the most favorable nucleic acid extraction that gives the PCR-amplifiable genomic DNA. Furthermore, automated nucleic acid extraction is an appealing alternative to labor-intensive manual methods. Operational complexity, defined as the number of steps required to obtain an extracted sample, is one of the criteria in the comparison. Here we are comparing the One BioMed’s automated X8 platform with the commercially available manual-operated kits from QIAGEN Mini Kit and Roche. We extracted DNA from rat fresh-frozen tissue (from different type of organs) in the matrices. After tissue pre-treatment, it is added to the One BioMed’s X8 pre-filled cartridge, and the QIAGEN QIAmp column respectively. We found that the results after subjecting the eluates to the Real Time PCR using BIORAD CFX are comparable.

Keywords: DNA extraction, frozen tissue, PCR, qPCR, rat

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Sopida Vacharasukpo, Sudarat Khwan-On

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This paper proposes a high step-up DC-DC converter topology for renewable energy system applications. The proposed converter employs only a single power switch instead of using several switches. Compared to the conventional DC-DC step-up converters the higher voltage gain with small output ripples can be achieved by using the proposed high step-up DC-DC converter topology. It can step up the low input voltage (20-50Vdc) generated from the photovoltaic modules to the high output voltage level approximately 600Vdc in order to supply the three-phase inverter fed the three-phase motor drive. In this paper, the operating principle of the proposed converter topology and its control strategy under the continuous conduction mode (CCM) are described. Finally, simulation results are shown to demonstrate the effectiveness of the proposed high step-up DC-DC converter with its control strategy to increase the voltage step-up conversion ratio.

Keywords: DC-DC converter, high step-up ratio, renewable energy, single switch

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Authors: Emad A. Mohammed

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Utilizing the capabilities of Data Mining and Artificial Intelligence in the prediction of the minimum miscibility pressure (MMP) required for multi-contact miscible (MCM) displacement of reservoir petroleum by hydrocarbon gas flooding using Fuzzy Logic models and Artificial Neural Network models will help a lot in giving accurate results. The factors affecting the (MMP) as it is proved from the literature and from the dataset are as follows: XC2-6: Intermediate composition in the oil-containing C2-6, CO2 and H2S, in mole %, XC1: Amount of methane in the oil (%),T: Temperature (°C), MwC7+: Molecular weight of C7+ (g/mol), YC2+: Mole percent of C2+ composition in injected gas (%), MwC2+: Molecular weight of C2+ in injected gas. Fuzzy Logic and Neural Networks have been used widely in prediction and classification, with relatively high accuracy, in different fields of study. It is well known that the Fuzzy Inference system can handle uncertainty within the inputs such as in our case. The results of this work showed that our proposed models perform better with higher performance indices than other emprical correlations.

Keywords: MMP, gas flooding, artificial intelligence, correlation

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Authors: Qi Wu, Dian-Yong Chen, Feng-Kun Guo, Gang Li

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In the past decade, a growing number of new hadron states have been observed, which are dubbed as XYZ states in the heavy quarkonium mass regions. In this work, we present our study on the production of some new hadron states. In particular, we investigate the processes Υ(5S,6S)→ Zb (10610)/Zb (10650)π, Bc→ Zc (3900)/Zc (4020)π and Λb→ Pc (4312)/Pc (4440)/Pc (4457)K. (1) For the production of Zb (10610)/Zb (10650) from Υ(5S,6S) decay, two types of bottom-meson loops were discussed within a nonrelativistic effective field theory. We found that the loop contributions with all intermediate states being the S-wave ground state bottom mesons are negligible, while the loops with one bottom meson being the broad B₀* or B₁' resonance could provide the dominant contributions to the Υ(5S)→ Zb⁽'⁾ π. (2) For the production of Zc (3900)/Zc (4020) from Bc decay, the branching ratios of Bc⁺→ Z (3900)⁺ π⁰ and Bc⁺→ Zc (4020)⁺ π⁰ are estimated to be of order of 10⁽⁻⁴⁾ and 10⁽⁻⁷⁾ in an effective Lagrangian approach. The large production rate of Zc (3900) could provide an important source of the production of Zc (3900) from the semi-exclusive decay of b-flavored hadrons reported by D0 Collaboration, which can be tested by the exclusive measurements in LHCb. (3) For the production of Pc (4312), Pc (4440) and Pc (4457) from Λb decay, the ratio of the branching fraction of Λb→ Pc K was predicted in a molecular scenario by using an effective Lagrangian approach, which is weakly dependent on our model parameter. We also find the ratios of the productions of the branching fractions of Λb→ Pc K and Pc→ J/ψ p can be well interpreted in the molecular scenario. Moreover, the estimated branching fractions of Λb→ Pc K are of order 10⁽⁻⁶⁾, which could be tested by further measurements in LHCb Collaboration.

