Search results for: molecular junction

Authors: R. O. Ocaya, J. J. Terblans

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The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C language, molecular dynamics, simulation, embedded atom method

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Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

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Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

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Authors: Bahattin Abay

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Thin film of polycyclic aromatic hydrocarbon rubrene, C₄₂H₂₈ (5,6,11,12-tetraphenyltetracene), has been surfaced on Moderately Doped (MD) n-InP substrate as an interfacial layer by means of spin coating technique for the electronic modification of Au/MD n-InP structure. Ex situ annealing has been carried out at 150 °C for three minutes under a brisk flow of nitrogen for the better adhesion of the deposited film with the substrate surface. Room temperature electrical characterization has been performed on the C₄₂H₂₈/MD n-InP hybrid junctions by current-voltage (I-V) and capacitance-voltage (C-V) measurement in the dark. It has been seen that the C₄₂H₂₈/MD n-InP structure demonstrated extraordinary rectifying behavior. An effective barrier height (BH) as high as 0.743 eV, along with an ideality factor very close to unity (n=1.203), has been achieved for C₄₂H₂₈/n-InP organic/inorganic device. A thin C₄₂H₂₈ interfacial layer between Au and MD n-InP also reduce the reverse leakage current by almost four orders of magnitude and enhance the BH about 0.278 eV. This good performance of the device is ascribed to the passivation effect of organic interfacial layer between Au and n-InP. By using C-V measurement, in addition, the value of BH of the C₄₂H₂₈/n-InP organic/inorganic hybrid junctions have been obtained as 0.796 eV. It has been seen that both of the BH value (0.743 and 0.796 eV) for the organic/inorganic hybrid junction obtained I-V and C-V measurement, respectively are significantly larger than that of the conventional Au/n-InP structure (0.465 and 0.503 eV). It was also seen that the device had good sensitivity to the light under 100 mW/cm² illumination conditions. The obtained results indicated that modification of the interfacial potential barrier for Metal/n-InP junctions might be attained using polycyclic aromatic hydrocarbon thin interlayer C₄₂H₂₈.

Keywords: I-V and C-V measurements, heterojunction, n-InP, rubrene, surface passivation

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Authors: R. Hocine, A. Boudjemai, A. Amrani, K. Belkacemi

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Temperature rising is a negative factor in almost all systems. It could cause by self heating or ambient temperature. In solar photovoltaic cells this temperature rising affects on the behavior of cells. The ability of a PV module to withstand the effects of periodic hot-spot heating that occurs when cells are operated under reverse biased conditions is closely related to the properties of the cell semi-conductor material. In addition, the thermal effect also influences the estimation of the maximum power point (MPP) and electrical parameters for the PV modules, such as maximum output power, maximum conversion efficiency, internal efficiency, reliability, and lifetime. The cells junction temperature is a critical parameter that significantly affects the electrical characteristics of PV modules. For practical applications of PV modules, it is very important to accurately estimate the junction temperature of PV modules and analyze the thermal characteristics of the PV modules. Once the temperature variation is taken into account, we can then acquire a more accurate MPP for the PV modules, and the maximum utilization efficiency of the PV modules can also be further achieved. In this paper, the three-Dimensional Transmission Line Matrix (3D-TLM) method was used to map the surface temperature distribution of solar cells while in the reverse bias mode. It was observed that some cells exhibited an inhomogeneity of the surface temperature resulting in localized heating (hot-spot). This hot-spot heating causes irreversible destruction of the solar cell structure. Hot spots can have a deleterious impact on the total solar modules if individual solar cells are heated. So, the results show clearly that the solar cells are capable of self-generating considerable amounts of heat that should be dissipated very quickly to increase PV module's lifetime.

Keywords: thermal effect, conduction, heat dissipation, thermal conductivity, solar cell, PV module, nodes, 3D-TLM

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Authors: Nouf Alharbi

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

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

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Authors: Gerardo Arias, Richard Wall, Jamie Stevens

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

Keywords: calliphoridae, molecular evolution, myiasis, obligate parasitism

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Authors: Jiahui Song

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The use of high-intensity, nanosecond electric pulses has been a recent development in biomedical. High-intensity (∼100 kV/cm), nanosecond duration-pulsed electric fields have been shown to induce cellular electroporation. This will lead to an increase in transmembrane conductivity and diffusive permeability. These effects will also alter the electrical potential across the membrane. The applications include electrically triggered intracellular calcium release, shrinkage of tumors, and temporary blockage of the action potential in nerves. In this research, the dynamics of pore formation with the presence of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations show pore formation occurs for a pulse with the amplitude of 0.5V/nm at 1ns at temperature 316°K. Also increasing temperatures facilitate pore formation. When the temperature is increased to 323°K, pore forms at 0.75ns with the pulse amplitude of 0.5V/nm. For statistical significance, a total of eight MD simulations are carried out with different starting molecular velocities for each simulation. Also, actual experimental observations are compared against MD simulation results.

