Search results for: molecular docking and dynamics

Authors: Paul C. Njoku, Archana Swati Njoku

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The study deals with the development of a mathematical model to characterize the oil production in Nigeria. This is calculated by initiating the dynamics of oil production in million barrels revenue plan cost of oil production in million nairas and unit cost of production from 1974-1982 in the contest of the federal Republic of Nigeria. This country export oil to other countries as well as importing specialized crude. The transport network from origin/destination tij to pairs is taking into account simulation runs, optimization have been considered in this study.

Keywords: mathematical oil model development dynamics, Nigeria, characterization barrels, dynamics of oil production

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

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

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

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Authors: Ambrish Singh

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

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

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Abbasali Raz, Javad Dadgar Pakdel, Kourosh Azizi, Aboozar Soltani, Mohammad Djaefar Moemenbellah-Fard

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Background: Maggot debridement therapy is an appropriate, effective, and controlled method using sterilized larvae of Luciliasericata (L.sericata) to treat wounds. Netrin-A is an enzyme in the Laminins family which secreted from salivary gland of L.sericata with a central role in neural regeneration and angiogenesis. This study aimed to production of new recombinant Netrin-A protein of Luciliasericata larvae by baculovirus expression vector system (BEVS) in SF9. Material and methods: In the first step, gene structure was subjected to the in silico studies, which were include determination of Antibacterial activity, Prion formation risk, homology modeling, Molecular docking analysis, and Optimization of recombinant protein. In the second step, the Netrin-A gene was cloned and amplified in pTG19 vector. After digestion with BamH1 and EcoR1 restriction enzymes, it was cloned in pFastBac HTA vector. It was then transformed into DH10Bac competent cells, and the recombinant Bacmid was subsequently transfected into insect Sf9 cells. The expressed recombinant Netrin-A was thus purified in the Ni-NTA agarose. This protein evaluation was done using SDS-PAGE and western blot, respectively. Finally, its concentration was calculated with the Bradford assay method. Results: The Bacmid vector structure with Netrin-A was successfully constructed and then expressed as Netrin-A protein in the Sf9 cell lane. The molecular weight of this protein was 52 kDa with 404 amino acids. In the in silico studies, fortunately, we predicted that recombinant LSNetrin-A have Antibacterial activity and without any prion formation risk.This molecule hasa high binding affinity to the Neogenin and a lower affinity to the DCC-specific receptors. Signal peptide located between amino acids 24 and 25. The concentration of Netrin-A recombinant protein was calculated to be 48.8 μg/ml. it was confirmed that the characterized gene in our previous study codes L. sericata Netrin-A enzyme. Conclusions: Successful generation of the recombinant Netrin-A, a secreted protein in L.sericata salivary glands, and because Luciliasericata larvae are used in larval therapy. Therefore, the findings of the present study could be useful to researchers in future studies on wound healing.

Keywords: blowfly, BEVS, gene, immature insect, recombinant protein, Sf9

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Authors: Salma M. Wakil

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

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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Authors: Nazeef, Suleiman, Umar, Danladi Muhammad, Ja'afar Ali, Zaliha Adamu Umar

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The population dynamics of Auchenoglanis occidentalis from the Dadin-Kowa reservoir were studied. Population dynamic parameters such as growth, mortality and recruitment patterns were analyzed using length frequency data over a 12-month period employing FiSAT II software. Findings revealed that LWR (b - constant) = 2.88, K = 0.72 -yr., L∞ = 40.91 cm and Tmax = 3.57 years and Ɵ’ = 3.14. Mortality indices revealed that natural mortality (M = 1.39), fishing mortality (F = 0.22) and exploitation ratio (E = 0.14), Lc/L∞ = 0.48, Emax = 0.64, while Lopt = 26.4 cm. Uni-modal recruitment peak observed with Lm = 27.3 cm. A restocking program is suitable to ensure its continuous existence as it seems to have a low population.

