Search results for: molecular topology

Authors: Tsu-Hsu Yen

Abstract:

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: Auwal Mustapha Imam

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The aim of the energy management system is to monitor and control utilization, access, optimize and manage energy availability. This can be realized through real-time analyses and energy sources and loads data control in a predictive way. Smart-home monitoring and control provide convenience and cost savings by controlling appliances, lights, thermostats and other loads. There may be different categories of loads in the various homes, and the homeowner may wish to control access to solar-generated energy to protect the storage from draining completely. Controlling the power system operation by managing the converter output power and controlling how it feeds the appliances will satisfy the residential load demand. The Internet of Things (IoT) provides an attractive technological platform to connect the two and make home automation and domestic energy utilization easier and more attractive. This paper presents the use of IoT-based control topology to monitor and control power distribution and consumption by DC loads connected to single-input multiple outputs (SIMO) DC-DC converter, thereby reducing leakages, enhancing performance and reducing human efforts. A SIMO converter was first developed and integrated with the IoT/Raspberry Pi control topology, which enables the user to monitor and control power scheduling and load forecasting via an Android app.

Keywords: flyback, converter, DC-DC, photovoltaic, SIMO

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

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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: Merouane Salhi, Toufik Zebbiche, Omar Abada

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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

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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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Authors: Ömer Tamer, Davut Avcı, Yusuf Atalay

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Novel picolinate complex of manganese(II) ion, [Mn(pic)2] [pic: picolinate or 2-pyridinecarboxylate], was prepared and fully characterized by single crystal X-ray structure determination. The manganese(II) complex was characterized by FT-IR, FT-Raman and UV–Vis spectroscopic techniques. The C=O, C=N and C=C stretching vibrations were found to be strong and simultaneously active in IR and spectra. In order to support these experimental techniques, density functional theory (DFT) calculations were performed at Gaussian 09W. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, the calculated data show that the predicted geometries can reproduce the structural parameters. The molecular modeling and calculations of IR, Raman and UV-vis spectra were performed by using DFT levels. Nonlinear optical (NLO) properties of synthesized complex were evaluated by the determining of dipole moment (µ), polarizability (α) and hyperpolarizability (β). Obtained results demonstrated that the manganese(II) complex is a good candidate for NLO material. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was analyzed using natural bond orbital (NBO) analysis. The highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) which is also known the frontier molecular orbitals were simulated, and obtained energy gap confirmed that charge transfer occurs within manganese(II) complex. Molecular electrostatic potential (MEP) for synthesized manganese(II) complex displays the electrophilic and nucleophilic regions. From MEP, the the most negative region is located over carboxyl O atoms while positive region is located over H atoms.

Keywords: DFT, picolinate, IR, Raman, nonlinear optic

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

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This study considers the selection of the most suitable in silico molecular descriptors that could be used for s-triazine pesticides characterization. Suitable descriptors among topological, geometrical and physicochemical are used for quantitative structure-retention relationships (QSRR) model establishment. Established models were obtained using linear regression (LR) and multiple linear regression (MLR) analysis. In this paper, MLR models were established avoiding multicollinearity among the selected molecular descriptors. Statistical quality of established models was evaluated by standard and cross-validation statistical parameters. For detection of similarity or dissimilarity among investigated s-triazine pesticides and their classification, principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used and gave similar grouping. This study is financially supported by COST action TD1305.

