Search results for: inorganic molecular crystals

Authors: Katerina H. Takova, Ivan N. Minkov, Gergana G. Zahmanova

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Molecular farming is the production of recombinant proteins in plants with the aim to use the protein as a purified product, crude extract or directly in the planta. Plants gain more attention as expression systems compared to other ones due to the cost effective production of pharmaceutically important proteins, appropriate post-translational modifications, assembly of complex proteins, absence of human pathogens to name a few. In addition, transient expression in plant leaves enables production of recombinant proteins within few weeks. Hepatitis E virus (HEV) is a causative agent of acute hepatitis. HEV causes epidemics in developing countries and is primarily transmitted through the fecal-oral route. Presently, all efforts for development of Hepatitis E vaccine are focused on the Open Read Frame 2 (ORF2) capsid protein as it contains epitopes that can induce neutralizing antibodies. For our purpose, we used the CMPV-based vector-pEAQ-HT for transient expression of HEV ORF2 in Nicotiana benthamina. Different molecular analysis (Western blot and ELISA) showed that HEV ORF2 capsid protein was expressed in plant tissue in high-yield up to 1g/kg of fresh leaf tissue. Electron microscopy showed that the capsid protein spontaneously assembled in low abundance virus-like particles (VLPs), which are highly immunogenic structures and suitable for vaccine development. The expressed protein was recognized by both human and swine HEV positive sera and can be used as a diagnostic reagent for the detection of HEV infection. Production of HEV capsid protein in plants is a promising technology for further HEV vaccine investigations. Here, we reported for a rapid high-yield transient expression of a recombinant protein in plants suitable for vaccine production as well as a diagnostic reagent. Acknowledgments -The authors’ research on HEV is supported with grants from the Project PlantaSYST under the Widening Program, H2020 as well as under the UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’ (BB/J004596/1). The authors want to thank Prof. George Lomonossoff (JIC, Norwich, UK) for his contribution.

Keywords: hepatitis E virus, plant molecular farming, transient expression, vaccines

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Authors: Omar Pillaca-Pullo, Arturo Alejandro-Paredes, Carol Flores-Fernandez, Marijuly Sayuri Kina, Amparo Iris Zavaleta

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Aqueous two-phase system (ATPS) is an interesting alternative for separating industrial enzymes due to it is easy to scale-up and low cost. Polyethylene glycol (PEG) mixed with potassium phosphate or magnesium sulfate is one of the most frequently polymer/salt ATPS used, but the consequences of its use is a high concentration of phosphates and sulfates in wastewater causing environmental issues. Citrate could replace these inorganic salts due to it is biodegradable and does not produce toxic compounds. On the other hand, statistical design of experiments is widely used for ATPS optimization and it allows to study the effects of the involved variables in the purification, and to estimate their significant effects on selected responses and interactions. The 24 factorial design with four central points (20 experiments) was employed to study the partition and purification of proteases produced by Pseudomonas sp. in PEG/citrate ATPS system. ATPS was prepared with different sodium citrate concentrations [14, 16 and 18% (w/w)], pH values (7, 8 and 9), PEG molecular weight (2,000; 4,000 and 6,000 g/mol) and PEG concentrations [18, 20 and 22 % (w/w)]. All system components were mixed with 15% (w/w) of the fermented broth and deionized water was added to a final weight of 12.5 g. Then, the systems were mixed and kept at room temperature until to reach two-phases separation. Volumes of the top and bottom phases were measured, and aliquots from both phases were collected for subsequent proteolytic activity and total protein determination. Influence of variables such as PEG molar mass (MPEG), PEG concentration (CPEG), citrate concentration (CSal) and pH were evaluated on the following responses: purification factor (PF), activity yield (Y), partition coefficient (K) and selectivity (S). STATISTICA program version 10 was used for the analysis. According to the obtained results, higher levels of CPEG and MPEG had a positive effect on extraction, while pH did not influence on the process. On the other hand, the CSal could be related with low values of Y because of the citrate ions have a negative effect on solubility and enzymatic structure. The optimum values of Y (66.4 %), PF (1.8), K (5.5) and S (4.3) were obtained at CSal (18%), MPEG (6,000 g/mol), CPEG (22%) and pH 9. These results indicated that the PEG/citrate system is accurate to purify these Pseudomonas sp. proteases from fermented broth as a first purification step.

Keywords: citrate, polyethylene glycol, protease, Pseudomonas sp

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Authors: Mini P. Singh, Jagat Ram, Archit Kumar, Tripti Rungta, Jasmine Khurana, Amit Gupta, R. K. Ratho

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Introduction: Human adenovirus is the most common agent involved in viral conjunctivitis. The clinical manifestations vary with different serotypes. The identification of the circulating strains followed by phylogenetic analysis can be helpful in understanding the origin and transmission of the disease. The present study aimed to carry out molecular epidemiology of the adenovirus types in the patients with conjunctivitis presenting to the eye centre of a tertiary care hospital in North India. Materials and Methods: The conjunctival swabs were collected from 23 suspected adenoviral conjunctivitis patients between April-August, 2014 and transported in viral transport media. The samples were subjected to nested PCR targeting hexon gene of human adenovirus. The band size of 956bp was eluted and 8 representative positive samples were subjected to sequencing. The sequences were analyzed by using CLUSTALX2.1 and MEGA 5.1 software. Results: The male: female ratio was found to be 3.6:1. The mean age of presenting patients was 43.95 years (+17.2). Approximately 52.1% (12/23) of patients presented with bilateral involvement while 47.8% (11/23) with unilateral involvement of the eye. Human adenovirus DNA could be detected in 65.2% (15/23) of the patients. The phylogenetic analysis revealed presence of serotype 8 in 7 patients and serotype 4 in one patient. The serotype 8 sequences showed 99-100% identity with Tunisian, Indian and Japanese strains. The adenovirus serotype 4 strains had 100% identity with strains from Tunisia, China and USA. Conclusion: Human adenovirus was found be an important etiological agent for conjunctivitis in our set up. The phylogenetic analysis showed that the predominant circulating strains in our epidemic keratoconjunctivitis were serotypes 8 and 4.

