Search results for: molecular dynamics simulation.

Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

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Authors: Parimalah Velo, Ahmad Zakaria

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Introduction: Monte Carlo simulations of preclinical imaging systems allow opportunity to enable new research that could range from designing hardware up to discovery of new imaging application. The simulation system which could accurately model an imaging modality provides a platform for imaging developments that might be inconvenient in physical experiment systems due to the expense, unnecessary radiation exposures and technological difficulties. The aim of present study is to validate the Monte Carlo simulation of thyroid phantom imaging using Geant4-GATE for Siemen’s e-cam single head gamma camera. Upon the validation of the gamma camera simulation model by comparing physical characteristic such as energy resolution, spatial resolution, sensitivity, and dead time, the GATE simulation of thyroid phantom imaging is carried out. Methods: A thyroid phantom is defined geometrically which comprises of 2 lobes with 80mm in diameter, 1 hot spot, and 3 cold spots. This geometry accurately resembling the actual dimensions of thyroid phantom. A planar image of 500k counts with 128x128 matrix size was acquired using simulation model and in actual experimental setup. Upon image acquisition, quantitative image analysis was performed by investigating the total number of counts in image, the contrast of the image, radioactivity distributions on image and the dimension of hot spot. Algorithm for each quantification is described in detail. The difference in estimated and actual values for both simulation and experimental setup is analyzed for radioactivity distribution and dimension of hot spot. Results: The results show that the difference between contrast level of simulation image and experimental image is within 2%. The difference in the total count between simulation and actual study is 0.4%. The results of activity estimation show that the relative difference between estimated and actual activity for experimental and simulation is 4.62% and 3.03% respectively. The deviation in estimated diameter of hot spot for both simulation and experimental study are similar which is 0.5 pixel. In conclusion, the comparisons show good agreement between the simulation and experimental data.

Keywords: gamma camera, Geant4 application of tomographic emission (GATE), Monte Carlo, thyroid imaging

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Authors: Rizwan H. Khan, Saima Nusrat

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Despite the fact that amyloid associated neurodegenerative diseases and non-neuropathic systemic amyloidosis have allured the research endeavors, as no curative drugs have been proclaimed up till now except for symptomatic cure. Therapeutic compounds which can diminish or disaggregate such toxic oligomers and fibrillar species have been examined and more are on its way. In the present study, we had reported an extensive biophysical, microscopic and computational study, revealing that L-3, 4-dihydroxyphenylalanine (L-Dopa) possess undeniable potency to inhibit heat induced human lysozyme (HL) amyloid fibrillation and also retain the fibril disaggregating potential. L-Dopa interferes in the amyloid fibrillogenesis process by interacting hydrophobically and also by forming hydrogen bonds with the amino acid residues found in amyloid fibril forming prone region of HL as elucidated by molecular docking results. L-Dopa also disaggregates the mature amyloid fibrils into some unorganised species. Thus, L-Dopa and related compounds can work as a promising inhibitor for the therapeutic advancement prospective against systemic amyloidosis.

Keywords: amyloids, disaggregation, human lysozyme, molecular docking

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Authors: Yanyan Yu, Haiping Ding, Pengjun Chen, Yiou Sun

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Fault depth is an important parameter to be determined in ground motion simulation, and peak ground velocity (PGV) demonstrates good application prospect. Using numerical simulation method, the variations of distribution and peak value of near-fault PGV with different fault depth were studied in detail, and the reason of some phenomena were discussed. The simulation results show that the distribution characteristics of PGV of fault-parallel (FP) component and fault-normal (FN) component are distinctly different; the value of PGV FN component is much larger than that of FP component. With the increase of fault depth, the distribution region of the FN component strong PGV moves forward along the rupture direction, while the strong PGV zone of FP component becomes gradually far away from the fault trace along the direction perpendicular to the strike. However, no matter FN component or FP component, the strong PGV distribution area and its value are both quickly reduced with increased fault depth. The results above suggest that the fault depth have significant effect on both FN component and FP component of near-fault PGV.