Keywords: molecular dynamics, high-intensity, nanosecond, electroporation

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Authors: Emma K. Sales, Nilda G. Butardo

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

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

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Authors: Surabhi Agrawal Kohli, Sunita Gupta, Esha Khanuja, Parul Garg, P. Gupta

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Background: Adenomyosis is a common gynaecological condition that affects the menstruating women. Uterine enlargement, dysmenorrhoea, and menorrhagia are regarded as the cardinal clinical symptoms of adenomyosis. Classically it was thought, compared with ultrasonography, when adenomyosis is suspected, MRI enables more accurate diagnosis of the disease. Materials and Methods: 172 subjects were enrolled after an informed consent that had complaints of HMB, dyspareunia, dysmenorrhea, and chronic pelvic pain. Detailed history of the enrolled subjects was taken, followed by a clinical examination. These patients were then subjected to TVS where myometrial echo texture, presence of myometrial cysts, blurring of endomyometrial junction was noted. MRI was followed which noted the presence of junctional zone thickness and myometrial cysts. After hysterectomy, histopathological diagnosis was obtained. Results: 78 participants were analysed. The mean age was 44.2 years. 43.5% had parity of 4 or more. heavy menstrual bleeding (HMB) was present in 97.8% and dysmenorrhea in 93.48 % of HPE positive patient. Transvaginal sonography (TVS) and MRI had a sensitivity of 89.13% and 80.43%, specificity of 90.62% and 84.37%, positive likelihood ratio of 9.51 and 5.15, negative likelihood ratio of 0.12 and 0.23, positive predictive value of 93.18% and 88.1%, negative predictive value of 85.29% and 75% and a diagnostic accuracy of 89.74% and 82.5%. Comparison of sensitivity (p=0.289) and specificity (p=0.625) showed no statistically significant difference between TVS and MRI. Conclusion: Prevalence of 30.23%. HMB with dysmenorrhoea and chronic pelvic pain helps in diagnosis. TVS (Endomyometrial junction blurring) is both sensitive and specific in diagnosing adenomyosis without need for additional diagnostic tool. Both TVS and MRI are equally efficient, however because of certain additional advantages of TVS over MRI, it may be used as the first choice of imaging. MRI may be used additionally in difficult cases as well as in patients with existing co-pathologies.

Keywords: adenomyosis, heavy menstrual bleeding, MRI, TVS

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Authors: Vivek Garg, Brajendra S. Sengar, Gaurav Siddharth, Nisheka Anadkat, Amitesh Kumar, Shailendra Kumar, Shaibal Mukherjee