Keywords: conjunctivitis, human adenovirus, molecular epidemiology, phylogenetics

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Authors: S. N. Harun, H. Ahmad

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A series of ruthenium(II) complexes, including two novel compounds [Ru(dppz)2(L)]2+ where dppz = dipyrido-[3,2-a:2’,3’-c]phenazine, and L = 2-phenylimidazo[4,5-f][1,10]phenanthroline (PIP) or 2-(4-hydroxyphenyl)imidazo[4,5-f][1,10]phenanthroline (p-HPIP) have been synthesized and characterized. The previously reported complexes [Ru(bpy)2L]2+ and [Ru(phen)2L]2+ were also prepared. All complexes were characterized by elemental analysis, 1H-NMR spectroscopy, ESI-Mass spectroscopy and FT-IR spectroscopy. The photophysical properties were analyzed by UV-Visible spectroscopy and fluorescence spectroscopy. [Ru(dppz)2(PIP)]2+ and [Ru(dppz)2(p-HPIP)]2+ displayed ‘molecular light-switch’ effect as they have high emission in acetonitrile but no emission in water. The cytotoxicity of all complexes against cancer cell lines Hela and MCF-7 were investigated through standard MTT assay. [Ru(dppz)2(PIP)]2+ showed moderate toxicity on both MCF-7 and Hela with IC50 of 37.64 µM and 28.02 µM, respectively. Interestingly, [Ru(dppz)2(p-HPIP)]2+ exhibited remarkable cytotoxicity results with IC50 of 13.52 µM on Hela and 11.63 µM on MCF-7 cell lines which are comparable to the infamous anti-cancer drug, cisplatin. The cytotoxicity of this complex series increased as the ligands size extended in order of [Ru(bpy)2(L)]2+ < [Ru(phen)2(L)]2+ < [Ru(dppz)2(L)]2+.

Keywords: ruthenium, cytotoxicity, molecular light-switch, anticancer

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Authors: Jatinder Kumar

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Ultrasonic machining is one of the most widely used non-traditional machining processes for machining of materials that are relatively brittle, hard and fragile such as advanced ceramics, refractories, crystals, quartz etc. There is a considerable lack of research on its application to the cost-effective machining of tough materials such as titanium. In this investigation, the application of USM process for machining of titanium (ASTM Grade-I) has been explored. Experiments have been conducted to assess the effect of different parameters of USM process on machining rate and tool wear rate as response characteristics. The process parameters that were included in this study are: abrasive grit size, tool material and power rating of the ultrasonic machine. It has been concluded that titanium is fairly machinable with USM process. Significant improvement in the machining rate can be realized by manipulating the process parameters and obtaining the optimum combination of these parameters.

Keywords: abrasive grit size, tool material, titanium, ultrasonic machining

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Authors: Nataša Kalajdžija, Strahinja Kovačević, Davor Lončar, Sanja Podunavac Kuzmanović, Lidija Jevrić

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In order to investigate the relationship between retention and structure, a quantitative Structure Retention Relationships (QSRRs) study was applied for the prediction of retention times of a set of 23 secoestrane derivatives in a reversed-phase thin-layer chromatography. After the calculation of molecular descriptors, a suitable set of molecular descriptors was selected by using step-wise multiple linear regressions. Artificial Neural Network (ANN) method was employed to model the nonlinear structure-activity relationships. The ANN technique resulted in 5-6-1 ANN model with the correlation coefficient of 0.98. We found that the following descriptors: Critical pressure, total energy, protease inhibition, distribution coefficient (LogD) and parameter of lipophilicity (miLogP) have a significant effect on the retention times. The prediction results are in very good agreement with the experimental ones. This approach provided a new and effective method for predicting the chromatographic retention index for the secoestrane derivatives investigated.

