Search results for: molecular dynamics

Authors: Wang-Xi Fan, Yi Ding, Zhong-Dan Tu, Kuo-Shien Huang, Chao-Ming Huang, Jen-Taut Yeh

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Original and/or functionalized activated nanocarbon particles with a quoted specific surface area of 100, 500, 1000 and 1400 m2/g, respectively, were used to investigate the influence of specific surface areas of activated nanocarbon on ultra drawing and ultimate tensile properties of ultrahigh molecular weight polyethylene (UHMWPE), UHMWPE/activated nanocarbon and UHMWPE/ functionalized activated nanocarbon fibers. The specific surface areas of well dispersed functionalized activated nanocarbon in UHMWPE/functionalized activated nanocarbon fibers can positively affect their ultra drawing, orientation, ultimate tensile properties and “micro-fibril” characteristics. Excellent orientation and ultimate tensile properties of UHMWPE/nanofiller fibers can be prepared by ultra drawing the UHMWPE/functionalized activated nanocarbon as-prepared fibers with optimal contents and compositions of functionalized activated nanocarbon. The ultimate tensile strength value of the best prepared UHMWPE/functionalized activated nanocarbon drawn fiber reached 8.0 GPa, which was about 2.86 times of that of the best-prepared UHMWPE drawn fiber prepared in this study. Specific surface area, morphological and Fourier transform infrared analyses of original and functionalized activated nanocarbon and/or investigations of thermal, orientation factor and ultimate tensile properties of as-prepared and/or drawn UHMWPE/functionalized activated nanocarbon fibers were performed to understand the above-improved ultra drawing and ultimate tensile properties of the UHMWPE/functionalized activated nanocarbon fibers.

Keywords: activated nanocarbon, specific surface areas, ultradrawing, ultrahigh molecular weight polyethylene

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: J. C. Moctezuma, V. Breña-Medina, Jose Luis Nunez-Yanez, Joseph P. McGeehan

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In this work we make a bifurcation analysis for a single compartment representation of Traub model, one of the most important conductance-based models. The analysis focus in two principal parameters: current and leakage conductance. Study of stable and unstable solutions are explored; also Hop-bifurcation and frequency interpretation when current varies is examined. This study allows having control of neuron dynamics and neuron response when these parameters change. Analysis like this is particularly important for several applications such as: tuning parameters in learning process, neuron excitability tests, measure bursting properties of the neuron, etc. Finally, a hardware implementation results were developed to corroborate these results.

Keywords: Traub model, Pinsky-Rinzel model, Hopf bifurcation, single-compartment models, bifurcation analysis, neuron modeling

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Authors: Ji-Hyon Kil, Kew-Cheol Shim, Kyoung-Ae Park, Kyoungho Kim

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Ambrosia trifida L. is designated as invasive alien species by the Act on the Conservation and Use of Biodiversity by the Ministry of Environment, Korea. The purpose of present paper was to investigate the inhibitory effects of aqueous extracts of A.trifida on the development of root hairs of Triticum aestivum L., and Allium tuberosum Rottler ex Spreng and the electrophoretic protein patterns of their radicles. The development of root hairs was inhibited by increasing of aqueous extract concentrations. Through SDS-PAGE, the electrophoretic protein bands of extracted proteins from their radicles were appeared in controls, but protein bands of specific molecular weight disappeared or weakened in treatments. In conclusion, inhibitory effects of A. trifida made two receptor species changed morphologically, and at the molecular level in early growth stage.

Keywords: Ambrosia trifida L., invasive alien species, inhibitory effect, root hair, electrophoretic protein, radicle

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Authors: Kamran Siddique, Hiroyuki Asada, Yoshifumi Ogami

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The use of Micro Gas Turbine (MGT) as the engine in Unmanned Aerobic Vehicles (UAVs) and power source in Robotics is widespread these days. Research has been conducted in the past decade or so to improve the performance of different components of MGT. This type of engine has interrelated components which have non-linear characteristics. Therefore, the overall engine performance depends on the individual engine element’s performance. Computational Fluid Dynamics (CFD) is one of the simulation method tools used to analyze or even optimize MGT system performance. In this study, the compressor of the MGT is designed, and performance optimization is being done using CFD. Performance of the micro compressor is improved in order to increase the overall performance of MGT. A high value of pressure ratio is to be achieved by studying the effect of change of different operating parameters like mass flow rate and revolutions per minute (RPM) and aerodynamical and geometrical parameters on the pressure ratio of the compressor. Two types of compressor designs are considered in this study; 3D centrifugal and ‘planar’ designs. For a 10 mm impeller, the planar model is the simplest compressor model with the ease in manufacturability. On the other hand, 3D centrifugal model, although more efficient, is very difficult to manufacture using current microfabrication resources. Therefore, the planar model is the best-suited model for a micro compressor. So. a planar micro compressor has been designed that has a good pressure ratio, and it is easy to manufacture using current microfabrication technologies. Future work is to fabricate the compressor to get experimental results and validate the theoretical model.