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CuInGaSe (CIGSe) is the dominant thin film solar cell technology. The band alignment of Buffer/CIGSe interface is one of the most crucial parameters for solar cell performance. In this article, the valence band offset (VBOff) and conduction band offset (CBOff) values of Cu(In0.70Ga0.30)Se/ 1 at.% Ga: Mg0.25Zn0.75O (GMZO) heterojunction, grown by dual ion beam sputtering system (DIBS), are calculated to understand the carrier transport mechanism at the heterojunction for the realization of all sputtered buffer-less solar cells. To determine the valence band offset (VBOff), ∆E_V at GMZO/CIGSe heterojunction interface, the standard method based on core-level photoemission is utilized. The value of ∆E_V can be evaluated by considering common core-level peaks. In our study, the values of (Valence band onset)VBOn, obtained by linear extrapolation method for GMZO and CIGSe films are calculated to be 2.86 and 0.76 eV. In the UPS spectra peak positions of Se 3d is observed in UPS spectra at 54.82 and 54.7 eV for CIGSe film and GMZO/CIGSe interface respectively, while the peak position of Mg 2p is observed at 50.09 and 50.12 eV for GMZO and GMZO/CIGSe interface respectively. The optical band gap of CIGSe and GMZO are obtained from absorption spectra procured from spectroscopic ellipsometry are 1.26 and 3.84 eV respectively. The calculated average values of ∆E_v and ∆E_C are estimated to be 2.37 and 0.21 eV, respectively, at room temperature. The calculated positive conduction band offset termed as a spike at the absorber junction is the required criterion for the high-efficiency solar cells for the efficient charge extraction from the junction. So we can conclude that the above study confirms GMZO thin films grown by the dual ion beam sputtering system are the suitable candidate for the CIGSe thin films based ultra-thin buffer-less solar cells. We investigated the band-offset properties at the GMZO/CIGSe heterojunction to verify the suitability of the GMZO for the realization of the buffer-less solar cells. The calculated average values of ∆E_V and ∆E_C are estimated to be 2.37 and 0.21 eV, respectively, at room temperature. The calculated positive conduction band offset termed as a spike at the absorber junction is the required criterion for the high-efficiency solar cells for the efficient charge extraction from the junction. So we can conclude that the above study confirms GMZO thin films grown by the dual ion beam sputtering system are the suitable candidate for the CIGSe thin films based ultra-thin buffer-less solar cells. Acknowledgment: We are thankful to DIBS, EDX, and XRD facility equipped at Sophisticated Instrument Centre (SIC) at IIT Indore. The authors B.S.S and A.K acknowledge CSIR and V.G acknowledge UGC, India for their fellowships. B.S.S is thankful to DST and IUSSTF for BASE Internship Award. Prof. Shaibal Mukherjee is thankful to DST and IUSSTF for BASE Fellowship and MEITY YFRF award. This work is partially supported by DAE BRNS, DST CERI, and DST-RFBR Project under India-Russia Programme of Cooperation in Science and Technology. We are thankful to Mukul Gupta for SIMS facility equipped at UGC-DAE Indore.

Keywords: CIGSe, DIBS, GMZO, solar cells, UPS

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Authors: Z. Bayat

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

Keywords: DFT, adamantane, QSAR, Kovat

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Authors: Seyyed Feisal Asbaghian Namin, Reza Pilafkan, Mahmood Kaffash Irzarahimi

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TThis paper considers vibration of single-layered graphene sheets using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), an open source software, is used to obtain fundamental frequencies. On the other hand, governing equations are derived using nonlocal elasticity and first order shear deformation theory (FSDT) and solved using generalized differential quadrature method (GDQ). The small-scale effect is applied in governing equations of motion by nonlocal parameter. The effect of different side lengths, boundary conditions and nonlocal parameter are inspected for aforementioned methods. Results are obtained from MD simulations is compared with those of the nonlocal elasticity theory to calculate appropriate values for the nonlocal parameter. The nonlocal parameter value is suggested for graphene sheets with various boundary conditions. Furthermore, it is shown that the nonlocal elasticity approach using classical plate theory (CLPT) assumptions overestimates the natural frequencies.

Keywords: graphene sheets, molecular dynamics simulations, fundamental frequencies, nonlocal elasticity theory, nonlocal parameter

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

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Authors: Roussin Lontio Fomekong, John Lambi Ngolui, Arnaud Dercorte

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Current years have seen increased interest in the synthesis of p/n metal oxide-based nano composites and their great potential in advanced applications, such as opto electronics, photo catalysis and gas sensors. The superior functional performances of the system combining p-type and n-types semiconducting oxyde in comparison to the corresponding single-phase metal oxides are mainly ascribed to the build-up of an inner electric field at the p/n junction interface.

Keywords: nanocomposite, semiconductors, p-n, heterojunction

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Authors: Muhammet Baldan, Emel Timuçin

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

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

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Authors: Ncoza Dlova, Tivani Mashamba-Thompson

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Garcinia livingstonei (Clusiaceae) extracts, morelloflavone- 7″- sulphate and sargaol were shown to be effective against hyper-pigmentation through inhibition of tyrosinase enzyme, in vitro . The aim of this study is to elucidate the structural mechanism through which morelloflavone- 7″- sulphate and sargaol binds human tyrosinase. Implementing a homology model to construct a tyrosinase model using the crystal structure of a functional unit from Octopus hemocyanin (PDB: 1JS8) as a reference template enabled us to create a human tyrosinase model. Molecular dynamics and binding free energy calculations were optimized to enable molecular dynamics simulation of the copper dependent inhibitors. Results show the importance of the hydrogen bond formation morelloflavone- 7″- sulphate and sargaol between compound and active site residues. Both complexes demonstrated the metallic coordination between compound and arginine residue as well as copper ions within the active site. The comprehensive molecular insight gained from this study should be vital in understanding the binding mechanism morelloflavone- 7″- sulphate and sargaol. Moreover, these results will assist in the design of novel of metal ion dependent enzyme inhibitors as potential anti-hyper-pigmentation disorder therapies.