Keywords: chemometrics, classification analysis, molecular descriptors, pesticides, regression analysis

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Authors: Maedeh Rahimnejad, Bahman Vahidi, Bahman Ebrahimi Hoseinzadeh, Fatemeh Yazdian, Puria Motamed Fath, Roghieh Jamjah

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Introduction: The intensive labor and high cost of developing new vehicles for controlled drug delivery highlights the need for a change in their discovery process. Computational models can be used to accelerate experimental steps and control the high cost of experiments. Methods: In this work, to better understand the interaction of anti-cancer drug and the nanocarrier with the cell membrane, we have done molecular dynamics simulation using NAMD. We have chosen paclitaxel for the drug molecule and dipalmitoylphosphatidylcholine (DPPC) as a natural phospholipid nanocarrier. Results: Next, center of mass (COM) between molecules and the van der Waals interaction energy close to the cell membrane has been analyzed. Furthermore, the simulation results of the paclitaxel interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane have been compared. Discussion: Analysis by molecular dynamics (MD) showed that not only the energy between the nanocarrier and the cell membrane is low, but also the center of mass amount decreases in the nanocarrier and the cell membrane system during the interaction; therefore they show significantly better interaction in comparison to the individual drug with the cell membrane.

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

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Authors: Malcolm Dinovitzer, Calvin Miller, Adam Hacker, Gabriel Wong, Zach Annen, Padmassun Rajakareyar, Jordan Mulvihill, Mostafa S.A. ElSayed

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The research work presented in this paper is developed by the Blended Wing Body (BWB) Unmanned Aerial Vehicle (UAV) team, a fourth-year capstone project at Carleton University Department of Mechanical and Aerospace Engineering. Here, a clean sheet UAV with BWB configuration is designed and optimized using Multiscale Design Optimization (MSDO) approach employing lattice materials taking into consideration design for additive manufacturing constraints. The BWB-UAV is being developed with a mission profile designed for surveillance purposes with a minimum payload of 1000 grams. To demonstrate the design methodology, a single design loop of a sample rib from the airframe is shown in details. This includes presentation of the conceptual design, materials selection, experimental characterization and residual thermal stress distribution analysis of additively manufactured materials, manufacturing constraint identification, critical loads computations, stress analysis and design optimization. A dynamic turbulent critical load case was identified composed of a 1-g static maneuver with an incremental Power Spectral Density (PSD) gust which was used as a deterministic design load case for the design optimization. 2D flat plate Doublet Lattice Method (DLM) was used to simulate aerodynamics in the aeroelastic analysis. The aerodynamic results were verified versus a 3D CFD analysis applying Spalart-Allmaras and SST k-omega turbulence to the rigid UAV and vortex lattice method applied in the OpenVSP environment. Design optimization of a single rib was conducted using topology optimization as well as MSDO. Compared to a solid rib, weight savings of 36.44% and 59.65% were obtained for the topology optimization and the MSDO, respectively. These results suggest that MSDO is an acceptable alternative to topology optimization in weight critical applications while preserving the functional requirements.

Keywords: blended wing body, multiscale design optimization, additive manufacturing, unmanned aerial vehicle

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Authors: M. Zemouli, K. Amara, M. Elkeurti, Y. Benallou

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We present the molecular dynamic simulations results of the structural and dynamical properties of the zinc-blende GaBi over a wide range of temperature (300-1000) K. Our simulation where performed in the framework of the three-body Tersoff potential, which accurately reproduces the lattice constants and elastic constants of the GaBi. A good agreement was found between our calculated results and the available theoretical data of the lattice constant, the bulk modulus and the cohesive energy. Our study allows us to predict the thermodynamic properties such as the specific heat and the lattice thermal expansion. In addition, this method allows us to check its ability to predict the phase transition of this compound. In particular, the transition pressure to the rock-salt phase is calculated and the results are compared with other available works.

Keywords: Gallium compounds, molecular dynamics simulations, interatomic potential thermodynamic properties, structural phase transition

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Authors: Jungyeol Hong, Dongjoo Park