Keywords: effective Lagrangian approach, hadron loops, molecular states, new hadron states

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Authors: Katherine Madero Valencia, Carlos Jaramillo, Elida Dueñas, Carlos Torres, María Del Pilar Delgado

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Asthma, described as a chronic inflammatory condition of the airways, courses accompanied by episodes known as exacerbations, characterized by a worsening of symptoms. Among the triggers, some allergen-irritative and infectious agents are found, including Chlamydophila pneumoniae which seems to play an increasingly important role. In this paper a PCR was used to detect C. pneumoniae in order to estimate the frequency of infections caused by this agent in pediatric patients with asthma exacerbations. C. pneumoniae distribution throughout the study period was also evaluated. 175 nasopharyngeal aspirates from children with asthma exacerbations were analyzed by PCR and sequencing. A global prevalence of C. pneumoniae of 53.71% was obtained. This study highlights a high circulation of C. pneumoniae during the study period, in children of all ages and especially in children under 5 years old. Molecular tests applied permit a rapid detection and improved our knowledge about these infections in children with asthma.

Keywords: Chlamydophila pneumoniae, detection, molecular techniques, pediatric asthma

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Authors: Asima Shah, F. A. Masoodi, Adil Gani, Bilal Ahmad Ashwar

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The present study was designed to evaluate the effect of γ-rays on the antioxidant and antiproliferative potential of β-glucan isolated from oats. The β-glucan was irradiated with 0, 2, 6, and 10 kGy by gamma ray. The samples were characterized by FT-IR, GPC, and quantitative estimation by Megazyme β-glucan assay kit. The average molecular weight of non-irradiated β-glucan was 199 kDa that decreased to 70 kDa at 10 kGy. Both FT-IR spectrum and chemical analysis revealed that the extracted β-glucan was pure having minor impurities. Antioxidant activity was evaluated by DPPH, lipid peroxidation, reducing power, metal chelating ability and oxidative DNA damage assays. Results revealed that the antioxidant activity of β-glucan increased with the increase in irradiation dose. Irradiated β-glucan also exhibited dose dependent cancer cell growth inhibition with irradiation doses. The study revealed that low molecular weight β-glucan with enhanced antioxidant and antiproliferative activities can be produced by a simple irradiation method.

Keywords: γ-irradiation, antioxidant activity, antiproliferative activity, β-glucan, oats

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Authors: Nattachote Rugthaicharoencheep

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This paper presents a feeder reconfiguration problem in distribution systems. The objective is to minimize the system power loss and to improve bus voltage profile. The optimization problem is subjected to system constraints consisting of load-point voltage limits, radial configuration format, no load-point interruption, and feeder capability limits. A method based on genetic algorithm, a search algorithm based on the mechanics of natural selection and natural genetics, is proposed to determine the optimal pattern of configuration. The developed methodology is demonstrated by a 33-bus radial distribution system with distributed generations and feeder capacitors. The study results show that the optimal on/off patterns of the switches can be identified to give the minimum power loss while respecting all the constraints.