Keywords: fish population dynamics, auchenoglanis occidentalis, FISAT II, natural mortality

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Authors: Afsheen Aman, Shah Ali Ul Qader

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

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

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Authors: Sang Ho Lee, Tae Heon Moon, Youn Taik Leem, Kwang Woo Nam

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Knowledge and IT inputs to other industrial production have become more important as a key factor for the competitiveness of national and regional economies, such as knowledge economies in smart cities. Knowledge and IT industries lead the industrial innovation and technical (r)evolution through low cost, high efficiency in production, and by creating a new value chain and new production path chains, which is referred as knowledge and IT dynamics. This study aims to investigate the knowledge and IT dynamics in Korea, which are analyzed through the input-output model and structural path analysis. Twenty-eight industries were reclassified into seven categories; Agriculture and Mining, IT manufacture, Non-IT manufacture, Construction, IT-service, Knowledge service, Non-knowledge service to take close look at the knowledge and IT dynamics. Knowledge and IT dynamics were analyzed through the change of input output coefficient and multiplier indices in terms of technical innovation, as well as the changes of the structural paths of the knowledge and IT to other industries in terms of new production value creation from 1985 and 2010. The structural paths of knowledge and IT explain not only that IT foster the generation, circulation and use of knowledge through IT industries and IT-based service, but also that knowledge encourages IT use through creating, sharing and managing knowledge. As a result, this paper found the empirical investigation on the knowledge and IT dynamics of the Korean economy. Knowledge and IT has played an important role regarding the inter-industrial transactional input for production, as well as new industrial creation. The birth of the input-output production path has mostly originated from the knowledge and IT industries, while the death of the input-output production path took place in the traditional industries from 1985 and 2010. The Korean economy has been in transition to a knowledge economy in the Smart City.

Keywords: knowledge and IT industries, input-output model, structural path analysis, dynamics of knowledge and it, knowledge economy, knowledge city and smart city

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Authors: Oleg Reva, Ilya Korotetskiy, Marina Lankina, Murat Kulmanov, Aleksandr Ilin

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Molecular docking approaches are widely used for design of new antibiotics and modeling of antibacterial activities of numerous ligands which bind specifically to active centers of indispensable enzymes and/or key signaling proteins of pathogens. Widespread drug resistance among pathogenic microorganisms calls for development of new antibiotics specifically targeting important metabolic and information pathways. A generally recognized problem is that almost all molecular targets have been identified already and it is getting more and more difficult to design innovative antibacterial compounds to combat the drug resistance. A promising way to overcome the drug resistance problem is an induction of reversion of drug resistance by supplementary medicines to improve the efficacy of the conventional antibiotics. In contrast to well established computer-based drug design, modeling of drug resistance reversion still is in its infancy. In this work, we proposed an approach to identification of compensatory genetic variants reducing the fitness cost associated with the acquisition of drug resistance by pathogenic bacteria. The approach was based on an analysis of the population genetic of Mycobacterium tuberculosis and on results of experimental modeling of the drug resistance reversion induced by a new anti-tuberculosis drug FS-1. The latter drug is an iodine-containing nanomolecular complex that passed clinical trials and was admitted as a new medicine against MDR-TB in Kazakhstan. Isolates of M. tuberculosis obtained on different stages of the clinical trials and also from laboratory animals infected with MDR-TB strain were characterized by antibiotic resistance, and their genomes were sequenced by the paired-end Illumina HiSeq 2000 technology. A steady increase in sensitivity to conventional anti-tuberculosis antibiotics in series of isolated treated with FS-1 was registered despite the fact that the canonical drug resistance mutations identified in the genomes of these isolates remained intact. It was hypothesized that the drug resistance phenotype in M. tuberculosis requires an adjustment of activities of many genes to compensate the fitness cost of the drug resistance mutations. FS-1 cased an aggravation of the fitness cost and removal of the drug-resistant variants of M. tuberculosis from the population. This process caused a significant increase in genetic heterogeneity of the Mtb population that was not observed in the positive and negative controls (infected laboratory animals left untreated and treated solely with the antibiotics). A large-scale search for linkage disequilibrium associations between the drug resistance mutations and genetic variants in other genomic loci allowed identification of target proteins, which could be influenced by supplementary drugs to increase the fitness cost of the drug resistance and deprive the drug-resistant bacterial variants of their competitiveness in the population. The approach will be used to improve the efficacy of FS-1 and also for computer-based design of new drugs to combat drug-resistant infections.

Keywords: complete genome sequencing, computational modeling, drug resistance reversion, Mycobacterium tuberculosis