Keywords: computational fluid dynamics, microfabrication, MEMS, unmanned aerobic vehicles

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Authors: Muhammet Baldan, Emel Timuçin

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Molecular solubility prediction plays a crucial role in various fields, such as drug discovery, environmental science, and material science. In this study, we compare the performance of five machine learning algorithms—linear regression, support vector machines (SVM), random forests, gradient boosting machines (GBM), and neural networks—for predicting molecular solubility using the AqSolDB dataset. The dataset consists of 9981 data points with their corresponding solubility values. MACCS keys (166 bits), RDKit properties (20 properties), and structural properties(3) features are extracted for every smile representation in the dataset. A total of 189 features were used for training and testing for every molecule. Each algorithm is trained on a subset of the dataset and evaluated using metrics accuracy scores. Additionally, computational time for training and testing is recorded to assess the efficiency of each algorithm. Our results demonstrate that random forest model outperformed other algorithms in terms of predictive accuracy, achieving an 0.93 accuracy score. Gradient boosting machines and neural networks also exhibit strong performance, closely followed by support vector machines. Linear regression, while simpler in nature, demonstrates competitive performance but with slightly higher errors compared to ensemble methods. Overall, this study provides valuable insights into the performance of machine learning algorithms for molecular solubility prediction, highlighting the importance of algorithm selection in achieving accurate and efficient predictions in practical applications.

Keywords: random forest, machine learning, comparison, feature extraction

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Authors: Chuan-Wen Liu, Min-Hsien Liu, Chung-Chieh Tai, Bing-Cheng Kuo, Cheng-Lung Chen, Huazhen Shen

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A recent surge in research on magnetic radar absorbing materials (RAMs) has presented researchers with new opportunities and challenges. This study was performed to gain a better understanding of the wave-absorbing phenomenon of magnetic RAMs. First, we hypothesized that the absorbing phenomenon is dependent on the particle shape. Using the Material Studio program and the micro-dot magnetic dipoles (MDMD) method, we obtained results from magnetic RAMs to support this hypothesis. The total MDMD energy of disk-like iron particles was greater than that of spherical iron particles. In addition, the particulate aggregation phenomenon decreases the wave-absorbance, according to both experiments and computational data. To conclude, this study may be of importance in terms of explaining the wave- absorbing characteristic of magnetic RAMs. Combining molecular dynamics simulation results and the theory of magnetization of magnetic dots, we investigated the magnetic properties of iron materials with different particle shapes and degrees of aggregation under external magnetic fields. The MDMD of the materials under magnetic fields of various strengths were simulated. Our results suggested that disk-like iron particles had a better magnetization than spherical iron particles. This result could be correlated with the magnetic wave- absorbing property of iron material.

Keywords: wave-absorbing property, magnetic material, micro-dot magnetic dipole, particulate aggregation

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Authors: Y. Saylan, F. Yılmaz, A. Denizli

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Rheumatoid arthritis (RA) which is the most common autoimmune disorder of the body's own immune system attacking healthy cells. RA has both articular and systemic effects.Until now romatiod factor (RF) assay is used the most commonly diagnosed RA but it is not specific. Anti-cyclic citrullinated peptide (anti-CCP) antibodies are IgG autoantibodies which recognize citrullinated peptides and offer improved specificity in early diagnosis of RA compared to RF. Anti-CCP antibodies have specificity for the diagnosis of RA from 91 to 98% and the sensitivity rate of 41-68%. Molecularly imprinted polymers (MIP) are materials that are easy to prepare, less expensive, stable have a talent for molecular recognition and also can be manufactured in large quantities with good reproducibility. Molecular recognition-based adsorption techniques have received much attention in several fields because of their high selectivity for target molecules. Quartz crystal microbalance (QCM) is an effective, simple, inexpensive approach mass changes that can be converted into an electrical signal. The applications for specific determination of chemical substances or biomolecules, crystal electrodes, cover by the thin films for bind or adsorption of molecules. In this study, we have focused our attention on combining of molecular imprinting into nanofilms and QCM nanosensor approaches and producing QCM nanosensor for anti-CCP, chosen as a model protein, using anti-CCP imprinted nanofilms. For this aim, anti-CCP imprinted QCM nanosensor was characterized by Fourier transform infrared spectroscopy, atomic force microscopy, contact angle measurements and ellipsometry. The non-imprinted nanosensor was also prepared to evaluate the selectivity of the imprinted nanosensor. Anti-CCP imprinted QCM nanosensor was tested for real-time detection of anti-CCP from aqueous solution. The kinetic and affinity studies were determined by using anti-CCP solutions with different concentrations. The responses related with mass shifts (Δm) and frequency shifts (Δf) were used to evaluate adsorption properties and to calculate binding (Ka) and dissociation (Kd) constants. To show the selectivity of the anti-CCP imprinted QCM nanosensor, competitive adsorption of anti-CCP and IgM was investigated.The results indicate that anti-CCP imprinted QCM nanosensor has a higher adsorption capabilities for anti-CCP than for IgM, due to selective cavities in the polymer structure.