Keywords: hyper-pigmentation disorders, dyschromia African skin, morelloflavone- 7″- sulphate, sagoal

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Authors: Adel A. Ghoneim

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Air conditioning devices are substantially utilized in the summer months, as a result maximum loads in Kuwait take place in these intervals. Peak energy consumption are usually more expensive to satisfy compared to other standard power sources. The primary objective of the current work is to enhance the performance of high concentrated photovoltaic (HCPV) systems in an attempt to minimize peak power usage in Kuwait using HCPV modules. High concentrated PV multi-junction solar cells provide a promising method towards accomplishing lowest pricing per kilowatt-hour. Nevertheless, these cells have various features that should be resolved to be feasible for extensive power production. A single diode equivalent circuit model is formulated to analyze multi-junction solar cells efficiency in Kuwait weather circumstances taking into account the effects of both the temperature and the concentration ratio. The diode shunt resistance that is commonly ignored in the established models is considered in the present numerical model. The current model results are successfully validated versus measurements from published data to within 1.8% accuracy. Present calculations reveal that the single diode model considering the shunt resistance provides accurate and dependable results. The electrical efficiency (η) is observed to increase with concentration to a specific concentration level after which it reduces. Implementing grid systems is noticed to increase with concentration to a certain concentration degree after which it decreases. Employing grid connected HCPV systems results in significant peak load reduction.

Keywords: grid connected, high concentrated photovoltaic systems, peak load, solar cells

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Authors: Mouna Baassi, Mohamed Moussaoui, Hatim Soufi, Sanchaita RajkhowaI, Ashwani Sharma, Subrata Sinha, Said Belaaouad

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Human Immunodeficiency Virus type 1 protease (HIV-1 PR) is one of the most challenging targets of antiretroviral therapy used in the treatment of AIDS-infected people. The performance of protease inhibitors (PIs) is limited by the development of protease mutations that can promote resistance to the treatment. The current study was carried out using statistics and bioinformatics tools. A series of thirty-three compounds with known enzymatic inhibitory activities against HIV-1 protease was used in this paper to build a mathematical model relating the structure to the biological activity. These compounds were designed by software; their descriptors were computed using various tools, such as Gaussian, Chem3D, ChemSketch and MarvinSketch. Computational methods generated the best model based on its statistical parameters. The model’s applicability domain (AD) was elaborated. Furthermore, one compound has been proposed as efficient against HIV-1 protease with comparable biological activity to the existing ones; this drug candidate was evaluated using ADMET properties and Lipinski’s rule. Molecular Docking performed on Wild Type and Mutant Type HIV-1 proteases allowed the investigation of the interaction types displayed between the proteases and the ligands, Darunavir (DRV) and the new drug (ND). Molecular dynamics simulation was also used in order to investigate the complexes’ stability, allowing a comparative study of the performance of both ligands (DRV & ND). Our study suggested that the new molecule showed comparable results to that of Darunavir and may be used for further experimental studies. Our study may also be used as a pipeline to search and design new potential inhibitors of HIV-1 proteases.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation.

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

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

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

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

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

Keywords: android, augmented reality, chemical learning, geometry

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Authors: Abdul Majid, Alia Jabeen, Nimra Zulifqar

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

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

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Authors: Jungkyun Im

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Nonsteroidal anti-inflammatory drugs (NSAIDs) are effective for relieving pain and reducing inflammation. They are nonselective inhibitors of two isoforms of COX, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), and thereby inhibiting the production of hormone-like lipid compounds such as, prostaglandins and thromboxanes which cause inflammation, pain, fever, platelet aggregation, etc. In addition, recently there are many research articles reporting the neuroprotective effect of NSAIDs in neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). However, the clinical use of NSAIDs in these diseases is limited by low brain distribution. Therefore, in order to assist the in-depth investigation on the pharmaceutical mechanism of flurbiprofen in neuroprotection and to make flurbiprofen a more potent drug to prevent or alleviate neurodegenerative diseases, delivery of flurbiprofen to brain should be effective and sufficient amount of flurbiprofen must penetrate the BBB thus gaining access into the patient’s brain. We have recently developed several types of guanidine-rich molecular carriers with high molecular weights and good water solubility that readily cross the blood-brain barrier (BBB) and display efficient distributions in the mouse brain. The G8 (having eight guanidine groups) molecular carrier based on D-sorbitol was found to be very effective in delivering anticancer drugs to a mouse brain. In the present study, employing the same molecular carrier, we prepared the flurbiprofen conjugate and studied its BBB permeation by mouse tissue distribution study. Flurbiprofen was attached to a molecular carrier with a fluorescein probe and multiple terminal guanidiniums. The conjugate was found to internalize into live cells and readily cross the BBB to enter the mouse brain. Our novel synthetic flurbiprofen conjugate will hopefully delivery NSAIDs into brain, and is therefore applicable to the neurodegenerative diseases treatment or prevention.