Keywords: lipophilicity, QSRR, RP TLC retention, secoestranes

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Authors: Jiancheng Zheng

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When metals are released into water from mining activities, they undergo changes chemically, physically and biologically and then may become more mobile and transportable along the waterway from their original sites. Natural colloids, including both organic and inorganic entities, are naturally occurring in any aquatic environment with sizes in the nanometer range. Natural colloids in a water system play an important role, quite often a key role, in binding and transporting compounds. When assessing and evaluating metals in natural waters, their sources, mobility, fate, and distribution patterns in the system are the major concerns from the point of view of assessing environmental contamination and pollution during resource development. There are a few ways to quantify colloids and accordingly study how metals distribute on different sizes of colloids. Current research results show that the presence of colloids can enhance the transport of some heavy metals in water, while heavy metals may also have an influence on the transport of colloids when cations in the water system change colloids and/or the ion strength of the water system changes. Therefore, studies into the relationship between different sizes of colloids and different metals in a water system are necessary and needed as natural colloids in water systems are complex mixtures of both organic and inorganic as well as biological materials. Their stability could be sensitive to changes in their shapes, phases, hardness and functionalities due to coagulation and deposition et al. and chemical, physical, and biological reactions. Because metal contaminants’ adsorption on surfaces of colloids is closely related to colloid properties, it is desired to fraction water samples as soon as possible after a sample is taken in the natural environment in order to avoid changes to water samples during transportation and storage. For this reason, this study carried out groundwater sample processing in the field, using Prep/Scale tangential flow filtration systems with 3-level cartridges (1 kDa, 10 kDa and 100 kDa). Groundwater samples from seven sites at Fort MacMurray, Alberta, Canada, were fractionated during the 2015 field sampling season. All samples were processed within 3 hours after samples were taken. Preliminary results show that although the distribution pattern of metals on colloids may vary with different samples taken from different sites, some elements often tend to larger colloids (such as Fe and Re), some to finer colloids (such as Sb and Zn), while some of them mainly in the dissolved form (such as Mo and Be). This information is useful to evaluate and project the fate and mobility of different metals in the groundwaters and possibly in environmental water systems.

Keywords: metal, colloid, groundwater, mobility, fractionation, sorption

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Authors: Kanchan Maji, Debasmita Pani, Sudip Dasgupta

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Calcium phosphate cement (CPC) due to its high bioactivity and optimum bioresorbability shows excellent bone regeneration capability. Despite it has limited applications as bone implant due to its macro-porous microstructure causing its poor mechanical strength. The reinforcement of apatitic CPCs with biocompatible fibre glass phase is an attractive area of research to improve its mechanical strength. Here we study the setting behaviour of Si-doped and un-doped alpha tri-calcium phosphate (α-TCP) based CPC and its reinforcement with the addition of E-glass fibre. Alpha tri-calcium phosphate powders were prepared by solid state sintering of CaCO3, CaHPO4 and tetra ethyl ortho silicate (TEOS) was used as silicon source to synthesise Si doped α-TCP powders. Alpha tri-calcium phosphate based CPC hydrolyzes to form hydroxyapatite (HA) crystals having excellent osteoconductivity and bone-replacement capability thus self-hardens through the entanglement of HA crystals. Setting time, phase composition, hydrolysis conversion rate, microstructure, and diametral tensile strength (DTS) of un-doped CPC and Si-doped CPC were studied and compared. Both initial and final setting time of the developed cement was delayed because of Si addition. Crystalline phases of HA (JCPDS 9-432), α-TCP (JCPDS 29-359) and β-TCP (JCPDS 9-169) were detected in the X-ray diffraction (XRD) pattern after immersion of CPC in simulated body fluid (SBF) for 0 hours to 10 days. The intensities of the α-TCP peaks of (201) and (161) at 2θ of 22.2°and 24.1° decreased when the time of immersion of CPC in SBF increased from 0 hours to 10 days, due to its transformation into HA. As Si incorporation in the crystal lattice stabilised the TCP phase, Si doped CPC showed a little slower rate of conversion into HA phase as compared to un-doped CPC. The SEM image of the microstructure of hardened CPC showed lower grain size of HA in un-doped CPC because of premature setting and faster hydrolysis of un-doped CPC in SBF as compared that in Si-doped CPC. Premature setting caused generation of micro and macro porosity in un-doped CPC structure which resulted in its lower mechanical strength as compared to that in Si-doped CPC. This lower porosity and greater compactness in the microstructure attributes to greater DTS values observed in Si-doped CPC. E-glass fibres of the average diameter of 12 μm were cut into approximately 1 mm in length and immersed in SBF to deposit carbonated apatite on its surface. This was performed to promote HA crystal growth and entanglement along the fibre surface to promote stronger interface between dispersed E-glass fibre and CPC matrix. It was found that addition of 10 wt% of E-glass fibre into Si-doped α-TCP increased the average DTS of CPC from 8 MPa to 15 MPa as the fibres could resist the propagation of crack by deflecting the crack tip. Our study shows that biocompatible E-glass fibre in optimum proportion in CPC matrix can enhance the mechanical strength of CPC without affecting its bioactivity.

Keywords: Calcium phosphate cement, biocompatibility, e-glass fibre, diametral tensile strength

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Authors: Rong Li, Brian D. Wirth, Bing Liu

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Graphite is the matrix, and structural material in the high temperature gas-cooled reactor exhibits an irradiation response. It is of significant importance to analyze the defect production and evaluate the role of graphite under irradiation. A vast experimental literature exists for graphite on the dimensional change, mechanical properties, and thermal behavior. However, simulations have not been applied to the atomistic perspective. Remarkably few molecular dynamics simulations have been performed to study the irradiation response in graphite. In this paper, irradiation-induced damage cascades in graphite were investigated with molecular dynamics simulation. Statistical results of the graphite defects were obtained by sampling a wide energy range (1–30 KeV) and 10 different runs for every cascade simulation with different random number generator seeds to the velocity scaling thermostat function. The chemical bonding in carbon was described using the adaptive intermolecular reactive empirical bond-order potential (AIREBO) potential coupled with the standard Ziegler–Biersack–Littmack (ZBL) potential to describe close-range pair interactions. This study focused on analyzing the number of defects, the final cascade morphology and the distribution of defect clusters in space, the length-scale cascade properties such as the cascade length and the range of primary knock-on atom (PKA), and graphite mechanical properties’ variation. It can be concluded that the number of surviving Frenkel pairs increased remarkably with the increasing initial PKA energy but did not exhibit a thermal spike at slightly lower energies in this paper. The PKA range and cascade length approximately linearly with energy which indicated that increasing the PKA initial energy will come at expensive computation cost such as 30KeV in this study. The cascade morphology and the distribution of defect clusters in space mainly related to the PKA energy meanwhile the temperature effect was relatively negligible. The simulations are in agreement with known experimental results and the Kinchin-Pease model, which can help to understand the graphite damage cascades and lifetime span under irradiation and provide a direction to the designs of these kinds of structural materials in the future reactors.