Keywords: network reconfiguration, distributed generation capacitor placement, loss reduction, genetic algorithm

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Authors: Mesbah Khaled, Bouraoui Ouissal, Benkiniouar Rachid, Belkhiri Lotfi

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Alstonia, which are tropical plants with a wide geographical distribution, have been divided into different sections by different authors based on previous studies of several species within the genus. Monachino divides Alstonia into 5 sections, while Pichon divides it into 3 sections. Several plants belonging to this genus, such as Alstonia brassii, have been used in traditional folk medicine to treat ailments such as fever, malaria and dysentery]. Previous studies focusing on the chemical composition of these plants have successfully identified indol alkaloids with cytotoxic, anti-diabetic and anti-inflammatory properties. The newly discovered monomers are structurally similar to the backbones of picralin, affinisin and macrolin. On the other hand, all recently isolated dimeric compounds have a macrolin moiety. In this study, a computational analysis was performed on a series of novel molecules, including both monomeric and dimeric compounds with different structural frameworks. This investigation represents the first computational study of these molecules using an in silico approach incorporating 2D-QSAR data. The analysis involved various computational techniques, including 2D-QSAR modelling, molecular docking studies and subsequent validation by molecular dynamics simulation and assessment of ADMET properties. The chemical composition was identified by 1D and 2D NMR. Eight new alkaloids were isolated, 5 monomers and 3 dimers. In this section, we focus on the biological activity of 4 new alkaloids belonging to two different skeletons, the affinisine skeleton.

Keywords: affinisine, talcarpine, macroline, cytotoxicity, alkaloids

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Authors: Virendra Nath, Vipin Kumar

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Background: TypeII Diabetes mellitus is a foremost health problem worldwide, predisposing to increased mortality and morbidity. Undesirable effects of the current medications have prompted the researcher to develop more potential drug(s) against the disease. The peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptors family and take part in a vital role in the regulation of metabolic equilibrium. They can induce or repress genes associated with adipogenesis, lipid, and glucose metabolism. Aims: Investigation of PPARα/γ agonistic hits were screened by hierarchical virtual screening followed by molecular dynamics simulation and knowledge-based structure-activity relation (SAR) analysis using approved PPAR α/γ dual agonist. Methods: The PPARα/γ agonistic activity of compounds was searched by using Maestro through structure-based virtual screening and molecular dynamics (MD) simulation application. Virtual screening of nuclear-receptor ligands was done, and the binding modes with protein-ligand interactions of newer entity(s) were investigated. Further, binding energy prediction, Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit along with the structural comparative analysis of approved PPARα/γ agonists with screened hit was done for knowledge-based SAR. Results and Discussion: The silicone chip-based approach recognized the most capable nine hits and had better predictive binding energy as compared to the reference drug compound (Tesaglitazar). In this study, the key amino acid residues of binding pockets of both targets PPARα/γ were acknowledged as essential and were found to be associated in the key interactions with the most potential dual hit (ChemDiv-3269-0443). Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit and found root mean square deviation (RMSD) stabile around 2Å and 2.1Å, respectively. Frequency distribution data also revealed that the key residues of both proteins showed maximum contacts with a potent hit during the MD simulation of 20 nanoseconds (ns). The knowledge-based SAR studies of PPARα/γ agonists were studied using 2D structures of approved drugs like aleglitazar, tesaglitazar, etc. for successful designing and synthesis of compounds PPARγ agonistic candidates with anti-hyperlipidimic potential.

Keywords: computational, diabetes, PPAR, simulation

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Authors: Ali Rahnamoun, Adri van Duin

Abstract:

The concept of high velocity particle impact on the spacecraft surface materials has been one of the important issues in the design of such materials. Among these particles, water clusters might be the most abundant and the most important particles to be studied. The importance of water clusters is that upon impact on the surface of the materials, they can cause damage to the material and also if they are sub-cooled water clusters, they can attach to the surface of the materials and cause ice accumulation on the surface which is very problematic in spacecraft and also aircraft operations. The dynamics of the collisions between amorphous silica structures and water clusters with impact velocities of 1 km/s to 10 km/s are studied using the ReaxFF reactive molecular dynamics simulation method. The initial water clusters include 150 water molecules and the water clusters are collided on the surface of amorphous fully oxidized and suboxide silica structures. These simulations show that the most abundant molecules observed on the silica surfaces, other than reflecting water molecules, are H3O+ and OH- for the water cluster impacts on suboxide and fully oxidized silica structures, respectively. The effect of impact velocity on the change of silica mass is studied. At high impact velocities the water molecules attach to the silica surface through a chemisorption process meaning that water molecule dissociates through the interaction with silica surface. However, at low impact velocities, physisorbed water molecules are also observed, which means water molecule attaches and accumulates on the silica surface. The amount of physisorbed waters molecules at low velocities is higher on the suboxide silica surfaces. The evolution of the temperatures of the water clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting water clusters increase to about 2000K, with individual molecules oocasionally reaching temperatures of over 8000K and thus will be prudent to consider the concept of electron excitation at these higher impact velocities which goes beyond the current ReaxFF ability.

Keywords: spacecraft materials, hypervelocity impact, reactive molecular dynamics simulation, amorphous silica

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Authors: Moulay Driss Mellaoui, Abdallah Imjjad, Rachid Boutiddar, Haydar Mohammad-Salim, Nivedita Acharjee, Hassan Bourzi, Souad El Issami, Khalid Abbiche, Hanane Zejli

Abstract:

We have investigated the underlying molecular processes involved in the [3+2] cycloaddition (32CA) reactions between N-methyl-C-(2-furyl) nitrone and three acetylene derivatives: 4b, 5b, and 6b. For this investigation, we utilized molecular electron density theory (MEDT) and density functional theory (DFT) methods at the B3LYP-D3/6 31G (d) computational level. These 32CA reactions, which exhibit a zwitterionic (zw-type) nature, proceed through a one-step mechanism with activation enthalpies ranging from 8.80 to 14.37 kcal mol−1 in acetonitrile and ethanol solvents. When the nitrone reacts with phenyl methyl propiolate (4b), two regioisomeric pathways lead to the formation of two products: P1,5-4b and P1,4-4b. On the other hand, when the nitrone reacts with dimethyl acetylene dicarboxylate (5b) and acetylene dicarboxylic acid (but-2-ynedioic acid) (6b), it results in the formation of a single product. Through topological analysis, we can categorize the nitrone as a zwitterionic three-atom component (TAC). Furthermore, the analysis of conceptual density functional theory (CDFT) indices classifies the 32CA reactions of the nitrone with 4b, 5b, and 6b as forward electron density flux (FEDF) reactions. The study of bond evolution theory (BET) reveals that the formation of new C-C and C-O covalent bonds does not initiate in the transition states, as the intermediate stages of these reactions display pseudoradical centers of the atoms already involved in bonding.

Keywords: 4-isoxazoline, DFT/B3LYP-D3, regioselectivity, cycloaddition reaction, MEDT, ELF

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Authors: Drissi Mokhtaria, Chouaih Abdelkader, Fodil Hamzaoui

Abstract:

Our work is about a comparison of experimental and theoretical results of the electron charge density distribution and the electrostatic potential around the M-Nitrophenol Molecule (m-NPH) kwon for its interesting physical characteristics. The molecular experimental results have been obtained from a high-resolution X-ray diffraction study. Theoretical investigations were performed under the Gaussian program using the Density Functional Theory at B3LYP level of theory at 6-31G*. The multipolar model of Hansen and Coppens was used for the experimental electron charge density distribution around the molecule, while we used the DFT methods for the theoretical calculations. The electron charge density obtained in both methods allowed us to find out the different molecular properties such us the electrostatic potential and the dipole moment which were finally subject to a comparison leading to an outcome of a good matching results obtained in both methods.

