Search results for: molecular sieve

Authors: Irlana C. do Mar, Thayna A. Ferreira, Dayane S. Rezende, Bruno A. M. Figueira, José M. R. Mercury

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This work presents a low-cost Mn starting material to synthesis manganese oxide octahedral molecular sieve with Mg²⁺ in the tunnel (Mg-OMS-1), based on the Mn residues from Carajás Mineral Province (Amazon, Brazil). After hydrothermal and cation exchange procedures, the Mn residues transformed to a single phase, Mg-OMS-1. The raw material and the synthesis processes were analyzed by means of X-ray diffraction (XRD), Scanning electron microscopy (SEM) and Infrared spectroscopy (FTIR). The tunnel structure was synthesized hydrothermally at 180 °C for three days without impurities. According to the XRD analysis, the formation of crystalline Mg-OMS-1 was identified through reflections at 9.8º, 12º and 18º (2θ), as well as a thermal stability around 300 ºC. The SEM analysis indicated that the final product presents good crystallinity with a homogeneous size. In addition, an intense and diagnostic FTIR band was identified at 515 cm⁻¹ related to the MnO₆ octahedral stretching vibrations.

Keywords: Mn residues , Octahedral Molecular Sieve, Synthesis, Characterization

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Authors: Cheng-Jui Li, Chien-Chou Tseng

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This study adopts Computational Fluid Dynamics (CFD) technique to build the multiphase flow numerical model where the interface between the flue gas and desulfurization liquid can be traced by Eulerian-Eulerian model. Inside the tower, the contact of the desulfurization liquid flow from the spray nozzles and flue gas flow can trigger chemical reactions to remove the sulfur dioxide from the exhaust gas. From experimental observations of the industrial scale plant, the desulfurization mechanism depends on the mixing level between the flue gas and the desulfurization liquid. In order to significantly improve the desulfurization efficiency, the mixing efficiency and the residence time can be increased by perforated sieve trays. Hence, the purpose of this research is to investigate the flow structure of sieve trays for the flue gas desulfurization by numerical simulation. In this study, there is an outlet at the top of FGD tower to discharge the clean gas and the FGD tower has a deep tank at the bottom, which is used to collect the slurry liquid. In the major desulfurization zone, the desulfurization liquid and flue gas have a complex mixing flow. Because there are four perforated plates in the major desulfurization zone, which spaced 0.4m from each other, and the spray array is placed above the top sieve tray, which includes 33 nozzles. Each nozzle injects desulfurization liquid that consists of the Mg(OH)2 solution. On each sieve tray, the outside diameter, the hole diameter, and the porosity are 0.6m, 20 mm and 34.3%. The flue gas flows into the FGD tower from the space between the major desulfurization zone and the deep tank can finally become clean. The desulfurization liquid and the liquid slurry goes to the bottom tank and is discharged as waste. When the desulfurization solution flow impacts the sieve tray, the downward momentum will be converted to the upper surface of the sieve tray. As a result, a thin liquid layer can be developed above the sieve tray, which is the so-called the slurry layer. And the volume fraction value within the slurry layer is around 0.3~0.7. Therefore, the liquid phase can't be considered as a discrete phase under the Eulerian-Lagrangian framework. Besides, there is a liquid column through the sieve trays. The downward liquid column becomes narrow as it interacts with the upward gas flow. After the flue gas flows into the major desulfurization zone, the flow direction of the flue gas is upward (+y) in the tube between the liquid column and the solid boundary of the FGD tower. As a result, the flue gas near the liquid column may be rolled down to slurry layer, which developed a vortex or a circulation zone between any two sieve trays. The vortex structure between two sieve trays results in a sufficient large two-phase contact area. It also increases the number of times that the flue gas interacts with the desulfurization liquid. On the other hand, the sieve trays improve the two-phase mixing, which may improve the SO2 removal efficiency.