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Authors: Akram Rasheed

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Background: Simulation in the health care field has been increasingly used over the last years in the training of resuscitation and life support practices. It has shown the advantage of improving the decision-making and technical skills through deliberate practice and return demonstration. Local Problem: This article reports on the integration of simulation-based training (SBT) in the training program about proper team dynamics and leadership skills during cardiopulmonary resuscitation (CPR) in the intensive care unit (ICU). Method and Intervention: Training of 180 critical care nurses was conducted using SBT between 1st January and 30th 2020. We had conducted 15 workshops, with the integration of SBT using high fidelity manikins and using demonstration and return-demonstration approach to train the nursing staff about proper team dynamics and leadership skills during CPR. Results: After completing the SBT session, all 180 nurses completed the evaluation form. The majority of evaluation items were rated over 95% for the effectiveness of the education; four items were less than 95% (88–94%). Lower rated items considered training and practice time, improved competency, and commitment to apply to learn. The team dynamics SBT was evaluated as an effective means to improve team dynamics and leadership skills during CPR in the intensive care unit (ICU). Conclusion: The use of simulation-based training to improve team dynamics and leadership skills is an effective method for better patient management during CPR. Besides skills competency, closed-loop communication, clear messages, clear roles, and assignments, knowing one’s limitations, knowledge sharing, constructive interventions, re-evaluating and summarizing, and mutual respect are all important concepts that should be considered during team dynamics training. However, participants reported the need for a repeated practice opportunity to build competency.

Keywords: cardiopulmonary resuscitation, high fidelity manikins, simulation-based training, team dynamics

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Authors: Elena K. Schneider, Johnny X. Huang, Vincenzo Carbone, Mark Baker, Mohammad A. K. Azad, Matthew A. Cooper, Jian Li, Tony Velkov

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Ivacaftor is a novel CF trans-membrane conductance regulator (CFTR) potentiator that improves the pulmonary function for cystic fibrosis patients bearing a G551D CFTR-protein mutation. Because ivacaftor is highly bound (>97%) to plasma proteins, there is the strong possibility that co-administered CF drugs that compete for the same plasma protein binding sites and impact the free drug concentration. This in turn could lead to drastic changes in the in vivo efficacy of ivacaftor and therapeutic outcomes. This study compares the binding affinity of ivacaftor and co-administered CF drugs for human serum albumin (HSA) and α1-acid glycoprotein (AGP) using surface plasmon resonance and fluorimetric binding assays that measure the displacement of site selective probes. Due to their high plasma protein binding affinities, drug-drug interactions between ivacaftor are to be expected with ducosate, montelukast, ibuprofen, dicloxacillin, omeprazole and loratadine. The significance of these drug-drug interactions is interpreted in terms of the pharmacodynamic/pharmacokinetic parameters and molecular docking simulations. The translational outcomes of the data are presented as recommendations for a staggered treatment regimen for future clinical trials which aims to maximize the effective free drug concentration and clinical efficacy of ivacaftor.

Keywords: human α-1-acid glycoprotein, binding affinity, human serum albumin, ivacaftor, cystic fibrosis

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Authors: Md. Samsuddin Ansari, Ashish Arora

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Every year 10 million people fall ill with one of the oldest diseases known as tuberculosis, caused by Mycobacterium tuberculosis. The success of M. tuberculosis as a pathogen is because of its ability to persist in host tissues. Multidrug resistance (MDR) mycobacteria cases increase every day, which is associated with efflux pumps controlled at the level of transcription. The transcription regulators of MDR transporters in bacteria belong to one of the following four regulatory protein families: AraC, MarR, MerR, and TetR. Phenolic acid decarboxylase repressor (PadR), like a family of transcription regulators, is closely related to the MarR family. Phenolic acid decarboxylase repressor (PadR) was first identified as a transcription factor involved in the regulation of phenolic acid stress response in various microorganisms (including Mycobacterium tuberculosis H37Rv). Recently research has shown that the PadR family transcription factors are global, multifunction transcription regulators. Rv0047c is a PadR subfamily-1 protein. We are exploring the biophysical and structural characterization of Rv0047c. The Rv0047 gene was amplified by PCR using the primers containing EcoRI and HindIII restriction enzyme sites cloned in pET-NH6 vector and overexpressed in DH5α and BL21 (λDE3) cells of E. coli following purification with Ni2+-NTA column and size exclusion chromatography. We did DSC to know the thermal stability; the Tm (transition temperature) of protein is 55.29ºC, and ΔH (enthalpy change) of 6.92 kcal/mol. Circular dichroism to know the secondary structure and conformation and fluorescence spectroscopy for tertiary structure study of protein. To understand the effect of pH on the structure, function, and stability of Rv0047c we employed spectroscopy techniques such as circular dichroism, fluorescence, and absorbance measurements in a wide range of pH (from pH-2.0 to pH-12). At low and high pH, it shows drastic changes in the secondary and tertiary structure of the protein. EMSA studies showed the specific binding of Rv0047c with its own 30-bp promoter region. To determine the effect of complex formation on the secondary structure of Rv0047c, we examined the CD spectra of the complex of Rv0047c with promoter DNA of rv0047. The functional role of Rv0047c was characterized by over-expressing the Rv0047c gene under the control of hsp60 promoter in Mycobacterium tuberculosis H37Rv. We have predicted the three-dimensional structure of Rv0047c using the Swiss Model and Modeller, with validity checked by the Ramachandra plot. We did molecular docking of Rv0047c with dnaA, through PatchDock following refinement through FireDock. Through this, it is possible to easily identify the binding hot-stop of the receptor molecule with that of the ligand, the nature of the interface itself, and the conformational change undergone by the protein pattern. We are using X-crystallography to unravel the structure of Rv0047c. Overall the studies show that Rv0047c may have transcription regulation along with providing an insight into the activity of Rv0047c in the pH range of subcellular environment and helps to understand the protein-protein interaction, a novel target to kill dormant bacteria and potential strategy for tuberculosis control.