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The primary purpose of this study is to develop a methodological framework to predict daily subway ridership at a station-level and to examine the association between subway ridership and bus demand incorporating commercial business facility in the vicinity of each subway station. The socio-economic characteristics, land-use, and built environment as factors may have an impact on subway ridership. However, it should be considered not only the endogenous relationship between bus and subway demand but also the characteristics of commercial business within a subway station’s sphere of influence, and integrated transit network topology. Regarding a statistical approach to estimate subway ridership at a station level, therefore it should be considered endogeneity and heteroscedastic issues which might have in the subway ridership prediction model. This study focused on both discovering the impacts of bus demand, commercial business characteristics, and network topology on subway ridership and developing more precise subway ridership estimation accounting for its statistical bias. The spatial scope of the study covers entire Seoul city in South Korea and includes 243 stations with the temporal scope set at twenty-four hours with one-hour interval time panels each. The data for subway and bus ridership was collected Seoul Smart Card data from 2015 and 2016. Three-Stage Least Square(3SLS) approach was applied to develop daily subway ridership model as capturing the endogeneity and heteroscedasticity between bus and subway demand. Independent variables incorporating in the modeling process were commercial business characteristics, social-economic characteristics, safety index, transit facility attributes, and dummies for seasons and time zone. As a result, it was found that bus ridership and subway ridership were endogenous each other and they had a significantly positive sign of coefficients which means one transit mode could increase another transportation mode’s ridership. In other words, two transit modes of subway and bus have a mutual relationship instead of the competitive relationship. The commercial business characteristics are the most critical dimension among the independent variables. The variables of commercial business facility rate in the paper containing six types; medical, educational, recreational, financial, food service, and shopping. From the model result, a higher rate in medical, financial buildings, shopping, and food service facility lead to increment of subway ridership at a station, while recreational and educational facility shows lower subway ridership. The complex network theory was applied for estimating integrated network topology measures that cover the entire Seoul transit network system, and a framework for seeking an impact on subway ridership. The centrality measures were found to be significant and showed a positive sign indicating higher centrality led to more subway ridership at a station level. The results of model accuracy tests by out of samples provided that 3SLS model has less mean square error rather than OLS and showed the methodological approach for the 3SLS model was plausible to estimate more accurate subway ridership. Acknowledgement: This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Science and ICT (2017R1C1B2010175).

Keywords: subway ridership, bus ridership, commercial business characteristic, endogeneity, network topology

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Authors: Koo-Yeon Kim, Eun-Hye Kim, Tae-Il Son

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Epidermal Growth Factor (EGF, Mw=6,045) has been reported to have high efficiency of wound repair and anti-wrinkle effect. However, the half-life of EGF in the body is too short to exert the biological activity effectively when applied in free form. Growth Factors can be stabilized by immobilization with carbohydrates from thermal and proteolytic degradation. Low molecular weight chitosan (LMCS) and its derivate prepared by hydrogen peroxide has high solubility. LM6A6DC was successfully prepared as a reactive carbohydrate for the stabilization of EGF by the reactions of LMCS with alkalization, tosylation, azidation and reduction. The structure of LM6A6DC was confirmed by FT-IR, 1H NMR and elementary analysis. For enhancing the stability of free EGF, EGF was attached with LM6A6DC by using water-soluble carbodiimide. EGF-LM6A6DC conjugates did not show any cytotoxicity on the Normal Human Dermal Fibroblast(NHDF) 3T3 proliferation at least under 100 ㎍/㎖. In the result, it was considered that LM6A6DC is suitable to immobilize of growth factor.

Keywords: epidermal growth factor (EGF), low-molecular-weight chitosan, immobilization

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Authors: M. Dehestani, M. Ghasemi-Kooch

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In this work, adsorption of chlorophylls a and b pigments in aqueous solution on the inner and outer surfaces of single-walled carbon nanotube (SWCNT) has been studied using molecular dynamics simulation. The linear interaction energy algorithm has been used to calculate the binding free energy. The results show that the adsorption of two pigments is fine on the both positions. Although there is the close similarity between these two pigments, their interaction with the nanotube is different. This result is useful to separate these pigments from one another. According to interaction energy between the pigments and carbon nanotube, interaction between these pigments-SWCNT on the inner surface is stronger than the outer surface. The interaction of SWCNT with chlorophylls phytol tail is stronger than the interaction of SWCNT with porphyrin ring of chlorophylls.