Keywords: anti-CCP, molecular imprinting, nanosensor, rheumatoid arthritis, QCM

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Authors: Fatimah Zawani Abdullah, Shereena Mohd Arif, Nurul Malim

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The study of molecular similarity search in chemical database is increasingly widespread, especially in the area of drug discovery. Similarity search is an application in the field of Chemoinformatics to measure the similarity between the molecular structure which is known as the query and the structure of chemical compounds in the database. Similarity search is also one of the approaches in virtual screening which involves computational techniques and scoring the probabilities of activity. The main objective of this work is to determine the best fingerprint when compared to the other five fingerprints selected in this study using PubChem chemical dataset. This paper will discuss the similarity searching process conducted using 6 types of descriptors, which are ECFP4, ECFC4, FCFP4, FCFC4, SRECFC4 and SRFCFC4 on 15 activity classes of PubChem dataset using Tanimoto coefficient to calculate the similarity between the query structures and each of the database structure. The results suggest that ECFP4 performs the best to be used with Tanimoto coefficient in the PubChem dataset.

Keywords: 2D fingerprints, Tanimoto, PubChem, similarity searching, chemoinformatics

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Authors: Prakash Persad, Kelvin Loutan, Trichelle Seepersad

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The Finite Element Method is commonly used in the analysis of flexible manipulators to predict elastic displacements and develop joint control schemes for reducing positioning error. In order to preserve simplicity, regular geometries, ideal joints and connections are assumed. This paper presents the dynamic FE analysis of a 4- degrees of freedom open chain manipulator, intended for striking a curved 3D surface percussion musical instrument. This was done utilizing the new MultiBody Dynamics Module in COMSOL, capable of modeling the elastic behavior of a body undergoing rigid body type motion.

Keywords: dynamic modeling, entertainment robots, finite element method, flexible robot manipulators, multibody dynamics, musical robots

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Authors: Janne Engblom, Elias Oikarinen

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A panel dataset is one that follows a given sample of individuals over time, and thus provides multiple observations on each individual in the sample. Panel data models include a variety of fixed and random effects models which form a wide range of linear models. A special case of panel data models are dynamic in nature. A complication regarding a dynamic panel data model that includes the lagged dependent variable is endogeneity bias of estimates. Several approaches have been developed to account for this problem. In this paper, the panel models were estimated using the Arellano-Bover/Blundell-Bond Generalized method of moments (GMM) estimator which is an extension of the Arellano-Bond model where past values and different transformations of past values of the potentially problematic independent variable are used as instruments together with other instrumental variables. The Arellano–Bover/Blundell–Bond estimator augments Arellano–Bond by making an additional assumption that first differences of instrument variables are uncorrelated with the fixed effects. This allows the introduction of more instruments and can dramatically improve efficiency. It builds a system of two equations—the original equation and the transformed one—and is also known as system GMM. In this study, Finnish housing price dynamics were examined empirically by using the Arellano–Bover/Blundell–Bond estimation technique together with ordinary OLS. The aim of the analysis was to provide a comparison between conventional fixed-effects panel data models and dynamic panel data models. The Arellano–Bover/Blundell–Bond estimator is suitable for this analysis for a number of reasons: It is a general estimator designed for situations with 1) a linear functional relationship; 2) one left-hand-side variable that is dynamic, depending on its own past realizations; 3) independent variables that are not strictly exogenous, meaning they are correlated with past and possibly current realizations of the error; 4) fixed individual effects; and 5) heteroskedasticity and autocorrelation within individuals but not across them. Based on data of 14 Finnish cities over 1988-2012 differences of short-run housing price dynamics estimates were considerable when different models and instrumenting were used. Especially, the use of different instrumental variables caused variation of model estimates together with their statistical significance. This was particularly clear when comparing estimates of OLS with different dynamic panel data models. Estimates provided by dynamic panel data models were more in line with theory of housing price dynamics.