Keywords: mycobacterium tuberculosis, phenolic acid decarboxylase repressor, Rv0047c, Circular dichroism, fluorescence spectroscopy, docking, protein-protein interaction

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Authors: Jiahui Song

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The application of an electric field can cause poration at cell membranes. This includes the outer plasma membrane, as well as the membranes of intracellular organelles. In order to analyze and predict such electroporation effects, it becomes necessary to first evaluate the electric fields and the transmembrane voltages. This information can then be used to assess changes in the pore formation energy that finally yields the pore distributions and their radii based on the Smolchowski equation. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into the pore formation energy equation. These changes make the pore formation energy E(r) self-adjusting in response to pore formation without causing uncontrolled growth and expansion. By using dynamic membrane tension, membrane electroporation in response to a 180kV/cm trapezoidal pulse with a 10 ns on time and 1.5 ns rise- and fall-times is discussed. Poration is predicted to occur at times beyond the peak at around 9.2 ns. Modeling also yields time-dependent distributions of the membrane pore population after multiple pulses. It shows that the pore distribution shifts to larger values of the radius with multiple pulsing. Molecular dynamics (MD) simulations are also carried out for a fixed field of 0.5 V/nm to demonstrate nanopore formation from a microscopic point of view. The result shows that the pore is predicted to be about 0.9 nm in diameter and somewhat narrower at the central point.

Keywords: high-intensity, nanosecond, dynamics, electroporation

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Authors: Nouf Alharbi

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The electrospray deposition technique became an important method that enables fragile, nonvolatile molecules to be deposited in situ in high vacuum environments. Furthermore, it is considered one of the ways to close the gap between basic surface science and molecular engineering, which represents a gradual change in the range of scientist research. Also, this paper talked about one of the most important techniques that have been developed and aimed for helping to further develop and characterize the electrospray by providing data collected using an image charge detection instrument. Image charge detection mass spectrometry (CDMS) is used to measure speed and charge distributions of the molecular ions. As well as, some data has been included using SIMION simulation to simulate the energies and masses of the molecular ions through the system in order to refine the mass-selection process.

Keywords: charge, deposition, electrospray, image, ions, molecules, SIMION

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Authors: Khachatur V. Nerkararyan, Sergey I. Bozhevolnyi

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We investigate relaxation dynamics of a quantum dipole emitter (QDE), e.g., a molecule or quantum dot, located near a metal nanoparticle (MNP) exhibiting a dipolar localized surface plasmon (LSP) resonance at the frequency of the QDE radiative transition. It is shown that under the condition of the QDE-MNP characteristic relaxation time being much shorter than that of the QDE in free-space but much longer than the LSP lifetime. It is also shown that energy dissipation in the QDE-MNP system is relatively weak with the probability of the photon emission being about 0.75, a number which, rather surprisingly, does not explicitly depend on the metal absorption characteristics. The degree of entanglement measured by the concurrency takes the maximum value, while the distances between the QDEs and metal ball approximately are equal.