Keywords: fault depth, near-fault, PGV, numerical simulation

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Authors: Sanghoon Bae, Hanju Cha

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Failed fuel detector (FFD) in research reactor is a very crucial instrument to detect the anomaly from failed fuels in the early stage around primary cooling system (PCS) outlet prior to the decay tank. FFD is considered as a mandatory sensor to ensure the integrity of fuel assemblies and mitigate the consequence from a failed fuel accident. For the effective function of FFD, the location of them should be determined by contemplating the effect from coolant flow around two outlets. For this, the analysis on computational flow dynamics (CFD) should be first performed how the coolant outlet flow including radioactive materials from failed fuels are mixed and discharged through the outlet plenum within certain seconds. The analysis result shows that the outlet flow is well mixed regardless of the position of failed fuel and ultimately illustrates the effect of detector location.

Keywords: computational flow dynamics (CFD), failed fuel detector (FFD), fresh fuel assembly (FFA), spent fuel assembly (SFA)

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Authors: Daniyar Seitenov, Nazim Mir-Nasiri

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Optimization of horizontal axis semi-exposed wind turbine has been performed using a shield protection that automatically protects the generator shaft at extreme wind speeds from over speeding, mechanical damage and continues generating electricity during the high wind speed conditions. A semi-exposed to wind generator has been designed and its structure has been described in this paper. The simplified point-force dynamic load model on the blades has been derived for normal and extreme wind conditions with and without shield involvement. Numerical simulation has been conducted at different values of wind speed to study the efficiency of shield application. The obtained results show that the maximum power generated by the wind turbine with shield does not exceed approximately the rated value of the generator, where shield serves as an automatic break for extreme wind speed values of 15 m/sec and above. Meantime the wind turbine without shield produced a power that is much larger than the rated value. The optimized horizontal axis semi-exposed wind turbine with shield protection is suitable for low and medium power generation when installed on the roofs of high rise buildings for harvesting wind energy. Wind shield works automatically with no power consumption. The structure of the generator with the protection, math simulation of kinematics and dynamics of power generation has been described in details in this paper.

Keywords: renewable energy, wind turbine, wind turbine optimization, high wind speed

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Authors: Alexander S. Andreev, Olga A. Peregudova

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In this paper, we propose a discrete tracking control of nonholonomic mobile robots with two degrees of freedom. The electro-mechanical model of a mobile robot moving on a horizontal surface without slipping, with two rear wheels controlled by two independent DC electric, and one front roal wheel is considered. We present back-stepping design based on the Euler approximate discrete-time model of a continuous-time plant. Theoretical considerations are verified by numerical simulation. The work was supported by RFFI (15-01-08482).

Keywords: actuator dynamics, back stepping, discrete-time controller, Lyapunov function, wheeled mobile robot

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Authors: Suyeb Ahmed Khan, Mahmood Mian

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Simulation plays an important role during all phases of the design and engineering of communications systems, from early stages of conceptual design through the various stages of implementation, testing, and fielding of the system. In the present paper, a simulation model has been constructed for the WCDMA system in order to evaluate the performance. This model describes multiusers effects and calculation of BER (Bit Error Rate) in 3G mobile systems using Simulink MATLAB 7.1. Gaussian Approximation defines the multi-user effect on system performance. BER has been analyzed with comparison between transmitting data and receiving data.

Keywords: WCDMA, simulations, BER, MATLAB

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Authors: Kiyoumars Roushangar, Shabnam Mirheidarian

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This study proposes metamodel approaches as a new intelligent technique for the explicit formulation of friction factors of water conveyance structures. For this purpose, experimental data of a movable bed flume with dune bed form were used. Analyzing the result clears the high capability of metamodel approaches (MNE= 0.05, R= 0.92) as a powerful tool for optimizing and explicit simulation of Manning's roughness coefficients of water conveyance structures compared to other nonlinear approaches.

Keywords: intelligent techniques, explicit simulation, roughness coefficient, water conveyance structure

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Authors: Marzieh Jafarzadeh, Fatemeh Rezaee