Keywords: Computational Fluid Dynamics (CFD), Eulerian-Eulerian Model, Flue Gas Desulfurization (FGD), perforated sieve tray

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Authors: Jeong-Hyun Hong, Wonsuk Choi, Hyungdal Park, Jinseok Kim, Junesun Kim

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Identifying the chronic functions of an implanted neural electrode is an important factor in acquiring neural signals through the electrode or restoring the nerve functions after peripheral nerve injury. The purpose of this study was to investigate the biocompatibility of the chronic implanted neural electrode into the sciatic nerve. To do this, a sieve-type neural electrode was implanted at proximal and distal ends of a transected sciatic nerve as an experimental group (Sieve group, n=6), and the end-to-end epineural repair was operated with the cut sciatic nerve as a control group (reconstruction group, n=6). All surgeries were performed on the sciatic nerve of the right leg in Sprague Dawley rats. Behavioral tests were performed before and 1, 4, 7, 10, 14, and weekly days until 5 months following surgery. Changes in sensory function were assessed by measuring paw withdrawal responses to mechanical and cold stimuli. Motor function was assessed by motion analysis using a Qualisys program, which showed a range of motion (ROM) related to the joints. Neurofilament-heavy chain and fibronectin expression were detected 5 months after surgery. In both groups, the paw withdrawal response to mechanical stimuli was slightly decreased from 3 weeks after surgery and then significantly decreased at 6 weeks after surgery. The paw withdrawal response to cold stimuli was increased from 4 days following surgery in both groups and began to decrease from 6 weeks after surgery. The ROM of the ankle joint was showed a similar pattern in both groups. There was significantly increased from 1 day after surgery and then decreased from 4 days after surgery. Neurofilament-heavy chain expression was observed throughout the entire sciatic nerve tissues in both groups. Especially, the sieve group was showed several neurofilaments that passed through the channels of the sieve-type neural electrode. In the reconstruction group, however, a suture line was seen through neurofilament-heavy chain expression up to 5 months following surgery. In the reconstruction group, fibronectin was detected throughout the sciatic nerve. However, in the sieve group, the fibronectin was observed only in the surrounding nervous tissues of an implanted neural electrode. The present results demonstrated that the implanted sieve-type neural electrode induced a focal inflammatory response. However, the chronic implanted sieve-type neural electrodes did not cause any further inflammatory response following peripheral nerve injury, suggesting the possibility of the chronic application of the sieve-type neural electrodes. This work was supported by the Basic Science Research Program funded by the Ministry of Science (2016R1D1A1B03933986), and by the convergence technology development program for bionic arm (2017M3C1B2085303).

Keywords: biocompatibility, motor functions, neural electrodes, peripheral nerve injury, sensory functions

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Authors: Massoud Farag Abouklaish

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The main aim of the present study is to investigate and classify the particle size distribution of sandy soils in Libya. More than fifty soil samples collected from many regions in North, West and South of Libya. Laboratory sieve analysis tests performed on disturbed soil samples to determine grain size distribution. As well as to provide an indicator of general engineering behavior and good understanding, test results are presented and analysed. In addition, conclusions, recommendations are made.

Keywords: Libya, grain size, sandy soils, sieve analysis tests

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

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

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

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Authors: Adebola Ajayi, Olakunle M. Makanjuola

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The effects of particle sizes of maize flour on the quality of traditional maize snack (Kokoro) were investigated. Maize flour of different sieve mesh sizes of 1.00mm, 1.9 mm, 1.4 mm, 1.68 mm and 2.0 mm was used to produce Kokoro. The samples were analysed for protein, fat, moisture content, crude fibre, ash and sensory evaluation. The various mixture obtained were separately processed into snacks following essential traditional method of production. The result of the sensory evaluation showed that Kokoro of sample 546 using 1.0mm mesh sieve size was the most preferred and sample 513 using 2.00 was least preferred. The result revealed that the more the maize was well blended the more acceptable the product is to the consumer.