Keywords: flurbiprofen, drug delivery, molecular carrier, organic synthesis

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Authors: Tsu-Hsu Yen

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The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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Authors: Amit Chaudhary, B. S. Yadav, P. K. Maurya, A. M., S. Srivastava, S. Singh, A. Mani

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Cold shock protein A (CspA) is major cold inducible protein present in Escherichia coli. The protein is involved in stabilizing secondary structure of RNA by working as chaperone during cold temperature. Two RNA binding motifs play key role in the stabilizing activity. This study aimed to investigate implications of low temperature on structure and RNA binding activity of E. coli CspA. Molecular dynamics simulations were performed to compare the stability of the protein at 37°C and 10 °C. The protein was mutated at RNA binding motifs and docked with RNA to assess the stability of both complexes. Results suggest that CspA as well as CspA-RNA complex is more stable at low temperature. It was also confirmed that RNP1 and RNP2 play key role in RNA binding.

Keywords: CspA, homology modelling, mutation, molecular dynamics simulation

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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: Riccardo Zanni, Maria Galvez-Llompart, Ramon Garcia-Domenech, Jorge Galvez

Abstract:

Biopesticides, such as naturally occurring chemicals, pheromones, fungi, bacteria and insect predators are often a winning choice in crop protection because of their environmental friendly profile. They are considered to have lower toxicity than traditional pesticides. After almost a century of pesticides use, resistances to traditional insecticides are wide spread, while those to bioinsecticides have raised less attention, and resistance management is frequently neglected. This seems to be a crucial mistake since resistances have already occurred for many marketed biopesticides. With an eye to the future, we present here a selection of new natural occurring chemicals as potential bioinsecticides. The molecules were selected using a consolidated mathematical paradigm called molecular topology. Several QSAR equations were depicted and subsequently applied for the virtual screening of hundred thousands molecules of natural origin, which resulted in the selection of new potential bioinsecticides. The most innovative aspect of this work does not only reside in the importance of the identification of new molecules overcoming biopesticides’ resistances, but on the possibility to promote shared knowledge in the field of green chemistry through this unique in silico discipline named molecular topology.

Keywords: green chemistry, QSAR, molecular topology, biopesticide

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Authors: G. R. Hashemi Tabar, G. R. Razmi, F. Mirshekar

Abstract:

Echinococcus granulosus have ten strains from G1 to G9. Each strain is related to special intermediated host. The morphology, epidemiology, treatment and control in these strains are different. There are many morphological and molecular methods to differentiate of Echinococcus strains. However, using both methods were provided better information about identification of each strain. The aim of study was to identify Echinococcus granulosus strain of hydrated cysts in slaughtered sheep using morphological and molecular methods in Mashhad area. In the present study, the infected liver and lung with hydatid cysts were collected and transferred to laboratory. The hydatid cyst liquid was extracted and morphological characters of rostellar hook protosclocies were measured using micrometer ocular. The total length of large blade length of large hooks, total length of small and blade length of small hooks, and number of hooks per protoscolex were 23± 0.3μm, 11.7±0.5 μm, 19.3±1.1 μm,8±1.1 and 33.7±0.7 μm, respectively. In molecular section of the study, DNA each samples was extracted with MBST Kit and development of PCR using special primers (EgF, EgR) which amplify fragment of ITS1 gen. The PCR product was digested with Bsh1236I enzyme. Based on pattern of PCR-RLFP results (four band forming), G1, G2 and G3 strain of Echinococcus granulosus were obtained. Differentiation of three strains was done using sequencing analysis and G1 strain was diagnosed. The agreement between the molecular results with morphometric characters of rosetellar hook was confirmed the presence of G1 strain of Echinococcus in the slaughtered sheep of Mashhad area.