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Introduction: The effect of ionizing radiation on human health can be effective for genomic integrity and cell viability. It also increases the risk of cancer and malignancy. Therefore, X-ray behavior and absorption dose calculation are considered. One of the applicable tools for calculating and evaluating the absorption dose in human tissues is Monte Carlo simulation. Monte Carlo offers a straightforward way to simulate and integrate, and because it is simple and straightforward, Monte Carlo is easy to use. The Monte Carlo BEAMnrc code is one of the most common diagnostic X-ray simulation codes used in this study. Method: In one of the understudy hospitals, a certain number of CT scan images of patients who had previously been imaged were extracted from the hospital database. BEAMnrc software was used for simulation. The simulation of the head of the device with the energy of 0.09 MeV with 500 million particles was performed, and the output data obtained from the simulation was applied for phantom construction using CT CREATE software. The percentage of depth dose (PDD) was calculated using STATE DOSE was then compared with international standard values. Results and Discussion: The ratio of surface dose to depth dose (D/Ds) in the measured energy was estimated to be about 4% to 8% for bone and 3% to 7% for bone marrow. Conclusion: MC simulation is an efficient and accurate method for simulating bone marrow and calculating the absorbed dose.

Keywords: Monte Carlo, absorption dose, BEAMnrc, bone marrow

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: William J. Crowther, Conor Marsh

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Object-based flow simulation allows fast computation of arbitrarily complex aerodynamic models made up of simple objects with limited flow interactions. The proposed approach is universally applicable to objects made from arbitrarily scaled ellipsoid primitives at arbitrary aerodynamic attitude and angular rate. The use of a component-based aerodynamic modelling approach increases efficiency by allowing selective inclusion of different physics models at run-time and allows extensibility through the development of new models. Insight into the numerical stability of the model under first order fixed-time step integration schemes is provided by stability analysis of the drag component. The compute cost of model components and functions is evaluated and compared against numerical benchmarks. Model static outputs are verified against theoretical expectations and dynamic behaviour using falling plate data from the literature. The model is applied to a range of case studies to demonstrate the efficacy of its application in extensibility, ease of use, and low computational cost. Dynamically complex multi-body systems can be implemented in a transparent and efficient manner, and we successfully demonstrate large scenes with hundreds of objects interacting with diverse flow fields.

Keywords: aerodynamics, real-time simulation, low-order model, flight dynamics

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: Kunj Parikh, S. Bhattacharya, V. Natarajan

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TCAD numerical simulation is one of the most tried and tested powerful tools for designing devices in semiconductor foundries worldwide. It has also been used to explain conduction in organic thin films where the processing temperature is often enough to make homogeneous samples (often imperfect, but homogeneously imperfect). In this report, we have presented the results of TCAD simulation in multi-grain thin films. The work has addressed the inhomogeneity in one dimension, but can easily be extended to two and three dimensions. The effect of grain boundaries has mainly been approximated as barriers located at the junction between two adjacent grains. The effect of the value of grain boundary barrier, the bulk traps, and the measurement temperature have been investigated.

Keywords: polycrystalline thin films, space charge limited conduction, Technology Computer-Aided Design (TCAD) simulation, traps

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Authors: J. L. Bhagoria, Ajeet Kumar Giri

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A computational investigation of various flow characteristics with artificial roughness in the form of V-types discrete ribs, heated wall of rectangular duct for turbulent flow with Reynolds number range (3800-15000) and p/e (5 to 12) has been carried out with k-e turbulence model is selected by comparing the predictions of different turbulence models with experimental results available in literature. The current study evaluates thermal performance behavior, heat transfer and fluid flow behavior in a v shaped duct with discrete roughened ribs mounted on one of the principal wall (solar plate) by computational fluid dynamics software (Fluent 6.3.26 Solver). In this study, CFD has been carried out through designing 3-demensional model of experimental solar air heater model analysis has been used to perform a numerical simulation to enhance turbulent heat transfer and Reynolds-Averaged Navier–Stokes analysis is used as a numerical technique and the k-epsilon model with near-wall treatment as a turbulent model. The thermal efficiency enhancement because of selected roughness is found to be 16-24%. The result predicts a significant enhancement of heat transfer as compared to that of for a smooth surface with different P’ and various range of Reynolds number.