Keywords: particle sizes, maize flour, quality, Kokoro

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Authors: Narendra Nath Patra

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Several recent studies reinforce the existence of a thick molecular disc in galaxies along with the dynamically cold thin disc. Assuming a two-component molecular disc, we model the disc of NGC 6946 as a four-component system consists of stars, HI, thin disc molecular gas, and thick disc molecular gas in vertical hydrostatic equilibrium. Following, we set up the joint Poisson-Boltzmann equation of hydrostatic equilibrium and solve it numerically to obtain a three-dimensional density distribution of different baryonic components. Using the density solutions and the observed rotation curve, we further build a three-dimensional dynamical model of the molecular disc and consecutively produce simulated CO spectral cube and spectral width profile. We find that the simulated spectral width profiles distinguishably differs for different assumed thick disc molecular gas fraction. Several CO spectral width profiles are then produced for different assumed thick disc molecular gas fractions and compared with the observed one to obtain the best fit thick disc molecular gas fraction profile. We find that the thick disc molecular gas fraction in NGC 6946 largely remains constant across its molecular disc with a mean value of 0.70 +/- 0.09. We also estimate the amount of extra-planar molecular gas in NGC 6946. We find 60% of the total molecular gas is extra-planar at the central region, whereas this fraction reduces to ~ 35% at the edge of the molecular disc. With our method, for the first time, we estimate the thick disc molecular gas fraction as a function of radius in an external galaxy with sub-kpc resolution.

Keywords: galaxies: kinematics and dynamic, galaxies: spiral, galaxies: structure , ISM: molecules, molecular data

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Authors: Seyyed Ershad Moradi, Javad Khodaveisi, Atefeh Nasrollahpour

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In this study, the highly ordered mesoporous carbon molecular sieve with high surface area and pore volume have been synthesized and modified by TiO₂ doping. The titanium oxide modified mesoporous carbon (Ti-OMC) was characterized by scanning electron microscope (SEM), BET surface area, DRS also XRD analysis (low and wide angle). Degradation experiments were conducted in batch mode with the variables such as amount of contact time, initial solution concentration, and solution pH. The optimal conditions for the degradation of methyl red (MR) were 100 mg/L dye concentration, pH of 7, and 0.12 mg/L of TiO₂ modified mesoporous carbon photocatalyst dosage.

Keywords: mesoporous carbon, photodegradation, surface modification, titanium oxide

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Authors: Jeoungsu Na, Jaehawn Lee, Changil Hong, Suhee Kim

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A molecular dynamics simulation in a converging-diverging nozzle was performed to study molecular collisions and their influence to average flow velocity according to a variety of vacuum levels. The static pressures and the dynamic pressure exerted by the molecule collision on the selected walls were compared to figure out the intensity variances of the directional flows. With pressure differences constant between the entrance and the exit of the nozzle, the numerical experiment was performed for molecular velocities and directional flows. The result shows that the velocities increased at the nozzle exit as the vacuum level gets higher in that area because less molecular collisions.

Keywords: cavitation, molecular collision, nozzle, vacuum, velocity increase

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Authors: L. Heidari, M. Jalili Ghazizade

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In recent years, different petrochemical complexes have been established to produce aromatic compounds. Among them, Nouri Petrochemical Complex (NPC) is the largest producer of aromatic raw materials in the world, and is located in south of Iran. Environmental concerns have been raised in this region due to generation of different types of solid waste generated in the process of aromatics production, and subsequently, industrial waste characterization has been thoroughly considered. The aim of this study is qualitative and quantitative characterization of industrial waste generated in the aromatics production process and determination of the best method for industrial waste management. For this purpose, all generated industrial waste during the production process was determined using a checklist. Four main industrial wastes were identified as follows: spent industrial soil, spent catalyst, spent molecular sieves and spent N-formyl morpholine (NFM) solvent. The amount of heavy metals and organic compounds in these wastes were further measured in order to identify the nature and toxicity of such a dangerous compound. Then industrial wastes were classified based on lab analysis results as well as using different international lists of hazardous waste identification such as EPA, UNEP and Basel Convention. Finally, the best method of waste disposal is selected based on environmental, economic and technical aspects. 