Keywords: graphite damage cascade, molecular dynamics, cascade morphology, cascade distribution

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Authors: Fekadu Melak, Tsegaye Girma Asere

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Trace element ions, such as Cr(VI) and F−, are of particular interest due to their environmental impact. Both ions exhibit an anionic nature in water that can show similar removal tendencies except for their significant differences in ionic radius. Accordingly, partial freezing was performed to examine freeze separation efficiencies of Cr(VI) and F– from aqueous solutions. Real groundwater and simulated wastewater were included to test effeciency of F– and Cr(VI), respectively. Parameters such as initial ion concentration, salt addition, and freeze duration were explored. Under optimal operating conditions, freeze separation efficiencies of 90 ± 0.12 to 97 ± 0.54% and 58 ± 0.23% to 60 ± 0.34% from 5 mg/L of Cr(VI) and F–, respectively, were demonstrated. The F– ion intercalation into the ice, initiating the decrement of freeze separation efficiency was observed in the salt addition processes. The influences of structuring-destructuring (kosmotropicity-chaotropicity) and the size-exclusion nature of ice crystals were used to explain the plausible mechanism in freeze separation efficiency trace elemental ions.

Keywords: Cr(VI), F-, partial freezing, size exclusion

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Authors: Manuel Salado, Mikel Rincón, Arkaitz Fidalgo, Roberto Fernandez, Senentxu Lanceros-Méndez

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Lithium-ion batteries (LIBs) are a promising technology for energy storage, but they suffer from safety concerns due to the use of flammable organic solvents in their liquid electrolytes. Solid-state electrolytes (SSEs) offer a potential solution to this problem, but they have their own limitations, such as poor ionic conductivity and high interfacial resistance. The aim of this research was to develop a new type of SSE based on metal-organic frameworks (MOFs) and ionic liquids (ILs). MOFs are porous materials with high surface area and tunable electronic properties, making them ideal for use in SSEs. ILs are liquid electrolytes that are non-flammable and have high ionic conductivity. A series of MOFs were synthesized, and their electrochemical properties were evaluated. The MOFs were then infiltrated with ILs to form a quasi-solid gel and solid xerogel SSEs. The ionic conductivity, interfacial resistance, and electrochemical performance of the SSEs were characterized. The results showed that the MOF-IL SSEs had significantly higher ionic conductivity and lower interfacial resistance than conventional SSEs. The SSEs also exhibited excellent electrochemical performance, with high discharge capacity and long cycle life. The development of MOF-IL SSEs represents a significant advance in the field of solid-state electrolytes. The high ionic conductivity and low interfacial resistance of the SSEs make them promising candidates for use in next-generation LIBs. The data for this research was collected using a variety of methods, including X-ray diffraction, scanning electron microscopy, and electrochemical impedance spectroscopy. The data was analyzed using a variety of statistical and computational methods, including principal component analysis, density functional theory, and molecular dynamics simulations. The main question addressed by this research was whether MOF-IL SSEs could be developed that have high ionic conductivity, low interfacial resistance, and excellent electrochemical performance. The results of this research demonstrate that MOF-IL SSEs are a promising new type of solid-state electrolyte for use in LIBs. The SSEs have high ionic conductivity, low interfacial resistance, and excellent electrochemical performance. These properties make them promising candidates for use in next-generation LIBs that are safer and have higher energy densities.

Keywords: energy storage, solid-electrolyte, ionic liquid, metal-organic-framework, electrochemistry, organic inorganic plastic crystal

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Authors: Lucas Sátiro Do Carmo, Betzabel Noemi Silva Carrera, Shigueo Watanabe, J. F. D. Chubaci

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Beryl is a silicate with chemical formula Be₃Al₂(SiO₃)₆ commonly found in Brazil. It has a few colored variations used as jewelry, like Aquamarine (blueish), Emerald (green) and Heliodor (yellow). The color of each variation depends on the dopant that is naturally present in the crystal lattice. In this work, Heliodor pellets of 5 mm diameter and 1 mm thickness have been produced and investigated using thermoluminescence (TL) to evaluate its potential for use as gamma ray’s dosimeter. The results show that the pellets exhibited a prominent TL peak at 205 °C that grows linearly with dose when irradiated from 1 Gy to 1000 Gy. A comparison has been made between powdered and sintered dosimeters. The results show that sintered pellets have higher sensitivity than powder dosimeter. The TL response of this mineral is satisfactory for radiation dosimetry applications in the studied dose range.