Keywords: metal nanoparticle, localized surface plasmon, quantum dipole emitter, relaxation dynamics

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Authors: Gerardo Arias, Richard Wall, Jamie Stevens

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Lucilia bufonivora Moniez, is an obligate parasite of toads and frogs widely distributed in Europe. Its sister taxon Lucilia silvarum Meigen behaves mainly as a carrion breeder in Europe, however it has been reported as a facultative parasite of amphibians. These two closely related species are morphologically almost identical, which has led to misidentification, and in fact, it has been suggested that the amphibian myiasis cases by L. silvarum reported in Europe should be attributed to L. bufonivora. Both species remain poorly studied and their taxonomic relationships are still unclear. The identification of the larval specimens involved in amphibian myiasis with molecular tools and phylogenetic analysis of these two closely related species may resolve this problem. In this work seventeen unidentified larval specimens extracted from toad myiasis cases of the UK, the Netherlands and Switzerland were obtained, their COX1 (mtDNA) and EF1-α (Nuclear DNA) gene regions were amplified and then sequenced. The 17 larval samples were identified with both molecular markers as L. bufonivora. Phylogenetic analysis was carried out with 10 other blowfly species, including L. silvarum samples from the UK and USA. Bayesian Inference trees of COX1 and a combined-gene dataset suggested that L. silvarum and L. bufonivora are separate sister species. However, the nuclear gene EF1-α does not appear to resolve their relationships, suggesting that the rates of evolution of the mtDNA are much faster than those of the nuclear DNA. This work provides the molecular evidence for successful identification of L. bufonivora and a molecular analysis of the populations of this obligate parasite from different locations across Europe. The relationships with L. silvarum are discussed.

Keywords: calliphoridae, molecular evolution, myiasis, obligate parasitism

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Authors: Emma K. Sales, Nilda G. Butardo

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The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated. Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP). Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest. These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: methylation, MSAP, somaclones, SSR, subculture, 2, 4-D

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Authors: Z. Bayat

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A quantitative structure–property relationship (QSPR) study was performed to develop models those relate the structures of 65 Kovats retention index (RI) of adamantane derivatives. Molecular descriptors derived solely from 3D structures of the molecular compounds. The usefulness of the quantum chemical descriptors, calculated at the level of the DFT theories using 6-311+G** basis set for QSAR study of adamantane derivatives was examined. The use of descriptors calculated only from molecular structure eliminates the need to experimental determination of properties for use in the correlation and allows for the estimation of RI for molecules not yet synthesized. The prediction results are in good agreement with the experimental value. A multi-parametric equation containing maximum Four descriptors at B3LYP/6-31+G** method with good statistical qualities (R2train=0.913, Ftrain=97.67, R2test=0.770, Ftest=3.21, Q2LOO=0.895, R2adj=0.904, Q2LGO=0.844) was obtained by Multiple Linear Regression using stepwise method.

Keywords: DFT, adamantane, QSAR, Kovat

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Authors: Malika Souada, Juanita Rausch, Benjamin Guinot, Christine Bugajny

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The increase of global commerce and tourism makes the shipping sector an important contributor of atmospheric pollution. Both, airborne particles and gaseous pollutants have negative impact on health and climate. This is especially the case in port cities, due to the proximity of the exposed population to the shipping emissions in addition to other multiple sources of pollution linked to the surrounding urban activity. The objective of this study is to determine the concentrations of fine particles (immission), specifically PM2.5, PM1, PM0.3, BC and sulphates, in a context where maritime passenger traffic plays an important role (port area of Bordeaux centre). The methodology is based on high temporal resolution measurements of pollutants, correlated with meteorological and ship movements data. Particles and gaseous pollutants from seven maritime passenger ships were sampled and analysed during the docking, manoeuvring and berthing phases. The particle mass measurements were supplemented by measurements of the number concentration of ultrafine particles (<300 nm diameter). The different measurement points were chosen by taking into account the local meteorological conditions and by pre-modelling the dispersion of the smoke plumes. The results of the measurement campaign carried out during the summer of 2021 in the port of Bordeaux show that the detection of concentrations of particles emitted by ships proved to be punctual and stealthy. Punctual peaks of ultrafine particle concentration in number (P#/m3) and BC (ng/m3) were measured during the docking phases of the ships, but the concentrations returned to their background level within minutes. However, it appears that the influence of the docking phases does not significantly affect the air quality of Bordeaux centre in terms of mass concentration. Additionally, no clear differences in PM2.5 concentrations between the periods with and without ships at berth were observed. The urban background pollution seems to be mainly dominated by exhaust and non-exhaust road traffic emissions. However, temporal high-resolution measurements suggest a probable emission of gaseous precursors responsible for the formation of secondary aerosols related to the ship activities. This was evidenced by the high values of the PM1/BC and PN/BC ratios, tracers of non-primary particle formation, during periods of ship berthing vs. periods without ships at berth. The research findings from this study provide robust support for port area air quality assessment and source apportionment.