Keywords: aromatic compounds, industrial soil, molecular sieve, normal formyl morpholine solvent

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Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

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Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

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Authors: Diana Larisa Vladoiu, Vasile Ostafe, Adriana Isvoran

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Molecular docking calculations reveal that pesticides provide favorable interactions with the bacterial chitinases. Pesticides interact with both hydrophilic and aromatic residues involved in the active site of the enzymes, their positions partially overlapping the substrate and the inhibitors locations. Molecular docking outcomes, in correlation with experimental literature data, suggest that the pesticides may be degraded or having an inhibitor effect on the activity of these enzymes, depending of the application dose and rate.

Keywords: chitinases, inhibition, molecular docking, pesticides

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Authors: Gayathri Devi V, Aravamudan Kannan, Amit Sircar

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In the inner fuel cycle system of a nuclear fusion reactor, the Hydrogen Isotopes Removal System (HIRS) plays a pivoted role. It enables the effective extraction of the hydrogen isotopes from the breeder purge gas which helps to maintain the tritium breeding ratio and sustain the fusion reaction. One of the components of HIRS, Cryogenic Molecular Sieve Bed (CMSB) columns with zeolites adsorbents are considered for the physisorption of hydrogen isotopes at 1 bar and 77 K. Even though zeolites have good thermal stability and reduced activation properties making them ideal for use in nuclear reactor applications, their modest capacity for hydrogen isotopes adsorption is a cause of concern. In order to enhance the adsorbent capacity in an informed manner, it is helpful to understand the adsorption phenomena at the quantum electronic structure level. Physicochemical modifications of the adsorbent material enhances the adsorption capacity through the incorporation of active sites. This may be accomplished through the incorporation of suitable metal ions in the zeolite framework. In this work, molecular hydrogen isotopes adsorption on the active sites of functionalized zeolites are investigated in detail using Density Functional Theory (DFT) study. This involves the utilization of hybrid Generalized Gradient Approximation (GGA) with dispersion correction to account for the exchange and correlation functional of DFT. The electronic energies, adsorption enthalpy, adsorption free energy, Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital (LUMO) energies are computed on the stable 8T zeolite clusters as well as the periodic structure functionalized with different active sites. The characteristics of the dihydrogen bond with the active metal sites and the isotopic effects are also studied in detail. Validation studies with DFT will also be presented for adsorption of hydrogen on metal ion functionalized zeolites. The ab-inito screening analysis gave insights regarding the mechanism of hydrogen interaction with the zeolites under study and also the effect of the metal ion on adsorption. This detailed study provides guidelines for selection of the appropriate metal ions that may be incorporated in the zeolites framework for effective adsorption of hydrogen isotopes in the HIRS.

Keywords: adsorption enthalpy, functionalized zeolites, hydrogen isotopes, nuclear fusion, physisorption

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Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

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Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular/nanoscale models is demonstrated.

Keywords: cement composite, mechanical properties, molecular dynamics, plasticizer additives

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Ferid Hammami

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The molecular geometries of the possible conformations of pyruvic acid-water complexes (PA-(H₂O)ₙ = 1- 4) have been fully optimized at DFT/B3LYP/6-311G ++ (d, p) levels of calculation. Among several optimized molecular clusters, the most stable molecular arrangements obtained when one, two, three, and four water molecules are hydrogen-bonded to a central pyruvic acid molecule are presented in this paper. Apposite topological and geometrical parameters are considered as primary indicators of H-bond strength. Atoms in molecules (AIM) analysis shows that pyruvic acid can form a ring structure with water, and the molecular structures are stabilized by both strong O-H...O and C-H...O hydrogen bonds. In large clusters, classical O-H...O hydrogen bonds still exist between water molecules, and a cage-like structure is built around some parts of the central molecule of pyruvic acid. The electrostatic potential energy map (MEP) and the HOMO-LUMO molecular orbital (highest occupied molecular orbital-lowest unoccupied molecular orbital) analysis has been performed for all considered complexes.