Keywords: dosimetry, beryl, gamma rays, sintered pellets, new material

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Authors: Mthokozisi Simelane

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Background: Malaria remains a life-threatening disease in tropical regions despite the advances in the treatment of this disease, it still remains a significant burden as some parasites have become resistant to the currently available drugs. This has created a necessity for the development of alternative, more efficient antimalarial drugs. Warburgia salutaris is a traditional medicinal plant used in malaria treatment by Zulu traditional healers. Materials and methods: The W. salutaris stem-bark was extracted with dichloromethane and the compound was isolated through column chromatography. The compound was identified and characterized by spectroscopic analysis (1H NMR, 13C NMR, IR and MS) and the structure was also confirmed by x-ray crystallography. The anti-plasmodial activity (in vitro) was studied on NF54 Plasmodium falciparum strain (CQS). Cytotoxicity was measured using the MTT assay on HEK239 and HEPG2 cell lines. Docking of Mukaadial acetate was conducted in AutoDock Vina. Structural modifications were conducted in UCSF Chimera and molecular interactions examined in LigPlot. Results: The compound, Mukaadial Acetate showed appreciable inhibition (IC50 0.44±0.10 µg/ml) of the parasite growth and cytotoxicity activity of 0.124±0.109 and 0.199±0.083 (µg/ml) on HEK293 and HEPG2 cells respectively. Molecular docking revealed that Mukaadial Acetate binds to the purine, pyrophosphate and ribose binding sites of the PfHGXPRT with an optimum binding conformation and forms hydrogen bond, steric and hydrophobic interactions with the residues inhabiting the respective binding sites. Conclusion: It is apparent that W. salutaris contains components (including Mukaadial Acetate) that exhibit antimalarial activity. This study scientifically validates the use of this plant in folk medicine.

Keywords: plasmodium falciparum, molecular docking, antimalarial activity, PfHGXPRT, Warburgia salutaris, mukaadial acetate

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Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: Samir Khene

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Present and future industrial uses of high critical temperature superconductors require high critical temperatures TC and strong current densities JC. These two aims constitute the two motivations of the scientific research in this domain. The most significant feature of any superconductor, from the viewpoint of uses, is the maximum electrical transport current density that this superconductor is capable of withstanding without loss of energy. In this work, vortices pinning in conventional and high-TC superconductors will be studied. Our experiments on vortices pinning in single crystals and nanoparticles of YBa2Cu3O7- and La1.85 Sr0.15CuO will be presented. It will be given special attention to the study of the YBa2Cu3O7- nanoparticles doped by ferromagnetic nanoparticles of Y3Fe5O12. The ferromagnetism and superconductivity coexistence in this compound will be demonstrated, and the influence of these ferromagnetic nanoparticles on the variations of the critical current density JC in YBa2Cu3O7- nanoparticles as a function of applied field H and temperature T will be studied.

Keywords: ferromagnetism, superconductivity, coexistence, magnetic material

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Authors: Abdelsabour G. A. Khaled, Galal A.R. El-Sherbeny, Ahmed M. Hassanein, Gameel M. G. Aly

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Classical methods of identification, based on agronomical characterization, are not always the most accurate way due to the instability of these characteristics under the influence of the different environments. In order to estimate the genetic diversity, molecular markers provided excellent tools. In this study, Genetic variation of nine Egyptian jojoba shrubs was tested using ISSR (inter simple sequences repeats), RAPD (random amplified polymorphic DNA) markers and based on the morphological characterization. The average of the percentage of polymorphism (%P) ranged between 58.17% and 74.07% for ISSR and RAPD markers, respectively. The range of genetic similarity percents among shrubs based on ISSR and RAPD markers were from 82.9 to 97.9% and from 85.5 to 97.8%, respectively. The average of PIC (polymorphism information content) values were 0.19 (ISSR) and 0.24 (RAPD). In the present study, RAPD markers were more efficient than the ISSR markers. Where the RAPD technique exhibited higher marker index (MI) average (1.26) compared to ISSR one (1.11). There was an insignificant correlation between the ISSR and RAPD data (0.076, P > 0.05). The dendrogram constructed by the combined RAPD and ISSR data gave a relatively different clustering pattern.

Keywords: correlation, molecular markers, polymorphism, marker index

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Authors: Nur Zahidah Rozaki, Desmond Ang Teck Chye

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Environment-friendly polymeric plasticisers for poly(vinyl chloride), PVC were synthesised using palm oil as the main raw material. The synthesis comprised of 2 steps: (i) transesterification of palm oil, followed by (ii) polycondensation between the products of transesterification with diacids. The synthesis involves four different formulations to produce plasticisers with different average molecular weight. Chemical structures of the plasticiser were studied using FTIR (Fourier-Transformed Infra-Red) and 1H-NMR (Proton-Nuclear Magnetic Resonance).The molecular weights of these palm oil-based polymers were obtained using GPC (Gel Permeation Chromatography). PVC was plasticised with the polymeric plasticisers through solvent casting technique using tetrahydrofuran, THF as the mutual solvent. Some of the tests conducted to evaluate the effectiveness of the plasticiser in the PVC film including thermal stability test using thermogravimetric analyser (TGA), differential scanning calorimetry (DSC) analysis to determine the glass transition temperature, Tg, and mechanical test to determine tensile strength, modulus and elongation at break of plasticised PVC using standard test method ASTM D882.

Keywords: alkyd, palm oil, plasticiser, pvc

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Authors: Soroor Ghaziof, Wei Gao

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Sol-enhanced Zn-Ni-Al2O3 nano-composite coatings were electroplated on mild steel by our newly developed sol-enhanced electroplating method. In this method, transparent Al2O3 sol was added into the acidic Zn-Ni bath to produced Zn-Ni-Al2O3 nano-composite coatings. The chemical composition, microstructure and mechanical properties of the composite and alloy coatings deposited at two different agitation speed were investigated. The structure of all coatings was single γ-Ni5Zn21 phase. The composite coatings possess refined crystals with higher microhardness compared to Zn-Ni alloy coatings. The wear resistance of Zn-Ni coatings was improved significantly by incorporation of alumina nano particles into the coatings. Higher agitation speed provided more uniform coatings with smaller grain sized and slightly higher microhardness. Considering composite coatings, high agitation speeds may facilitate co-deposition of alumina in the coatings.