Keywords: CFD, solar collector, airheater, thermal efficiency

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Bruno Coelho Lima, Joao F.A. Martos, Paulo G. P. Toro, Israel S. Rego

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The shock tube is a ground-facility widely used in aerospace and aeronautics science and technology for studies on gas dynamic and chemical-physical processes in gases at high-temperature, explosions and dynamic calibration of pressure sensors. A shock tube in its simplest form is comprised of two separate tubes of equal cross-section by a diaphragm. The diaphragm function is to separate the two reservoirs at different pressures. The reservoir containing high pressure is called the Driver, the low pressure reservoir is called Driven. When the diaphragm is broken by pressure difference, a normal shock wave and non-stationary (named Incident Shock Wave) will be formed in the same place of diaphragm and will get around toward the closed end of Driven. When this shock wave reaches the closer end of the Driven section will be completely reflected. Now, the shock wave will interact with the boundary layer that was created by the induced flow by incident shock wave passage. The interaction between boundary layer and shock wave force the separation of the boundary layer. The aim of this paper is to make an analysis of influences of separation of the boundary layer in the reservoir pressure in the shock tube. A comparison among CDF (Computational Fluids Dynamics), experiments test and analytical analysis were performed. For the analytical analysis, some routines in Python was created, in the numerical simulations (Computational Fluids Dynamics) was used the Ansys Fluent, and the experimental tests were used T1 shock tube located in IEAv (Institute of Advanced Studies).

Keywords: boundary layer separation, moving shock wave, shock tube, transient simulation

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Authors: Yue Shuai Zhao, Rong Ping Shao, Wei Sun, Guo Hua Ren, Yong Wang, Li Chen Sun

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A large-scale cryopump (DN1250) used in large vacuum leak detecting system was designed and its performance experimentally investigated by Beijing Institute of Spacecraft Environment Engineering. The cryopump was cooled by four closed cycle helium refrigerators (two dual stage refrigerators and two single stage refrigerators). Detailed numerical analysis of the heat transfer in the first stage array and the second stage array were performed by using computational fluid dynamic method (CFD). Several design parameters were considered to find the effect on the temperature distribution and the cooldown time. The variation of thermal conductivity and heat capacity with temperature was taken into account. The thermal analysis method based on numerical techniques was introduced in this study, the heat transfer in the first stage array and the second stage cryopanel was carefully analyzed to determine important considerations in the thermal design of the cryopump. A performance test system according to the RNEUROP standards was built to test main performance of the cryopump. The experimental results showed that the structure of first stage array which was optimized by the method could meet the requirement of the cryopump well. The temperature of the cryopanel was down to 10K within 300 min, and the result of the experiment was accordant with theoretical analysis' conclusion. The test also showed that the pumping speed for N2 of the pump was up to 57,000 L/s, and the crossover was over than 300,000 Pa•L.

Keywords: cryopump, temperature distribution, thermal analysis, CFD Simulation

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Authors: Heval Serhat Uluk, Sam M. Dakka, Kuldeep Singh, Richard Jefferson-Loveday

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This paper will focus on the suitability of a trapped vortex combustor as a candidate for gas turbine combustor objectives to minimize pressure drop across the combustor and investigate aerodynamic performance. Non-reacting simulation of axisymmetric cavity trapped vortex combustors were simulated to investigate the pressure drop for various cavity aspect ratios of 0.3, 0.6, and 1 and for air mass flow rates of 14 m/s, 28 m/s, and 42 m/s. A numerical study of an axisymmetric trapped vortex combustor was carried out by using two-dimensional and three-dimensional computational domains. A comparison study was conducted between Reynolds Averaged Navier Stokes (RANS) k-ε Realizable with enhanced wall treatment and RANS k-ω Shear Stress Transport (SST) models to find the most suitable turbulence model. It was found that the k-ω SST model gives relatively close results to experimental outcomes. The numerical results were validated and showed good agreement with the experimental data. Pressure drop rises with increasing air mass flow rate, and the lowest pressure drop was observed at 0.6 cavity aspect ratio for all air mass flow rates tested, which agrees with the experimental outcome. A mixing enhancement study showed that 30-degree angle air injectors provide improved fuel-air mixing.