Keywords: dynamic model, fixed effects, panel data, price dynamics

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Authors: Taher S. Ababneh, Taghreed M. A. Jazzazi, Tareq M. A. Alshboul

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The inhibiting action against aluminum corrosion by three derivatives of 1,8-bis (benzylideneamino) naphthalene (BN) Schiff base has been investigated by means of DFT quantum chemical calculations at the B3LYP/6-31G(d) level of theory. The derivatives (CBN, NBN and MBN) were prepared from the condensation reaction of 1,8-diaminonaphthalene with substituted benzaldehyde (4-CN, 3-NO₂ and 3,4-(OMe)₂, respectively). Calculations were conducted to study the adsorption of each Schiff base on aluminum surface to evaluate its potential as a corrosion inhibitor. The computational structural features and electronic properties of each derivative such as relative energies and energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) have been reported. Thermodynamic functions and quantum chemical parameters such as the hardness of the inhibitor, the softness and the electrophilicity index were calculated to determine the derivative of the highest inhibition efficiency.

Keywords: corrosion, aluminum, DFT calculation, 1, 8-diaminonaphthalene, benzaldehyde

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Authors: L. P. Gomes, G. F. Araújo, Y. M. L. Cordeiro, C. T. Andrade, E. M. Del Aguila, V. M. F. Paschoalin

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The application of nanoscale materials and nanostructures is an emerging area, these since materials may provide solutions to technological and environmental challenges in order to preserve the environment and natural resources. To reach this goal, the increasing demand must be accompanied by 'green' synthesis methods. Chitosan is a natural, nontoxic, biopolymer derived by the deacetylation of chitin and has great potential for a wide range of applications in the biological and biomedical areas, due to its biodegradability, biocompatibility, non-toxicity and versatile chemical and physical properties. Chitosan also presents high antimicrobial activities against a wide variety of pathogenic and spoilage microorganisms. Ultrasonication is a common tool for the preparation and processing of polymer nanoparticles. It is particularly effective in breaking up aggregates and in reducing the size and polydispersity of nanoparticles. High-intensity ultrasonication has the potential to modify chitosan molecular weight and, thus, alter or improve chitosan functional properties. The aim of this study was to evaluate the influence of sonication intensity and time on the changes of commercial chitosan characteristics, such as molecular weight and its potential antibacterial activity against Gram-negative bacteria. The nanoparticles (NPs) were produced from two commercial chitosans, of medium molecular weight (CS-MMW) and low molecular weight (CS-LMW) from Sigma-Aldrich®. These samples (2%) were solubilized in 100 mM sodium acetate pH 4.0, placed on ice and irradiated with an ultrasound SONIC ultrasonic probe (model 750 W), equipped with a 1/2" microtip during 30 min at 4°C. It was used on constant duty cycle and 40% amplitude with 1/1s intervals. The ultrasonic degradation of CS-MMW and CS-LMW were followed up by means of ζ-potential (Brookhaven Instruments, model 90Plus) and dynamic light scattering (DLS) measurements. After sonication, the concentrated samples were diluted 100 times and placed in fluorescence quartz cuvettes (Hellma 111-QS, 10 mm light path). The distributions of the colloidal particles were calculated from the DLS and ζ-potential are measurements taken for the CS-MMW and CS-LMW solutions before and after (CS-MMW30 and CS-LMW30) sonication for 30 min. Regarding the results for the chitosan sample, the major bands can be distinguished centered at Radius hydrodynamic (Rh), showed different distributions for CS-MMW (Rh=690.0 nm, ζ=26.52±2.4), CS-LMW (Rh=607.4 and 2805.4 nm, ζ=24.51±1.29), CS-MMW30 (Rh=201.5 and 1064.1 nm, ζ=24.78±2.4) and CS-LMW30 (Rh=492.5, ζ=26.12±0.85). The minimal inhibitory concentration (MIC) was determined using different chitosan samples concentrations. MIC values were determined against to E. coli (106 cells) harvested from an LB medium (Luria-Bertani BD™) after 18h growth at 37 ºC. Subsequently, the cell suspension was serially diluted in saline solution (0.8% NaCl) and plated on solid LB at 37°C for 18 h. Colony-forming units were counted. The samples showed different MICs against E. coli for CS-LMW (1.5mg), CS-MMW30 (1.5 mg/mL) and CS-LMW30 (1.0 mg/mL). The results demonstrate that the production of nanoparticles by modification of their molecular weight by ultrasonication is simple to be performed and dispense acid solvent addition. Molecular weight modifications are enough to provoke changes in the antimicrobial potential of the nanoparticles produced in this way.