Keywords: microhardness, sol-enhanced electroplating, wear resistance, Zn-Ni-Al2O3 composite coatings

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Authors: Maria Fontenele, Claude-Gilles Dussap, Vincent Dumouilla, Baptiste Boit

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Roquette Frères is a producer of plant-based ingredients that employs many processes to extract relevant molecules and often transforms them through chemical and physical processes to create desired ingredients with specific functionalities. In this context, Roquette encounters numerous multi-component complex systems in their processes, including fibers, proteins, and carbohydrates, in an aqueous environment. To develop, control, and optimize both new and old processes, Roquette aims to develop new in silico tools. Currently, Roquette uses process modelling tools which include specific thermodynamic models and is willing to develop computational methodologies such as molecular dynamics simulations to gain insights into the complex interactions in such complex media, and especially hydrogen bonding interactions. The issue at hand concerns aqueous mixtures of polyols with high dry matter content. The polyols mannitol and sorbitol molecules are diastereoisomers that have nearly identical chemical structures but very different physicochemical properties: for example, the solubility of sorbitol in water is 2.5 kg/kg of water, while mannitol has a solubility of 0.25 kg/kg of water at 25°C. Therefore, predicting liquid-solid equilibrium properties in this case requires sophisticated solution models that cannot be based solely on chemical group contributions, knowing that for mannitol and sorbitol, the chemical constitutive groups are the same. Recognizing the significance of solvation phenomena in polyols, the GePEB (Chemical Engineering, Applied Thermodynamics, and Biosystems) team at Institut Pascal has developed the COSMO-UCA model, which has the structural advantage of using quantum mechanics tools to predict formation and phase equilibrium properties. In this work, we use molecular dynamics simulations to elucidate the behavior of polyols in aqueous solution. Specifically, we employ simulations to compute essential metrics such as radial distribution functions and hydrogen bond autocorrelation functions. Our findings illuminate a fundamental contrast: sorbitol and mannitol exhibit disparate hydrogen bond lifetimes within aqueous environments. This observation serves as a cornerstone in elucidating the divergent physicochemical properties inherent to each compound, shedding light on the nuanced interplay between their molecular structures and water interactions. We also present a methodology to predict the physicochemical properties of complex solutions, taking as sole input the three-dimensional structure of the molecules in the medium. Finally, by developing knowledge models, we represent some physicochemical properties of aqueous solutions of sorbitol and mannitol.

Keywords: COSMO models, hydrogen bond, molecular dynamics, thermodynamics

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Authors: Shilpi, Indu Gaur, Neha Bhadauria, Susmita Goswami, Prabir K. Paul

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Cultivation and consumption of organically grown fruits and vegetables have increased by several folds. However, the presence of Human Enteric Pathogens on the surface of organically grown vegetables causing Gastro-intestinal diseases, are most likely due to contaminated water and fecal matter of farm animals. Human Enteric Pathogens are adapted to colonize the human gut, and also colonize plant surface. Microbes on plant surface communicate with each other to establish quorum sensing. The cross talk study is important because the enteric pathogens on phylloplane have been reported to mask the beneficial resident bacteria of plant. In the present study, HEPs and bacterial colonizers were identified using 16s rRNA sequencing. Microbial colonization patterns after interaction between Human Enteric Pathogens and natural bacterial residents on tomato phylloplane was studied. Tomato plants raised under aseptic conditions were inoculated with a mixture of Serratia fonticola and Klebsiella pneumoniae. The molecules involved in cross-talk between Human Enteric Pathogens and regular bacterial colonizers were isolated and identified using molecular techniques and HPLC. The colonization pattern was studied by leaf imprint method after 48 hours of incubation. The associated protein-protein interaction in the host cytoplasm was studied by use of crosslinkers. From treated leaves the crosstalk molecules and interaction proteins were separated on 1D SDS-PAGE and analyzed by MALDI-TOF-TOF analysis. The study is critical in understanding the molecular aspects of HEP’s adaption to phylloplane. The study revealed human enteric pathogens aggressively interact among themselves and resident bacteria. HEPs induced establishment of a signaling cascade through protein-protein interaction in the host cytoplasm. The study revealed that the adaptation of Human Enteric Pathogens on phylloplane of Solanum lycopersicum involves the establishment of complex molecular interaction between the microbe and the host including microbe-microbe interaction leading to an establishment of quorum sensing. The outcome will help in minimizing the HEP load on fresh farm produce, thereby curtailing incidences of food-borne diseases.