Keywords: aerodynamic, computational fluid dynamics, propulsion, trapped vortex combustor

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

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Complexes of ionic liquids with different heterocyclic-rings were synthesized by ion exchange reactions with pure salmon DNA. Ionic liquids (ILs) like 1-hexyl-3-methylimidazolium chloride, 1-butyl-4-methylpyridinium chloride and 1-ethyl-1-methylpyrrolidinium bromide were used. The ILs were built into helical state and confirmed by IR spectrometric techniques. Patterns of UV-Vis, photoluminescence, IR, and CD spectra indicated inclusion of small molecules into DNA structure. Molecular weight and radii of gyrations values of ILs-DNA complexes chains were established by HPSEC–MALLS–RI method. Modification DNA with 1-ethyl-1-methylpyrrolidinium bromide gives more uniform material and leads to elimination of high molecular weight chains. Thus, the incorporation DNA double helical structure with both 1-hexyl-3-methylimidazolium chloride and 1-butyl-4-methylpyridinium chloride exhibited higher molecular weight values. Scanning electron microscopy images indicate formation of nanofibre structures in all DNA complexes. Fluorescence depends strongly on the environment in which the chromophores are inserted and simultaneously on the molecular interactions with the biopolymer matrix. The most intensive emission was observed for DNA-imidazole ring complex. Decrease in intensity UV-Vis peak absorption is a consequence of a reduction in the spatial order of polynucleotide strands and provides different π–π stacking structure. Changes in optical properties confirmed by spectroscopy methods make DNA-ILs complexes potential biosensor applications.

Keywords: biopolymers, biosensors, cationic surfactant, DNA, DNA-gels

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Authors: Hariti Rafika, Fekih Malika, Saighi Mohamed

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During the period storage of liquefied natural gas, stability is necessarily affected by natural convection along the walls of the tank with thermal insulation is not perfectly efficient. In this paper, we present the numerical simulation of heat transfert by natural convection double diffusion,in unsteady laminar regime in a storage tank. The storage tank contains a liquefied natural gas (LNG) in its gaseous phase. Fluent, a commercial CFD package, based on the numerical finite volume method, is used to simulate the flow. The gas is just on the surface of the liquid phase. This numerical simulation allowed us to determine the temperature profiles, the stream function, the velocity vectors and the variation of the heat flux density in the vapor phase in the LNG storage tank volume. The results obtained for a general configuration, by numerical simulation were compared to those found in the literature.

Keywords: numerical simulation, natural convection, heat gains, storage tank, liquefied natural gas

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Authors: A. Kudrev

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The duplex Poly(A)-Poly(U) denaturation in an aqueous solutions in mixtures with the tetracationic MeTMPyP4 (Me = 2H, Zn(II); TMPyP4 is 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin), was investigated by monitoring the changes in the UV-Vis absorbance spectrum with increasing temperatures from 20°С to 70°С (рН 7.0, I=0.15M). The absorbance data matrices were analyzed with a versatile chemometric procedure that provides the melting profile (distribution of species) and the pure spectrum for each chemical species present along the heating experiment. As revealed by the increase of Tm, the duplex structure was stabilized by these porphyrins. The values of stabilization temperature ΔTm in the presence of these porphyrins are relatively large, 1.2-8.4 °C, indicating that the porphyrins contribute differently in stabilizing the duplex Poly(A)-Poly(U) structure. Remarkable is the fact that the porphyrin TMPyP4 was less effective in the stabilization of the duplex structure than the metalloporphyrin Zn(X)TMPyP4 which suggests that metallization play an important role in porphyrin-RNA binding. Molecular Dynamics Simulations has been used to illustrate melting of the duplex dsRNA bound with a porphyrin molecule.

Keywords: melting, Poly(A)-Poly(U), TMPyP4, Zn(X)TMPyP4

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Authors: A. R. Momeninezhad

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Erosion of Slurry Pumps in Related Industries, is one of the major costs in their production process. Many factories in extractive industries try to find ways to diminish this cost. In this paper, we consider the flow pattern modifications by geometric variations made of numerical simulation of flow inside pump casing, which is one of the most important parts analyzed for erosion. The mentioned pump is a cyclone centrifugal slurry pump, which is operating in Sarcheshmeh Copper Industries in Kerman-Iran, named and tagged as HM600 cyclone pump. Simulation shows many improvements in local wear information and situations for better and more qualified design of casing shape and impeller position, before and after geometric corrections. By theory of liquid-solid two-phase flow, the local wear defeats are analyzed and omitted.