Keywords: characterization, fine particulate matter, harbour air quality, shipping impacts

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Authors: Ariesny Vera, Rodrigo Montecinos

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The rare-earth elements (REEs) or rare-earth metals (REMs), correspond to seventeen chemical elements composed by the fifteen lanthanoids, as well as scandium and yttrium. Lanthanoids corresponds to lanthanum and the f-block elements, from cerium to lutetium. Scandium and yttrium are considered rare-earth elements because they have ionic radii similar to the lighter f-block elements. These elements were called rare earths because they are simply more difficult to extract and separate individually than the most metals and, generally, they do not accumulate in minerals, they are rarely found in easily mined ores and are often unfavorably distributed in common ores/minerals. REEs show unique chemical and physical properties, in comparison to the other metals in the periodic table. Nowadays, these physicochemical properties are utilized in a wide range of synthetic, catalytic, electronic, medicinal, and military applications. Because of their applications, the global demand for rare earth metals is becoming progressively more important in the transition to a self-sustaining society and greener economy. However, due to the difficult separation between lanthanoid ions, the high cost and pollution of these processes, the scientists search the development of a method that combines selectivity and quantitative separation of lanthanoids from the leaching liquor, while being more economical and environmentally friendly processes. This motivation has favored the design and development of more efficient and environmentally friendly cation extractors with the incorporation of compounds as ionic liquids, membrane inclusion polymers (PIM) and supramolecular systems. Supramolecular chemistry focuses on the development of host-guest systems, in which a host molecule can recognize and bind a certain guest molecule or ion. Normally, the formation of a host-guest complex involves non-covalent interactions Additionally, host-guest interactions can be influenced among others effects by the structural nature of host and guests. The different macrocyclic hosts for lanthanoid species that have been studied are crown ethers, cyclodextrins, cucurbituryls, calixarenes and pillararenes.Among all the factors that can influence and affect lanthanoid (III) coordination, perhaps the most basic of them is the systematic control using macrocyclic substituents that promote a selective coordination. In this sense, macrocycles pillar[n]arenes (P[n]As) present a relatively easy functionalization and they have more π-rich cavity than other host molecules. This gives to P[n]As a negative electrostatic potential in the cavity which would be responsible for the selectivity of these compounds towards cations. Furthermore, the cavity size, the linker, and the functional groups of the polar headgroups could be modified in order to control the association of lanthanoid cations. In this sense, different P[n]As systems, specifically derivatives of the pentamer P[5]A functionalized with amide, amine, phosphate and sulfate derivatives, have been designed in terms of experimental synthesis and molecular dynamics, and the interaction between these P[5]As and some lanthanoid ions such as La³+, Eu³+ and Lu³+ has been studied by physicochemical characterization by 1H-NMR, ITC and fluorescence in the case of Eu³+ systems. The molecular dynamics study of these systems was developed in hexane as solvent, also taking into account the lanthanoid ions mentioned above, and the respective comparison studies between the different ions.

Keywords: lanthanoids, macrocycles, pillar[n]arenes, rare-earth metal extraction, supramolecular chemistry, supramolecular complexes.

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Authors: O. B. Iskender, K. V. Ling, V. Dubanchet, L. Simonini

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This paper presents a Guidance and Control (G&C) strategy to address spacecraft maneuvering problem for future Rendezvous and Docking (RVD) missions. The proposed strategy allows safe and propellant efficient trajectories for space servicing missions including tasks such as approaching, inspecting and capturing. This work provides the validation test results of the G&C laws using a Hardware-In-the-Loop (HIL) setup with two robotic mockups representing the chaser and the target spacecraft. Through this paper, the challenges of the relative motion control in space are first summarized, and in particular, the constraints imposed by the mission, spacecraft and, onboard processing capabilities. Second, the proposed algorithm is introduced by presenting the formulation of constrained Model Predictive Control (MPC) to optimize the fuel consumption and explicitly handle the physical and geometric constraints in the system, e.g. thruster or Line-Of-Sight (LOS) constraints. Additionally, the coupling between translational motion and rotational motion is addressed via dual quaternion based kinematic description and accordingly explained. The resulting convex optimization problem allows real-time implementation capability based on a detailed discussion on the computational time requirements and the obtained results with respect to the onboard computer and future trends of space processors capabilities. Finally, the performance of the algorithm is presented in the scope of a potential future mission and of the available equipment. The results also cover a comparison between the proposed algorithms with Linear–quadratic regulator (LQR) based control law to highlight the clear advantages of the MPC formulation.