Keywords: crosslinkers, human enteric pathogens (HEPs), phylloplane, quorum sensing

Procedia PDF Downloads 275

Authors: Abdelouahab Diafat, Meribai Abdelmalek, Ahmed Bahloul

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phytoremediation is the use of plants to remove or degrade organic or inorganic contaminants from soil and water this work aims to study the potential effect of malva sylvestris for the phytoremediation of soils contaminated by Zn. plants were grown in pots containing soil artificially contaminated with Zn at concentrations of 100, 200, and 300 mg/kg. the results obtained show that the Zn concentrations used have a negative effect on the growth of this plant the search for the metal carried out by the technique of atomic absorption spectrometry shows that this plant accumulates a small quantity of this metal. it can be concluded that the malva sylvestris plant tolerates Zn contaminated soils but it is not considered as a zinc hyperaccumulator plant

Keywords: phytoremidiation, Zn-contaminated soils, Malva Sylvestris, phytoextraction

Procedia PDF Downloads 79

Authors: Sang Hun Park, Moung Young Lee, Su Min Yu, Hyun Sang Jo, Ji Hyeon Kim, Chul Gyu Song

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A near-infrared light source used as a light source in the fluorescence imaging system is suitable for use in real-time during the operation since it has no interference in surgical vision. However, fluorescence images do not have depth information. In this paper, we configured the device with the research on molecular imaging systems for monitoring thrombus imaging using fluorescence and photoacoustic. Fluorescence imaging was performed using a phantom experiment in order to search the exact location, and the Photoacoustic image was in order to detect the depth. Fluorescence image obtained when evaluated through current phantom experiments when the concentration of the contrast agent is 25μg / ml, it was confirmed that it looked sharper. The phantom experiment is has shown the possibility with the fluorescence image and photoacoustic image using an indocyanine green contrast agent. For early diagnosis of cardiovascular diseases, more active research with the fusion of different molecular imaging devices is required.

Keywords: fluorescence, photoacoustic, indocyanine green, carotid artery

Procedia PDF Downloads 598

Authors: Sh. Gofurov, O. Ismailova, U. Makhmanov, A. Kokhkharov

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The refractometric method has been used to determine optical properties of concentration features of aqueous solutions of ethanol, tetrahydrofuran and dimethylformamide at the room temperature. Changes in dielectric permittivity of aqueous solutions of ethanol, tetrahydrofuran and dimethylformamide in a wide range of concentrations (0÷1.0 molar fraction) have been studied using molecular dynamics method. The curves depending on the concentration of experimental data on excess refractive indices and excess dielectric permittivity were compared. It has been shown that stable heteromolecular complexes in binary solutions are formed in the concentration range of 0.3÷0.4 mole fractions. The real and complex part of dielectric permittivity was obtained from dipole-dipole autocorrelation functions of molecules. At the concentrations of C = 0.3 / 0.4 m.f. the heteromolecular structures with hydrogen bonds are formed. This is confirmed by the extremum values of excessive dielectric permittivity and excessive refractive index of aqueous solutions.

Keywords: refractometric method, aqueous solution, molecular dynamics, dielectric constant

Procedia PDF Downloads 259

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

Procedia PDF Downloads 178

Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major concern to fruit and vegetable production in the USA. Timely detection and identification of these agricultural pests facilitate the possibility of eradication from newly invaded areas. They spread primarily as larvae in infested fruits carried in commerce or personal baggage. Identification of larval stages to species level is difficult but necessary to determine pest loads and their pathways into the USA. The main focus of this study is the New World genus, Anastrepha. Many of its constituent taxa are pests of major economic importance. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed. Elongation factor 1 alpha sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level.

Keywords: anastrepha, diptera, elongation factor, fruit fly

Procedia PDF Downloads 203

Authors: Abhishek Kumar Gupta

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Atomistic Molecular Dynamics (MD) Simulations have been performed to study the effect of monovalent salt i.e. NaCl concentration (Cs) and chain degree of neutralization (f) on the structure and dynamics of anionic poly(methacrylic acid) (PMA) in dilute aqueous solutions. In the present study, the attention is to unveil the conformational structure, hydrogen-bonding, local polyion-counterion structure, h-bond dynamics, chain dynamics and thermodynamic enthalpy of solvation of a-PMA in dilute aqueous solutions as a function of salt concentration, Cs and f. The results have revealed that at low salt concentration, the conformational radius of gyration (Rg) increases and then decreases reaching a maximum in agreement with the reported light scattering experimental results. The Rg at f = 1 shows a continual decrease and acquire a plateau value at higher salt concentration in agreement with results obtained by light scattering experiments. The radial distribution functions between PMA, salt and water atoms has been computed with respect to atom and centre-of-mass to understand the intermolecular structure in detail. The results pertaining to PMA chain conformations and hydrogen bond autocorrelation function showcasing the h-bond dynamics will be presented. The results pertaining to chain dynamics will be presented. The results pertaining to counterion condensation on the PMA chain shows greater condensation of Na+ ions on to the carboxylate ions with increase in salt concentration. Moreover, the solvation enthalpy of the system as a function of salt concentration will be presented.

Keywords: conformations, molecular dynamics simulations, NaCl concentration, radial distribution functions

Procedia PDF Downloads 110

Authors: Jiahui Song

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The use of very high electric fields (~ 100kV/cm or higher) with pulse durations in the nanosecond range has been a recent development. The electric pulses have been used as tools to generate electroporation which has many biomedical applications. Most of the studies of electroporation have ignored possible thermal effects because of the small duration of the applied voltage pulses. However, it has been predicted membrane temperature gradients ranging from 0.2×109 to 109 K/m. This research focuses on thermal gradients that drives for electroporative enhancements, even though the actual temperature values might not have changed appreciably from their equilibrium levels. The dynamics of pore formation with the application of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. Different temperatures are assigned to various regions to simulate the appropriate temperature gradients. The GROMACS provides the force fields for the lipid membranes, which is taken to comprise of dipalmitoyl-phosphatidyl-choline (DPPC) molecules. The water model mimicks the aqueous environment surrounding the membrane. Velocities of water and membrane molecules are generated randomly at each simulation run according to a Maxwellian distribution. For statistical significance, a total of eight MD simulations are carried out with different starting molecular velocities for each simulation. MD simulation shows no pore is formed in a 10-ns snapshot for a DPPC membrane set at a uniform temperature of 295 K after a 0.4 V/nm electric field is applied. A nano-sized pore is clearly seen in a 10-ns snapshot on the same geometry but with the top and bottom membrane surfaces kept at temperatures of 300 and 295 K, respectively. For the same applied electric field, the formation of nanopores is clearly demonstrated, but only in the presence of a temperature gradient. MD simulation results show enhanced electroporative effects arising from thermal gradients. The study suggests the temperature gradient is a secondary driver, with the electric field being the primary cause for electroporation.