Keywords: electron charge density, m-nitrophenol, nonlinear optical compound, electrostatic potential, optimized geometric

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Authors: Samir Al-Zobaidi

Abstract:

This study attempts to understand the effect of different UV irradiation methods on the intercalation of LDPE/MMT nanocomposites, and its molecular behavior at certain isothermal crystallization temperature. Three different methods of UV exposure were employed using single composition of LDPE/MMT nanocomposites. All samples were annealed for 5 hours at a crystallization temperature of 100°C. The crystallization temperature was chosen to be at large supercooling temperature to ensure quick and complete crystallization. The raw material of LDPE consisted of two stable monoclinic and orthorhombic phases according to XRD results. The thermal behavior of both phases acted differently when UV exposure method was changed. The monoclinic phase was more dependent on the method used compared to the orthorhombic phase. The intercalation of clay, as well as, the non-isothermal crystallization temperature, has also shown a clear dependency on the type of UV exposure. A third phase that is thermally less stable was also observed. Its respond to UV irradiation was greater since it contains low molecular weight entities which make it more vulnerable to any UV exposure.

Keywords: LDPE/MMt nanocomposites, crystallization, UV irradiation, intercalation

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Authors: Gomti Devi

Abstract:

Photoisomerization has been attracting to researchers due to its wide range of applications in optical switches, polymeric chains, liquid-crystalline systems and bilayer membranes etc. Azobenzene is a photochromic molecule which exhibits a reversible isomerisation process between its trans and cis isomers of different stability. An investigation has been conducted of the effects of temperature on intensity and position of Raman band of N=N, C-N stretching modes of Azobenzene (AZBN). It was found that the N=N stretching mode of Raman band shape shifts to lower frequency region with the increase in temperature. The Raman intensity was also decreased with the increase of temperature. The change in bandwidth with the increase in temperature has been studied. The FTIR spectrum of the molecule is recorded so as to complement the Raman spectra. In order to investigate the possibility of undergoing dimerization and trimerization as well as the stability of this molecule, ab initio calculation for geometry optimization and vibrational wavenumber calculation have been performed. Theoretically calculated values are found in good agreement with the experimental results.

Keywords: azobenzene, temperature, ab-initio, frequency

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Authors: K. Frahtia, I. Mihoubi, S. Picot

Abstract:

Leishmaniasis is a group of parasitic disease with a varied clinical expression caused by flagellate protozoa of the Leishmania genus. These diseases are transmitted to humans and animals by the sting of a vector insect, the female sandfly. Among the groups of dipteral disease vectors, Phlebotominae occupy a prime position and play a significant role in human pathology, such as leishmaniasis that affects nearly 350 million people worldwide. The vector control operation launched by health services throughout the country proves to be effective since despite the prevalence of the disease remains high especially in rural areas, leishmaniasis appears to be declining in Algeria. In this context, this study mainly concerns molecular detection of Leishmania from the vector. Furthermore, a molecular diagnosis has also been made on skin samples taken from patients in the region of Constantine, located in the North-East of Algeria. Concerning the vector, 5858 sandflies were captured, including 4360 males and 1498 females. Male specimens were identified based on their morphological. The morphological identification highlighted the presence of the Phlebotomus genus with a prevalence of 93% against 7% represented by the Sergentomyia genus. About the identified species, P. perniciosus is the most abundant with 59.4% of the male identified population followed by P. longicuspis with 24.7% of the workforce. P. perfiliewi is poorly represented by 6.7% of specimens followed by P. papatasi with 2.2% and 1.5% S. dreyfussi. Concerning skin samples, 45/79 (56.96%) collected samples were found positive by real-time PCR. This rate appears to be in sharp decline compared to previous years (alert peak of 30,227 cases in 2005). Concerning the detection of Leishmania from sandflies by RT-PCR, the results show that 3/60 PCR performed genus are positive with melting temperatures corresponding to that of the reference strain (84.1 +/- 0.4 ° C for L. infantum). This proves that the vectors were parasitized. On the other side, identification by RT-PCR species did not give any results. This could be explained by the presence of an insufficient amount of leishmanian DNA in the vector, and therefore support the hypothesis of the regression of leishmaniasis in Constantine.

Keywords: Algeria, molecular diagnostic, phlebotomus, real time PCR

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