Keywords: autonomous vehicles, embedded optimization, real-time experiment, rendezvous and docking, space robotics

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Authors: Keaghan Brown

Abstract:

The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Rahul Shrivastava, Manish Tripathi, Mohmmad Yasir, Shailesh Singh

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Life style changes and depletion in atmospheric ozone layer in recent decades lead to increase in skin cancer including both melanoma and nonmelanomas. Natural products which were obtained from different plant species have the potential of anti skin cancer activity. In regard of this, present study focuses the potential effect of Glycosmis pentaphylla against anti skin cancer activity. Different Phytochemical constituents which were present in the roots of Glycosmis pentaphylla were identified and were used as ligands after sketching of their structures with the help of ACD/Chemsketch. These ligands are screened for their anticancer potential with proteins which are involved in skin cancer effects with the help of pyrx software. After performing docking studies, results reveal that Noracronycine secondary metabolite of Glycosmis pentaphylla shows strong affinity of their binding energy with Ribosomal S6 Kinase 2 (2QR8) protein. Ribosomal S6 Kinase 2 (2QR8) has an important role in the cell proliferation and transformation mediated through by N-terminal kinase domain and was induced by the tumour promoters such as epidermal growth factor. It also plays a key role in the neoplastic transformation of human skin cells and in skin cancer growth. Noracronycine interact with THR-493 and MET-496 residue of Ribosomal S6 Kinase 2 protein with binding energy ΔG = -8.68 kcal/mole. Thus on the basis of this study we can say that Noracronycine which present in roots of Glycosmis pentaphylla can be used as lead compound against skin cancer.

Keywords: glycosmis pentaphylla, pyrx, ribosomal s6 kinase, skin cancer

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Authors: Jie Ji, Jing Xu, Yuehong Zhuang, Xiangqing Kang, Ying Qian, Ping Zhou, Di Xue

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Background: In 2014, there were 28,341 health professionals in Pudong new area of Shanghai and the number per 1000 population was 5.199, 55.55% higher than that in 2006. But it was always less than the average number of health professionals per 1000 population in Shanghai from 2006 to 2014. Therefore, allocation planning for the health professionals in Pudong new area has become a high priority task in order to meet the future demands of health care. In this study, we constructed an objective-based system dynamics model to forecast the number of health professionals in Pudong new area of Shanghai in 2020. Methods: We collected the data from health statistics reports and previous survey of human resources in Pudong new area of Shanghai. Nine experts, who were from health administrative departments, public hospitals and community health service centers, were consulted to estimate the current and future status of nine variables used in the system dynamics model. Based on the objective of the number of health professionals per 1000 population (8.0) in Shanghai for 2020, the system dynamics model for health professionals in Pudong new area of Shanghai was constructed to forecast the number of health professionals needed in Pudong new area in 2020. Results: The system dynamics model for health professionals in Pudong new area of Shanghai was constructed. The model forecasted that there will be 37,330 health professionals (6.433 per 1000 population) in 2020. If the success rate of health professional recruitment changed from 20% to 70%, the number of health professionals per 1000 population would be changed from 5.269 to 6.919. If this rate changed from 20% to 70% and the success rate of building new beds changed from 5% to 30% at the same time, the number of health professionals per 1000 population would be changed from 5.269 to 6.923. Conclusions: The system dynamics model could be used to simulate and forecast the health professionals. But, if there were no significant changes in health policies and management system, the number of health professionals per 1000 population would not reach the objectives in Pudong new area in 2020.

Keywords: allocation planning, forecast, health professional, system dynamics

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Authors: Young June Yoon

Abstract:

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

Keywords: tissues, mechanics, mechanical properties, wave propagation

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Authors: Muhammet Baldan, Emel Timuçin

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Generally, absorption and bioavailability increase if solubility increases; therefore, it is crucial to predict them in drug discovery applications. Molecular descriptors and Molecular properties are traditionally used for the prediction of water solubility. There are various key descriptors that are used for this purpose, namely Drogan Descriptors, Morgan Descriptors, Maccs keys, etc., and each has different prediction capabilities with differentiating successes between different data sets. Another source for the prediction of solubility is structural features; they are commonly used for the prediction of solubility. However, there are little to no studies that combine three or more properties or descriptors for prediction to produce a more powerful prediction model. Unlike available models, we used a combination of those features in a random forest machine learning model for improved solubility prediction to better predict and, therefore, contribute to drug discovery systems.