Keywords: pyruvic acid, PA-water complex, hydrogen bonding, DFT, AIM, MEP, HOMO-LUMO

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Authors: Eseldin Keleb

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In the pharmaceutical industry particle size distribution is an important parameter for the characterization of pharmaceutical powders. The powder flowability, reactivity and compatibility, which have a decisive impact on the final product, are determined by particle size and size distribution. Therefore, the aim of this study was to evaluate the influence of processing parameters on the particle size distribution measurements. Different Size fractions of α-lactose monohydrate and 5% polyvinylpyrrolidone were prepared by wet granulation and were used for the preparation of samples. The influence of sieve load (50, 100, 150, 200, 250, 300, and 350 g), processing time (5, 10, and 15 min), sample size ratios (high percentage of small and large particles), type of disturbances (vibration and shaking) and process reproducibility have been investigated. Results obtained showed that a sieve load of 50 g produce the best separation, a further increase in sample weight resulted in incomplete separation even after the extension of the processing time for 15 min. Performing sieving using vibration was rapider and more efficient than shaking. Meanwhile between day reproducibility showed that particle size distribution measurements are reproducible. However, for samples containing 70% fines or 70% large particles, which processed at optimized parameters, the incomplete separation was always observed. These results indicated that sieving reliability is highly influenced by the particle size distribution of the sample and care must be taken for samples with particle size distribution skewness.

Keywords: sieving, reliability, particle size distribution, processing parameters

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Authors: Monika R. Bhoi, R. F. Sutar, Bhaumik B. Patel

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The objective of this research paper is to obtain the premium quality of cinnamon bark powder through cryogenic grinding technology. The effect of grinding temperature (0, -20, -40, -60, -80 and -100˚C), feed rate (8, 9 and 10 kg/h), and sieve size (0.8, 1.0 and 1.5 mm) were evaluated with respect to grinding time, volatile oil content, particle size, energy consumption, and liquid nitrogen consumption. Cryogenic grinding process parameters were optimized to obtain premium quality cinnamon bark powder was carried out using three factorial completely randomized design. The optimization revealed that grinding of cinnamon bark at -80⁰C temperature using 0.8 mm sieve size and 10 kg/h feed rate resulted in premium quality cinnamon bark powder containing volatile oil 3.01%. In addition, volatile oil retention in cryogenically ground powder was 88.23%, whereas control (ambient grinding) had 33.11%. Storage study of premium quality cryogenically ground powder was carried out under accelerated storage conditions (38˚C & 90% R.H). Accelerated storage of cryoground powder was found to be advantageous over the conventional ground for extended storage of the ground cinnamon powder with retention of its nutritional quality. Hence, grinding of spices at optimally low cryogenic temperature is a promising technology for the production of its premium quality powder economically.

Keywords: cinnamon bark, cryogenic grinding, feed rate, volatile oil

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Authors: Mei Hong, Wei Liu, Xuemin Dai, Yanxiong Pan, Xiangling Ji

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Polyamic acid (PAA) is the precursor of polyimide (PI) prepared by a two-step method, its molecular weight and molecular weight distribution not only play an important role during the preparation and processing, but also influence the final performance of PI. However, precise characterization on molecular weight of PAA is still a challenge because of the existence of very complicated interactions in the solution system, including the electrostatic interaction, hydrogen bond interaction, dipole-dipole interaction, etc. Thus, it is necessary to establisha suitable strategy which can completely suppress these complex effects and get reasonable data on molecular weight. Herein, the gel permeation chromatography (GPC) coupled with differential refractive index (RI) and multi-angle laser light scattering (MALLS) detectors were applied to measure the molecular weight of (6FDA-DMB) PAA using different mobile phases, LiBr/DMF, LiBr/H3PO4/THF/DMF, LiBr/HAc/THF/DMF, and LiBr/HAc/DMF, respectively. It was found that combination of LiBr with HAc can shield the above-mentioned complex interactions and is more conducive to the separation of PAA than only addition of LiBr in DMF. LiBr/HAc/DMF was employed for the first time as a mild mobile phase to effectively separate PAA and determine its molecular weight. After a series of conditional experiments, 0.02M LiBr/0.2M HAc/DMF was fixed as an optimized mobile phase to measure the relative and absolute molecular weights of (6FDA-DMB) PAA prepared, and the obtained Mw from GPC-MALLS and GPC-RI were 35,300 g/mol and 125,000 g/mol, respectively. Particularly, such a mobile phase is also applicable to other PAA samples with different structures, and the final results on molecular weight are also reproducible.