Keywords: Echinococcus granulosus, Hydatid cyst, PCR, sheep

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Authors: Anna Yagodnitsyna, Alexander Kovalev, Artur Bilsky

Abstract:

The efficiency of certain technological processes in two-phase microfluidics such as emulsion production, nanomaterial synthesis, nitration, extraction processes etc. depends on two-phase flow regimes in microchannels. For practical application in chemistry and biochemistry it is very important to predict the expected flow pattern for a large variety of fluids and channel geometries. In the case of immiscible liquids, the plug flow is a typical and optimal regime for chemical reactions and needs to be predicted by empirical data or correlations. In this work flow patterns of immiscible liquid-liquid flow in a rectangular microchannel with T-junction are investigated. Three liquid-liquid flow systems are considered, viz. kerosene – water, paraffin oil – water and castor oil – paraffin oil. Different flow patterns such as parallel flow, slug flow, plug flow, dispersed (droplet) flow, and rivulet flow are observed for different velocity ratios. New flow pattern of the parallel flow with steady wavy interface (serpentine flow) has been found. It is shown that flow pattern maps based on Weber numbers for different liquid-liquid systems do not match well. Weber number multiplied by Ohnesorge number is proposed as a parameter to generalize flow maps. Flow maps based on this parameter are superposed well for all liquid-liquid systems of this work and other experiments. Plug length and velocity are measured for the plug flow regime. When dispersed liquid wets channel walls plug length cannot be predicted by known empirical correlations. By means of particle tracking velocimetry technique instantaneous velocity fields in a plug flow regime were measured. Flow circulation inside plug was calculated using velocity data that can be useful for mass flux prediction in chemical reactions.

Keywords: flow patterns, hydrodynamics, liquid-liquid flow, microchannel

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Authors: Merouane Salhi, Toufik Zebbiche, Omar Abada

Abstract:

When the stagnation pressure of perfect gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with this pressure. The gas does not remain perfect. Its state equation change and it becomes a real gas. In this case, the effects of molecular size and inter molecular attraction forces intervene to correct the state equation. The aim of this work is to show and discuss the effect of stagnation pressure on supersonic thermo dynamical, physical and geometrical flow parameters, to find a general case for real gas. With the assumptions that Berthelot’s state equation accounts for molecular size and inter molecular force effects, expressions are developed for analyzing supersonic flow for thermally and calorically imperfect gas lower than the dissociation molecules threshold. The designs parameters for supersonic nozzle like thrust coefficient depend directly on stagnation parameters of the combustion chamber. The application is for air. A computation of error is made in this case to give a limit of perfect gas model compared to real gas model.

Keywords: supersonic flow, real gas model, Berthelot’s state equation, Simpson’s method, condensation function, stagnation pressure

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Authors: Zeeshan Ahmed, Ajinkya Sarode, Pratik Basarkar, Atul Bhargav, Debjyoti Banerjee

Abstract:

The use of CO₂ in oil recovery and in CO₂ capture and storage is gaining traction in recent years. These applications involve heat transfer between CO₂ and the base fluid, and hence, there arises a need to improve the thermal conductivity of CO₂ to increase the process efficiency and reduce cost. One way to improve the thermal conductivity is through nanoparticle addition in the base fluid. The nanofluid model in this study consisted of copper (Cu) nanoparticles in varying concentrations with CO₂ as a base fluid. No experimental data are available on thermal conductivity of CO₂ based nanofluid. Molecular dynamics (MD) simulations are an increasingly adopted tool to perform preliminary assessments of nanoparticle (NP) fluid interactions. In this study, the effect of the formation of a nanolayer (or molecular layering) at the gas-solid interface on thermal conductivity is investigated using equilibrium MD simulations by varying NP diameter and keeping the volume fraction (1.413%) of nanofluid constant to check the diameter effect of NP on the nanolayer and thermal conductivity. A dense semi-solid fluid layer was seen to be formed at the NP-gas interface, and the thickness increases with increase in particle diameter, which also moves with the NP Brownian motion. Density distribution has been done to see the effect of nanolayer, and its thickness around the NP. These findings are extremely beneficial, especially to industries employed in oil recovery as increased thermal conductivity of CO₂ will lead to enhanced oil recovery and thermal energy storage.

Keywords: copper-CO2 nanofluid, molecular dynamics simulation, molecular interfacial layer, thermal conductivity

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