Keywords: solubility, random forest, molecular descriptors, maccs keys

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

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Aqueous suspensions of DNA were illuminated with linearly polarized visible light and ultraviolet for 5, 15, 20 and 40 h. In order to check the nature of modification, DNA interactions were characterized by FTIR spectroscopy. For each illuminated sample, weight average molecular weight and hydrodynamic radius were measured by high pressure size exclusion chromatography. Resulting optical changes for illuminated DNA were investigated using UV-Vis spectra and photoluminescent. Optical properties show potential application in sensors based on modified DNA. Then selected DNA-surfactant complexes were illuminated with electromagnetic radiation for 5h. Molecular structure, optical characteristic were examinated for obtained complexes. Illumination led to changes of complexes physicochemical properties as compared with native DNA. Observed changes were induced by rearrangement of the molecular structure of DNA chains.

Keywords: biopolymers, deoxyribonucleic acid, ionic liquids, linearly polarized visible light, ultraviolet

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Authors: Somit Dutta, Pallab Kar, Arnab Kumar Chakraborty, Arnab Sen, Tapas Kumar Chaudhuri

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In the present study three species of Clerodendrum; Clerodendrum indicum, Volkameria inermis and Clerodendrum colebrookianum were used to investigate the possible activity against oxidative stress. A detailed in-vivo and in-vitro antioxidant profiling, directly associated with inflammation-related carcinogenesis, has been executed with a motive to evaluate the free radical scavenging activity of Clerodendrum extract. Measurement of cell viability and ROS generation in HEK-293 (Human Embryonic Kidney Cell Line) cells was also estimated. The immune cell proliferative properties (MTT) and in-vitro assay for evaluation of their antioxidant activities including hydroxyl radical, nitric oxide, singlet oxygen, peroxinitrate and hydrogen peroxide, etc. were investigated. GC-MS and FTIR analyses have been performed to identify the active biological compounds. These active biological compounds were further studied to assess their potential medicinal properties, aided by molecular docking and interaction analysis between the active compounds and different proteins related to oxidative stress leading to progression of carcinogenesis. The research article clearly demonstrates the role of ROS in various phases of carcinogenesis. Therefore, the antioxidant and free radical scavenging capacity of all the Clerodendrum species might prove beneficial for the immune system. It might be concluded that this plant species offers great promise for cancer prevention and therapy due to the presence of several bioactive compounds and potent antioxidant capacity of C. colebrookianum.

Keywords: antioxidant, cancer, oxidative stress, reactive oxygen species (ROS)

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Authors: F. S. Irwansyah, I. Farida, Y. Maulana

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Studying chemistry requires the ability to understand three levels of understanding in the form of macroscopic, submicroscopic and symbolic, but the lack of emphasis on the submicroscopic level leads to the understanding of chemical concepts becoming incomplete, due to the limitations of the tools capable of providing visualization of submicroscopic concepts. The purpose of this study describes the stages of making augmented reality learning media on the concept of molecular geometry and analyze the feasibility test result of augmented reality learning media on the concept of molecular geometry. This research uses Research and Development (R & D) method which produces a product of AR learning media on molecular geometry concept and test the effectiveness of the product. Research stages include concept analysis and learning indicators, design development, validation, feasibility, and limited testing. The stages of validation and limited trial are aimed to get feedback in the form of assessment, suggestion and improvement on learning aspect, material substance aspect, visual communication aspect and software engineering aspects and media feasibility in terms of media creation purpose to be used in learning. The results of the overall feasibility test obtained r-calculation 0,7-0,9 with the interpretation of high feasibility value, whereas the result of limited trial got the percentage of eligibility with the average value equal to 70,83-92,5%. This percentage indicates that AR's learning media product on the concept of molecular geometry, deserves to be used as a learning resource.

Keywords: android, augmented reality, chemical learning, geometry

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Authors: Abdul Majid, Alia Jabeen, Nimra Zulifqar

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The inorganic molecular crystal (IMCs) due to their unusual structure has grabbed a lot of attention due to anisotropy in crystal structure. The IMCs consist of the molecular structures joined together via weak forces. Therefore, a difference between the bonding between the inter-cage and intra-cage interactions exists. To look closely at the bonding and interactions, we investigated interactions between two cages of Sb2O3 structure. The interactions were characterized via Extended Transition State-Natural Orbital for Chemical Valence-method (ETS-NOCV), Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results revealed strong intra-cage covalent bonding while weak van der Waals (vdWs) interactions along inter-cages exits. This structure cannot be termed as layered material although they have anisotropy in bonding and presence of weak vdWs interactions but its bulk is termed as inorganic layered clusters. This is due to the fact that the free standing sheet/films with these materials are not possible. This type of structures may be the most feasible to be used for the system to deal with high pressures and stress bearing materials.

Keywords: inorganic molecular crystals, density functional theory, cages, interactions

Procedia PDF Downloads 95