Keywords: flow pattern, slurry pump, simulation, wear

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Authors: Jérémy Philippe, Lucien Baldas, Batoul Attar, Jean-Charles Mare

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The proposed communication deals with the research and development of a rotary direct-drive servo valve for aerospace applications. A key challenge of the project is to downsize the electromagnetic torque motor by reducing the torque required to drive the rotary spool. It is intended to optimize the spool and the sleeve geometries by combining a Computational Fluid Dynamics (CFD) approach with commercial optimization software. The present communication addresses an important phase of the project, which consists firstly of gaining confidence in the simulation results. It is well known that the force needed to pilot a sliding spool valve comes from several physical effects: hydraulic forces, friction and inertia/mass of the moving assembly. Among them, the flow force is usually a major contributor to the steady-state (or Root Mean Square) driving torque. In recent decades, CFD has gradually become a standard simulation tool for studying fluid-structure interactions. However, in the particular case of high-pressure valve design, the authors have experienced that the calculated overall hydraulic force depends on the parameterization and options used to build and run the CFD model. To solve this issue, the authors have selected the standard case of the linear spool valve, which is addressed in detail in numerous scientific references (analytical models, experiments, CFD simulations). The first CFD simulations run by the authors have shown that the evolution of the equivalent discharge coefficient vs. Reynolds number at the metering orifice corresponds well to the values that can be predicted by the classical analytical models. Oppositely, the simulated flow force was found to be quite different from the value calculated analytically. This drove the authors to investigate minutely the influence of the studied domain and the setting of the CFD simulation. It was firstly shown that the flow recirculates in the inlet and outlet channels if their length is not sufficient regarding their hydraulic diameter. The dead volume on the uncontrolled orifice side also plays a significant role. These examples highlight the influence of the geometry of the fluid domain considered. The second action was to investigate the influence of the type of mesh, the turbulence models and near-wall approaches, and the numerical solver and discretization scheme order. Two approaches were used to determine the overall hydraulic force acting on the moving spool. First, the force was deduced from the momentum balance on a control domain delimited by the valve inlet and outlet and the spool walls. Second, the overall hydraulic force was calculated from the integral of pressure and shear forces acting at the boundaries of the fluid domain. This underlined the significant contribution of the viscous forces acting on the spool between the inlet and outlet orifices, which are generally not considered in the literature. This also emphasized the influence of the choices made for the implementation of CFD calculation and results analysis. With the step-by-step process adopted to increase confidence in the CFD simulations, the authors propose a set of best practices and recommendations for the efficient use of CFD to design high-pressure spool valves.

Keywords: computational fluid dynamics, hydraulic forces, servovalve, rotary servovalve

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Authors: Michel Wakim, Rodrigo Rivera Tinoco

Abstract:

Supersonic ejector is an economical device that use high pressure vapor to compress a low pressure vapor without any rotating parts or external power sources. Entrainment ratio is a major characteristic of the ejector performance, so the ejector performance is highly dependent on its geometry. The aim of this paper is to design ejector geometry, based on pre-specified operating conditions, and to study the flow behavior inside the ejector by using computational fluid dynamics ‘CFD’ by using ‘ANSYS FLUENT 15.0’ software. In the first section; 1-D mathematical model is carried out to predict the ejector geometry. The second part describes the flow behavior inside the designed model. CFD is the most reliable tool to reveal the mixing process at different parts of the supersonic turbulent flow and to study the effect of the geometry on the effective ejector area. Finally, the results show the effect of the geometry on the entrainment ratio.

Keywords: computational fluids dynamics, ejector, entrainment ratio, geometry optimization, performance

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Authors: Fouzia Perveen, Rumana Qureshi

Abstract:

The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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Authors: Isha Sharawat, R. P. Dahiya, T. R. Sreekrishnan

Abstract:

One of the environmental challenges in India is urban wastewater management as regulations and infrastructural development has not kept pace with the urbanization and growing population. The quality of life of people is also improving with the rapid growth of the gross domestic product. This has contributed to the enhancement in the per capita water requirement and consumption. More domestic water consumption generates more wastewater. The scarcity of potable water is making the situation quite serious, and water supply has to be regulated in most parts of the country during summer. This requires elaborate and concerted efforts to efficiently manage the water resources and supply systems. In this article, a system dynamics modelling approach is used for estimating the water demand and wastewater generation in a district headquarter city of North India. Projections are made till the year 2035. System dynamics is a software tool used for formulation of policies. On the basis of the estimates, policy scenarios are developed for sustainable development of water resources in conformity with the growing population. Mitigation option curtailing the water demand and wastewater generation include population stabilization, water reuse and recycle and water pricing. The model is validated quantitatively, and sensitivity analysis tests are carried out to examine the robustness of the model.