Keywords: adsorption, chlorophyll, interaction, molecular dynamics simulation, nanotube

Procedia PDF Downloads 201

Authors: M. Zemouli, K. Amara, M. Elkeurti, Y. Benallou

Abstract:

We present a theoretical study of the structural, elastic and thermodynamic properties of the zinc-blende AlBi for a wide temperature range. The simulation calculation is performed in the framework of the molecular dynamics method using the three-body Tersoff potential which reproduces provide, with reasonable accuracy, the lattice constants and elastic constants. Our results for the lattice constant, the bulk modulus and cohesive energy are in good agreement with other theoretical available works. Other thermodynamic properties such as the specific heat and the lattice thermal expansion can also be predicted. In addition, this method allows us to check its ability to predict the phase transition of this compound. In particular, the transition pressure to the rock-salt phase is calculated and the results are compared with other available works.

Keywords: aluminium compounds, molecular dynamics simulations, interatomic potential, thermodynamic properties, structural phase transition

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Authors: D. S. Malatesh, K. J. Ananda, C. Ansar Kamran, K. Ganesh Udupa

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Dirofilaria repens is a mosquito-borne filarioid nematode of dogs and other carnivores and accidentally affects humans. D. repens is reported in many countries, including India. Subcutaneous dirofilariosis caused by D. repens is a zoonotic disease, widely distributed throughout Europe, Asia, and Africa, with higher prevalence reported in dogs from Sri Lanka (30-60%), Iran (61%) and Italy (21-25%). Dirofilariasis in dogs was diagnosed by detection of microfilariae in blood. Identification of different Dirofilaria species was done by using molecular methods like polymerase chain reaction (PCR). Even though many researchers reported molecular evidence of D. repens across India, to our best knowledge there is no data available on molecular diagnosis of D. repens in dogs and its zoonotic implication in Karnataka state a southern state in India. The aim of the present study was to identify the Dirofilaria species occurring in dogs from Karnataka, India. Out of 310 samples screened for the presence of microfilariae using traditional diagnostic methods, 99 (31.93%) were positive for the presence of microfilariae. Based on the morphometry, the microfilariae were identified as D. repens. For confirmation of species, the samples were subjected to PCR using pan filarial primers (DIDR-F1, DIDR-R1) for amplification of internal transcribed spacer region 2 (ITS2) of the ribosomal DNA. The PCR product of 484 base pairs on agarose gel was indicative of D. repens. Hence, a single PCR reaction using pan filarial primers can be used to differentiate filarial species found in dogs. The present study confirms that dirofilarial species occurring in dogs from Karnataka is D. repens and further sequencing studies are needed for genotypic characterization of D. repens.

Keywords: Dirofilaria repens, molecular characterization, polymerase chain reaction, Karnataka, India

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Authors: Boda Sreenivas, Lyathakula Ravindranath, Kanugula Srishailam, Byru Venkatram Reddy

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Extensive research into the optimized structure and molecular properties of 3-Flouro-2-methylbenzoicacid(FMB), 3-Chloro-2-methoxybenzoicacid (CMB), and 3-Bromo-2-methylbenzoicacid (BMB) was carried out using FT-IR, FT-Raman and UV-Visible spectra, as well as theoretically using the DFT approach with B3LYPfunctional in conjunction with 6-311++G(d,p) basis set. The optimized structure was determined by evaluating torsional scans about free rotation bonds. Structure parameters, harmonic vibrational frequencies, potential energy distribution(PED), and infrared and Raman intensities were computed. The computational results from the DFT approach, such asFT-IR, FT-Raman, and UV-Visible spectra, were compared with the experimental results and found good agreement. Observed and calculated frequencies agreed with an rms error of 8.42, 6.60, and 6.95 cm-1 for FMB, CMB, and BMB, respectively. Unambiguous vibrational assignments were made for all fundamentals using PED and eigenvectors. The electronic HOMO-LUMO, H-bonding, and strong conjugative interactions across different molecular entities are discussed using experimental and simulated Ultraviolet-Visible spectra. The title molecules' molecular properties such as dipole moment, mean polarizability, and first-order hyperpolarizability, were calculated to study their non-linear optical (NLO) behavior. The chemical reactivity descriptors and mapped electrostatic surface potential (MESP) were also evaluated. Natural bond orbital (NBO) analysis was used to examine the stability of molecules resulting from hyperconjugative interactions and charge delocalization.