Keywords: nanosecond, electroporation, thermal effects, molecular dynamics

Procedia PDF Downloads 76

Authors: Catherine Vasnetsov, Victor Vasnetsov

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Context: Thermo-responsive polymers are materials that undergo significant changes in their physical properties in response to temperature changes. These polymers have gained significant attention in research due to their potential applications in various industries and medicine. However, the molecular mechanisms underlying their behavior are not well understood, particularly in relation to cosolvency, which is crucial for practical applications. Research Aim: This study aimed to theoretically investigate the phenomenon of cosolvency in long-chain polymers using the Flory-Huggins statistical-mechanical framework. The main objective was to understand the interactions between the polymer, solvent, and cosolvent under different conditions. Methodology: The research employed a combination of Monte Carlo computer simulations and advanced machine-learning methods. The Flory-Huggins mean field theory was used as the basis for the simulations. Spinodal graphs and ternary plots were utilized to develop an initial computer model for predicting polymer behavior. Molecular dynamic simulations were conducted to mimic real-life polymer systems. Machine learning techniques were incorporated to enhance the accuracy and reliability of the simulations. Findings: The simulations revealed that the addition of very low or very high volumes of cosolvent molecules resulted in smaller radii of gyration for the polymer, indicating poor miscibility. However, intermediate volume fractions of cosolvent led to higher radii of gyration, suggesting improved miscibility. These findings provide a possible microscopic explanation for the cosolvency phenomenon in polymer systems. Theoretical Importance: This research contributes to a better understanding of the behavior of thermo-responsive polymers and the role of cosolvency. The findings provide insights into the molecular mechanisms underlying cosolvency and offer specific predictions for future experimental investigations. The study also presents a more rigorous analysis of the Flory-Huggins free energy theory in the context of polymer systems. Data Collection and Analysis Procedures: The data for this study was collected through Monte Carlo computer simulations and molecular dynamic simulations. The interactions between the polymer, solvent, and cosolvent were analyzed using the Flory-Huggins mean field theory. Machine learning techniques were employed to enhance the accuracy of the simulations. The collected data was then analyzed to determine the impact of cosolvent volume fractions on the radii of gyration of the polymer. Question Addressed: The research addressed the question of how cosolvency affects the behavior of long-chain polymers. Specifically, the study aimed to investigate the interactions between the polymer, solvent, and cosolvent under different volume fractions and understand the resulting changes in the radii of gyration. Conclusion: In conclusion, this study utilized theoretical modeling and computer simulations to investigate the phenomenon of cosolvency in long-chain polymers. The findings suggest that moderate cosolvent volume fractions can lead to improved miscibility, as indicated by higher radii of gyration. These insights contribute to a better understanding of the molecular mechanisms underlying cosolvency in polymer systems and provide predictions for future experimental studies. The research also enhances the theoretical analysis of the Flory-Huggins free energy theory.

Keywords: molecular modelling, flory-huggins, cosolvency, stimuli-responsive polymers

Procedia PDF Downloads 67

Authors: F. Ambreen, A.Naheed

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Osteoarthritis (OA) is a degenerative disorder affecting millions of people worldwide. Nitric oxide (NO) was found to play a catabolic role in the development of osteoarthritis. It is a toxic free radical gas generated during the metabolism of L-arginine by the enzyme Nitric oxide synthase (NOS). Inducible Nitric Oxide Synthase (iNOS) is one of the isoform of NOS, and its overexpression leads to the excessive formation of NO that results in pathophysiological joint conditions. Several synthetic anti-inflammatory drugs and inhibitors are present to date, but all showed side effects and complications. Therefore, the pursuit of natural disease-modifying drugs remains a top priority. Curcumin is an active component of turmeric, and the past few decades have witnessed intense research devoted to the antioxidant and anti-inflammatory properties of curcumin. The present study focused on curcumin and its derivatives in the search for new iNOS inhibitors for the treatment of osteoarthritis. We conducted a molecular docking study on curcumin and its four derivatives; cyclocurcumin, tetrahydrocurcumin, demethoxycurcumin and curcumin monoglucoside with iNOS using CLC Drug discovery work bench 3.02. We selected two co-crystallized ligands for this study; tetrahydrobiopterin and N-omega-propyl-L-arginine present in complex with the enzyme iNOS. Results showed the best binding affinity of N-omega-propyl-L-arginine with cyclocurcumin and curcumin monoglucoside that exhibit binding energies of -65.2 kcal/mol and -68 kcal/mol respectively. Whereas with tetrahydrobiopterin, best binding scores of -64.7 kcal/mol and -62.2 kcal/mol were found with tetrahydrocurcumin and demethoxycurcumin respectively. This information could open doors of research for the designing of novel drugs using herbs such as curcumin for the treatment of inflammatory joint diseases.

Keywords: curcumin, iNOS, molecular docking, osteoarthritis

Procedia PDF Downloads 126