Keywords: system dynamics, wastewater, water pricing, water recycle

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Authors: Igor B. Sivaev

Abstract:

Design of molecular machines is an extraordinary growing and very important area of research that it was recognized by awarding Sauvage, Stoddart and Feringa the Nobel Prize in Chemistry in 2016 'for the design and synthesis of molecular machines'. Based on the type of motion being performed, molecular machines can be divided into two main types: molecular motors and molecular switches. Molecular switches are molecules or supramolecular complexes having bistability, i.e., the ability to exist in two or more stable forms, among which may be reversible transitions under external influence (heating, lighting, changing the medium acidity, the action of chemicals, exposure to magnetic or electric field). Molecular switches are the main structural element of any molecular electronics devices. Therefore, the design and the study of molecules and supramolecular systems capable of performing mechanical movement is an important and urgent problem of modern chemistry. There is growing interest in molecular switches and other devices of molecular electronics based on transition metal complexes; therefore choice of suitable stable organometallic unit is of great importance. An example of such unit is bis(dicarbollide) complexes of transition metals [3,3’-M(1,2-C₂B₉H₁₁)₂]ⁿ⁻. The control on the ligand rotation in such complexes can be reached by introducing substituents which could provide stabilization of certain rotamers due to specific interactions between the ligands, on the one hand, and which can participate as Lewis bases in complex formation with external metals resulting in a change in the rotation angle of the ligands, on the other hand. A series of isomeric methyl sulfide derivatives of cobalt bis(dicarbollide) complexes containing methyl sulfide substituents at boron atoms in different positions of the pentagonal face of the dicarbollide ligands [8,8’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻, rac-[4,4’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[4,7’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ were synthesized by the reaction of CoCl₂ with the corresponding methyl sulfide carborane derivatives [10-MeS-7,8-C₂B₉H₁₁)₂]⁻ and [10-MeS-7,8-C₂B₉H₁₁)₂]⁻. In the case of asymmetrically substituted cobalt bis(dicarbollide) complexes the corresponding rac- and meso-isomers were successfully separated by column chromatography as the tetrabutylammonium salts. The compounds obtained were studied by the methods of ¹H, ¹³C, and ¹¹B NMR spectroscopy, single crystal X-ray diffraction, cyclic voltammetry, controlled potential coulometry and quantum chemical calculations. It was found that in the solid state, the transoid- and gauche-conformations of the 8,8’- and 4,4’-isomers are stabilized by four intramolecular CH···S(Me)B hydrogen bonds each one (2.683-2.712 Å and 2.709-2.752 Å, respectively), whereas gauche-conformation of the 4,7’-isomer is stabilized by two intramolecular CH···S hydrogen bonds (2.699-2.711 Å). The existence of the intramolecular CH·S(Me)B hydrogen bonding in solutions was supported by the 1H NMR spectroscopy. These data are in a good agreement with results of the quantum chemical calculations. The corresponding iron and nickel complexes were synthesized as well. The reaction of the methyl sulfide derivatives of cobalt bis(dicarbollide) with various labile transition metal complexes results in rupture of intramolecular hydrogen bonds and complexation of the methyl sulfide groups with external metal. This results in stabilization of other rotational conformation of cobalt bis(dicarbollide) and can be used in design of molecular switches. This work was supported by the Russian Science Foundation (16-13-10331).

Keywords: molecular switches, NMR spectroscopy, single crystal X-ray diffraction, transition metal bis(dicarbollide) complexes, quantum chemical calculations

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Authors: Ali M. EL-Soll

Abstract:

Physical properties of Sarir waxy crude oil was investigated, pour-point was determined using ASTM D-79 procedure, paraffin content and carbon number distribution of the paraffin was determined using gas liquid Chromatography(GLC), polymeric additives were prepared and their structures were confirmed using IR spectrophotometer. The molecular weight and molecular weigh distribution of these additives were determined by gel permeation chromatography (GPC). the performance of the synthesized additives as pour-point depressants was evaluated, for the mentioned crude oil.

Keywords: sarir, waxy, crude, pour point, depressants

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