Keywords: ftir/raman spectra, DFT, NLO, homo-lumo, NBO, halogenated benzoic acids

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Authors: M. Dehestani, F. Kamali, M. Klantari Pour, L. Zeidabadi-Nejad

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Chemical bonding between polyethylene glycol (PEG) with pharmaceutical proteins called pegylation is one of the most effective methods of improving the pharmacological properties. The covalent attachment of polyethylene glycol (PEG) to proteins will increase their pharmacologic properties. For the formation of a combination of pegylated protein should first be activated PEG and connected to the protein. Interferons(IFNs) are a family of cytokines which show antiviral effects in front of the biological and are responsible for setting safety system. In this study, the nature and properties of the interaction between active positions of IFNs and polyethylene glycol have been investigated using molecular dynamics simulation. The main aspect of this theoretical work focuses on the achievement of valuable data on the reaction pathways of PEG-IFNs and the transition state energy. Our results provide a new perspective on the interactions, chemical properties and reaction pathways between IFNs and PEG.

Keywords: interaction, interferons, molecular dynamics simulation, polyethylene glycol

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Authors: Mahdi Asghari

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The cavitation phenomenon is the formation and production of micro-bubbles and eventually the bursting of the micro-bubbles inside the liquid fluid, which results in localized high pressure and temperature, causing physical and chemical fluid changes. This pressure and temperature are predicted to be 2000 atmospheres and 5000 °C, respectively. As a result of small bubbles bursting from this process, temperature and pressure increase momentarily and locally, so that the intensity and magnitude of these temperatures and pressures provide the energy needed to break the molecular bonds of heavy compounds such as fuel oil. In this paper, we study the theory of cavitation and the methods of cavitation production by acoustic and hydrodynamic methods and the necessary mechanical equipment and reactors for industrial application of the hydrodynamic cavitation method to break down the molecular bonds of the fuel oil and convert it into useful and economical products.

Keywords: Cavitation, Hydrodynamic Cavitation, Cavitation Reactor, Fuel Oil

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Authors: A. Rezaei, M. Huisman, W. Van Paepegem

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Atomic interactions in molecular systems are mainly studied by particle mechanics. Nevertheless, researches have also put on considerable effort to simulate them using continuum methods. In early 2000, simple equivalent finite element models have been developed to study the mechanical properties of carbon nanotubes and graphene in composite materials. Afterward, many researchers have employed similar structural simulation approaches to obtain mechanical properties of nanostructured materials, to simplify interface behavior of fiber-reinforced composites, and to simulate defects in carbon nanotubes or graphene sheets, etc. These structural approaches, however, are limited to small deformations due to complicated local rotational coordinates. This article proposes a method for the finite element simulation of molecular mechanics. For ease in addressing the approach, here it is called Structural Finite Element Molecular Modeling (SFEMM). SFEMM method improves the available structural approaches for large deformations, without using any rotational degrees of freedom. Moreover, the method simulates molecular conformation, which is a big advantage over the previous approaches. Technically, this method uses nonlinear multipoint constraints to simulate kinematics of the atomic multibody interactions. Only truss elements are employed, and the bond potentials are implemented through constitutive material models. Because the equilibrium bond- length, bond angles, and bond-torsion potential energies are intrinsic material parameters, the model is independent of initial strains or stresses. In this paper, the SFEMM method has been implemented in ABAQUS finite element software. The constraints and material behaviors are modeled through two Fortran subroutines. The method is verified for the bond-stretch, bond-angle and bond-torsion of carbon atoms. Furthermore, the capability of the method in the conformation simulation of molecular structures is demonstrated via a case study of a graphene sheet. Briefly, SFEMM builds up a framework that offers more flexible features over the conventional molecular finite element models, serving the structural relaxation modeling and large deformations without incorporating local rotational degrees of freedom. Potentially, the method is a big step towards comprehensive molecular modeling with finite element technique, and thereby concurrently coupling an atomistic domain to a solid continuum domain within a single finite element platform.