Keywords: Polyamic acids, Polyelectrolyte effects, Gel permeation chromatography, Mobile phase, Molecular weight

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

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In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

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Authors: K. Veluraja

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Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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Authors: Amir Bahrami

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In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index or a descriptor index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters of a graph which characterize its topology and are usually graph invariant. Topological indices are used for example in the development of quantitative structure-activity relationships (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure. In this paper some descriptor index (descriptor index) of single-walled carbon nanotubes, is determined.

Keywords: chemical graph theory, molecular topology, molecular descriptor, single-walled carbon nanotubes

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Authors: Upasana Pattnaik, Akshaya Kumar Sabat

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The compaction properties, unconfined compressive strength (UCS), soaked California bearing ratio (CBR), hydraulic conductivity, and swelling pressure of lime stabilized expansive soil-shredded waste tyre mixes have been discussed in this paper. Shredded waste tyres, passing 4.75 mm Indian Standard (IS) sieve and retained on 75µ IS sieve have been used in the experimental programme. First of all expansive soil-shredded waste tyre mixes were prepared by adding shredded waste tyre from 0 to 20% at an increment of 5%.Standard Proctor compaction, UCS and soaked CBR tests were conducted on these mixes. The optimum percentage of shredded waste tyre found out was 10%.In the second phase of the experiment, lime was added to sample having optimum percentage of expansive soil and shredded waste tyre from 2 to 6% at an increment of 1%.Compaction, UCS, soaked CBR, hydraulic conductivity, and swelling pressure tests were conducted on lime stabilized expansive soil-shredded waste tyre mixes. The optimum percentage of lime for stabilization was found out to be 5%.At the optimum percentage of lime the stabilized expansive soil-shredded waste tyre mix had increased strength, reduced hydraulic conductivity and swelling pressure.

Keywords: expansive soil, hydraulic conductivity, lime, shredded waste tyre, soaked california bearing ratio

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Authors: Sunatda Arayachukiat, Shogo Nobukawa, Masayuki Yamaguchi

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A new self-healing material was developed utilizing molecular entanglements for poly(vinyl butyral) (PVB) containing plasticizers. It was found that PVB shows autonomic self-healing behavior even below the glass transition temperature Tg because of marked molecular motion at surface. Moreover, the plasticizer addition enhances the chain mobility, leading to good healing behavior.

Keywords: Poly(vinyl butyral) (PVB), rheological properties, self-healing behaviour, molecular diffusion

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Authors: Rajandeep Kaur, Rajeev Gupta

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Background: Chronic myeloid leukemia (CML) is the most common leukaemia in India. The annual incidence of chronic myeloid leukemia in India was originally reported to be 0.8 to 2.2 per 1,00,000 population. CML is a clonal disorder that is usually easily diagnosed because the leukemic cells of more than 95% of patients have a distinctive cytogenetic abnormality, the Philadelphia chromosome (Ph1). The approval of tyrosine kinase inhibitors (TKIs), which target BCR-ABL1 kinase activity, has significantly reduced the mortality rate associated with chronic myeloid leukemia (CML) and revolutionized treatment. Material and Methods: 80 diagnosed cases of CML were taken. Investigations were done. Bone marrow and molecular studies were also done and with EUTOS, patients were stratified into low and high-risk groups and then treatment with Imatinib was given to all patients and the molecular response was evaluated at 6 months and 12 months follow up with BCR-ABL by RT-PCR quantitative assay. Results: In the study population, out of 80 patients in the study population, 40 were females and 40 were males, with M: F is 1:1. Out of total 80 patients’ maximum patients (54) were in 31-60 years age group. Our study showed a most common symptom of presentation is abdominal discomfort followed by fever. Out of the total 80 patients, 25 (31.3%) patients had high EUTOS scores and 55 (68.8%) patients had low EUTOS scores. On 6 months follow up 36.3% of patients had Complete Molecular Response, 16.3% of patients had Major Molecular Response and 47.5% of patients had No Molecular Response but on 12 months follow up 71.3% of patients had Complete Molecular Response, 16.25% of patients had Major Molecular Response and 12.5% patients had No Molecular Response. Conclusion: In this study, we found a significant correlation between EUTOS score and Molecular response at 6 months and 12 months follow up after Imatinib therapy.