Keywords: finite element, large deformation, molecular mechanics, structural method

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Authors: Bakhtishod Matmuratov, Sakhiba Madraximova, Rakhmat Esanov, Alimjan Matchanov

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Studies have been performed to obtain complexes of glycyrrhizic acid and kinetins in a 2:1 ratio. The complex of glycyrrhizic acid and kinetins in a 2:1 ratio was considered evidence of the formation of a molecular complex by determining the molecular masses using chromato-mass spectroscopy and analyzing the IR spectra.

Keywords: monoammonium salt of glycyrrhizic acid, glycyrrhizic acid, supramolecular complex, isomolar series, IR spectroscopy

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Authors: M. Shahina, K. Fakruddin, C. M. Subhan, S. Rangappa

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In this work, two mixtures with equal concentrations of 1) 4ꞌ-(6-(4-(pentylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(hexyloxy) benzylidene) amino) phenyl 4-butoxy benzoate and 2) 4ꞌ - (6-(4-(hexylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(octyloxy) benzylidene) amino) phenyl 4-butoxy benzoate, have been prepared. The transition temperature and optical texture are observed by using thermal microscopy. Density and birefringence studies are carried out on the above liquid crystalline mixtures. Using density and refractive indices data, the molecular polarizabilities are evaluated by using well-known Vuks and Neugebauer models. The molecular polarizability is also evaluated theoretically by Lippincott δ function model. The results reveal that the polarizability values are same in both experimental and theoretical methods.

Keywords: liquid crystals, optical textures, transition temperature, birefringence, polarizability

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Authors: Noureddine Benharkat, Abdelkader Chouaih, Nourdine Boukabcha

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A thiourea derivative compound was synthesized and subjected to structural analysis using single-crystal X-ray diffraction (XRD). The crystallographic data unveiled its crystallization in the P21/c space group within the monoclinic system. Examination of the dihedral angles indicated a notable non-planar structure. To support and interpret these resulats, density functional theory (DFT) calculations were conducted utilizing the B3LYP functional along with a 6–311 G (d, p) basis set. Additionally, to assess the contribution of intermolecular interactions, Hirshfeld surface analysis and 2D fingerprint plots were employed. Various types of interactions, whether weak intramolecular or intermolecular, within a molecule can significantly impact its stability. The distinctive signature of non-covalent interactions can be detected solely through electron density analysis. The NCI-RDG analysis was employed to investigate both repulsive and attractive van der Waals interactions while also calculating the energies associated with intermolecular interactions and their characteristics. Additionally, a molecular docking study was studied to explain the structure-activity relationship, revealing that the title compound exhibited an affinity energy of -6.8 kcal/mol when docked with B-DNA (1BNA).

Keywords: computational chemistry, density functional theory, crystallography, molecular docking, molecular structure, powder x-ray diffraction, single crystal x-ray diffraction

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Authors: Sumit Sharma, Rakesh Chandra, Pramod Kumar, Navin Kumar

Abstract:

Molecular dynamics (MD) simulation has been used to study the effect of carbon nanofiber (CNF) volume fraction (Vf) and aspect ratio (l/d) on mechanical properties of CNF reinforced polypropylene (PP) composites. Materials Studio 5.5 has been used as a tool for finding the modulus and damping in composites. CNF composition in PP was varied by volume from 0 to 16%. Aspect ratio of CNF was varied from l/d=5 to l/d=100. To the best of the knowledge of the authors, till date there is no study, either experimental or analytical, which predict damping for CNF-PP composites at the nanoscale. Hence, this will be a valuable addition in the area of nanocomposites. Results show that with only 2% addition by volume of CNF in PP, E11 increases 748%. Increase in E22 is very less in comparison to the increase in E11. With increase in CNF aspect ratio (l/d) till l/d=60, the longitudinal loss factor (η11) decreases rapidly. Results of this study have been compared with those available in literature.