Keywords: chronic myeloid leukemia, European treatment and outcome study score, hematological response, molecular response, tyrosine kinase inhibitor

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Authors: M. Bhattarai, B. B. Rana, M. Kamimukai, I. Takamure, T. Kawano, M. Murai

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The sd1-d allele at the sd1 locus on chromosome 1, originating from Taiwanese variety Dee-geo-woo-gen, has been playing important role for developing short-culm and lodging-resistant indica varieties such as IR36 in rice. The dominant allele SD1 for long culm at the locus is differentiated into SD1-in and SD1-ja which are harbored in indica and japonica subspecies’s, respectively. The sd1-d of an indica variety IR36 was substituted with SD1-in or SD1-ja by recurrent backcrosses of 17 times with IR36, and two isogenic tall lines regarding the respective dominant alleles were developed by using an indica variety IR5867 and a japonica one ‘Koshihikari’ as donors, which were denoted by '5867-36' and 'Koshi-36', respectively. The present study was conducted to examine the effect of sd1-d on yield and related traits as compared with SD1-in and SD1-ja, by using the two isogenic tall lines. Seedlings of IR36 and the two isogenic lines were transplanted on an experimental field of Kochi University, by the planting distance of 30 cm × 15 cm with two seedlings per hill, on May 3, 2017. Chemical fertilizers were supplied by basal application and top-dressing at a rate of 8.00, 6.57 and 7.52 g/m², respectively, for N, P₂O₅ and K₂O in total. Yield, yield components, and other traits were measured. Culm length (cm) was in the order of 5867-36 (101.9) > Koshi-36 (80.1) > IR36 (60.0), where '>' indicates statistically significant difference at the 5% level. Accordingly, sd1-d reduced culm by 41.9 and 20.1 cm, compared with SD1-in and SD1-ja, respectively, and the effect of elongating culm was higher in the former allele than in the latter one. Total brown rice yield (g/m²), including unripened grains, was in the order of IR36 (611) ≧ 5867-36 (586) ≧ Koshi-36 (572), indicating non-significant differences among them. Yield-1.5mm sieve (g/m²) was in the order of IR36 (596) ≧ 5867-36 (575) ≧ Koshi-36 (558). Spikelet number per panicle was in the order of 5867-36 (89.2) ≧ IR36 (84.7) ≧ Koshi-36 (79.8), and 5867-36 > Koshi-36. Panicle number per m² was in the order of IR36 (428) ≧ Koshi-36 (403) ≧ 5867-36 (353), and IR36 > 5867-36, suggesting that sd1-d increased number of panicles compared with SD1-in. Ripened-grain percentage-1.5mm sieve was in the order of Koshi-36 (86.0) ≧ 5867-36 (85.0) ≧ IR36 (82.7), and Koshi-36 > IR36. Thousand brown-rice-grain weight-1.5mm sieve (g) was in the order of 5867-36 (21.5) > Koshi-36 (20.2) ≧ IR36 (19.9). Total dry weight at maturity (g/m²) was in the order of 5867-36 (1404 ) ≧ IR36 (1310) ≧ Kosihi-36 (1290). Harvest index of total brown rice (%) was in the order of IR36 (39.6) > Koshi-36 (37.7) > 5867-36 (35.5). Hence, sd1-d did not exert significant effect on yield in indica genetic background. However, lodging was observed from the late stage of maturity in 5867-36 and Koshi-36, particularly in the former, which was principally due to their long culms. Consequently, sd1-d enables higher yield with higher fertilizer application, by enhancing lodging resistance, particularly in indica subspecies.

Keywords: rice, dwarfing gene, sd1-d, SD1-in, SD1-ja, yield

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

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Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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Authors: Jannes Quer, Amir Niknejad, Marcus Weber

Abstract:

Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

Abstract:

In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

Procedia PDF Downloads 528