Keywords: carbon nanofiber, elasticity, mechanical properties, molecular dynamics

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Authors: Alya Harichane, Abderraouf Achour, Abdelbaki Benmounah

Abstract:

The main difficulty encountered in the formulation of high-performance concrete (HPC) consists in choosing the most efficient cement-superplasticizer pair allowing to obtain maximum water reduction, good workability of the concrete in the fresh state, and very good mechanical resistance in the hardened state. The aim of this work is to test the efficiency of three polycarboxylate ether-based superplasticizers (PCE) marketed in Algeria with CEMI 52.5 R cement and to study the effect of chemical structure of PCE on zeta potential, rheological and mechanical properties of cement pastes. The property of the polymers in cement was tested by a Malvern Zetasizer 2000 apparatus and VT 550 viscometer. Results showed that the zeta potential and its rheological properties are related to the molecular weight and the density carboxylic of PCE. The PCE with a moderate molecular weight and the highest carboxylic groups had the best dispersion (high value of zeta potential) and lowest viscosity. The effect of the chemical structure of PCEs on mechanical properties is evaluated by the formulation of cement mortar with these PCEs. The result shows that there is a correlation between the zeta potential of polymer and the compressive strength of cement paste.

Keywords: molecular weight, polycarboxylate-ether superplasticizer, rheology, zeta potential

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Authors: Chaudhari S. G., Saxena, S.

Abstract:

We systematically and quantitatively investigated the effect of glucose as a model of natural molecular crowding agent on the structure and thermodynamics of Watson-Crick base paired three duplexes (named as D1, D2 and D3) of different base compositions and lengths. Structural analyses demonstrated that duplexes (D1 and D2) folded into B-form with different cations in the absence and presence of glucose while duplex (D3) folded into mixed A and B-form. Moreover, we demonstrated that the duplex was more stable in the absence of glucose, and marginally destabilized in its presence because glucose act as a weak structure breaker on the tetrahedral network of water. In the absence of glucose, the values of ΔG°25 for duplex (D1) were -13.56, -13.76, -12.46, and -12.36 kcal/mol, for duplex (D2) were -13.64, -12.93, -12.86, and -12.30 kcal/mol, for duplex (D3) were -10.05, -11.76, -9.91, -9.70 kcal/mol in the presence of Na+, K+, Na+ + Mg++ and K+ + Mg++ respectively. At high concentration of glucose (1:10000), there was increase in ΔG°25 for duplex (D1) -12.47, -12.37, -11.96, -11.55 kcal/mol, for duplex (D2) -12.37, -11.47, -11.98, -11.01 kcal/mol and for duplex (D3) -8.47, -9.17, -9.16, -8.66 kcal/mol. Our results provide the information that structure and stability of DNA duplex depends on the structure of molecular crowding agent present in its close vicinity. In this study, I have taken the hydration of simple sugar as an essential model for understanding interactions between hydrophilic groups and interfacial water molecules and its effect on hydrogen bonded DNA duplexes. On the basis of these relatively simple building blocks I hope to gain some insights for understanding more generally the properties of sugar–water–salt systems with DNA duplexes.

Keywords: natural molecular crowding, DNA Duplex, structure of DNA, bioengineering and life sciences

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

Abstract:

Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

Abstract:

The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory

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Authors: Mahdi Golriz

Abstract:

The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

Procedia PDF Downloads 124