Keywords: antimicrobial agent, chitosan, green production, nanoparticles

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Authors: Kristina Sutiene, Lina Dapkute

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The paper investigates the current demographic trends that exert the sustainability of pension systems in most EU regions. Several drivers usually compose the demographic challenge, coming from the structure and trends of population in the country. As the case of research, three main variables of demographic risk in Lithuania have been singled out and have been used in making up the analysis. Over the last two decades, the country has presented a peculiar demographic situation characterized by pessimistic fertility trends, negative net migration rate and rising life expectancy that make the significant changes in labor-age population. This study, therefore, sets out to assess the relative impact of these risk factors both individually and in aggregate, while assuming economic trends to evolve historically. The evidence is presented using data of pension funds that operate in Lithuania and are financed by defined-contribution plans. To achieve this goal, the discrete-time pension fund’s value model is developed that reflects main operational modalities: contribution income from current participants and new entrants, pension disbursement and administrative expenses; it also fluctuates based on returns from investment activity. Age-structured Leslie population dynamics model has been integrated into the main model to describe the dynamics of fertility, migration and mortality rates upon age. Validation has concluded that Leslie model adequately fits the current population trends in Lithuania. The elasticity of pension system is examined using Loimaranta efficiency as a measure for comparison of plausible long-term developments of demographic risks. With respect to the research question, it was found that demographic risks have different levels of influence on future value of aggregated pension funds: The fertility rates have the highest importance, while mortality rates give only a minor impact. Further studies regarding the role of trying out different economic scenarios in the integrated model would be worthwhile.

Keywords: asset liability modelling, Leslie model, pension funds, population dynamics

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Authors: Malik Sajjad Mehmood, Aisha Ali, Hamna Khan, Tariq Yasin, Masroor Ikram

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Ultra-high molecular weight polyethylene (UHMWPE) is one of the polymers belongs to polyethylene (PE) family having monomer –CH2– and average molecular weight is approximately 3-6 million g/mol. Due its chemical, mechanical, physical and biocompatible properties, it has been extensively used in the field of electrical insulation, medicine, orthopedic, microelectronics, engineering, chemistry and the food industry etc. In order to alter/modify the properties of UHMWPE for particular application of interest, certain various procedures are in practice e.g. treating the material with high energy irradiations like gamma ray, e-beam, and ion bombardment. Radiation treatment of UHMWPE induces free radicals within its matrix, and these free radicals are the precursors of chain scission, chain accumulation, formation of double bonds, molecular emission, crosslinking etc. All the aforementioned physical and chemical processes are mainly responsible for the modification of polymers properties to use them in any particular application of our interest e.g. to fabricate LEDs, optical sensors, antireflective coatings, polymeric optical fibers, and most importantly for radiation dosimetry applications. It is therefore, to check the feasibility of using UHMWPE for radiation dosimetery applications, the compressed sheets of UHMWPE were irradiated at room temperature (~25°C) for total dose values of 30 kGy and 100 kGy, respectively while one were kept un-irradiated as reference. Transmittance data (from 400 nm to 800 nm) of e-beam irradiated UHMWPE and its hybrids were measured by using Muller matrix spectro-polarimeter. As a result significant changes occur in the absorption behavior of irradiated samples. To analyze these (radiation induced) changes in polymer matrix Urbach edge method and modified Tauc’s equation has been used. The results reveal that optical activation energy decreases with irradiation. The values of activation energies are 2.85 meV, 2.48 meV, and 2.40 meV for control, 30 kGy, and 100 kGy samples, respectively. Direct and indirect energy band gaps were also found to decrease with irradiation due to variation of C=C unsaturation in clusters. We believe that the reported results would open new horizons for radiation dosimetery applications.

Keywords: electron beam, radiation dosimetry, Tauc’s equation, UHMWPE, Urbach method

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Authors: Idenyi Goshen Peter, Oludayo Tade

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Traffic robbery is a prevalent issue in Lagos State, impacting commuters and transport workers, necessitating an examination of victimization experiences and offender-victim dynamics. The research aim is to investigate the nature of traffic robbery victimization experiences, strategies employed by offenders, and the extent of the crime as reported in newspapers. Utilizing content analysis, the study examines 167 traffic robbery cases from 2015 to 2023 reported in five newspapers using the routine activity theory to understand the dynamics between offenders and victims. The research discusses the victimization experience and convergence of the offenders and victims, it documents the extent of the crime as captured by various newspapers (Vanguard, Punch. Tribune, Sun and Guardian ), and it also interrogates the strategies, methods deployed by traffic robbers. The study addresses the nature, strategies, and extent of traffic robbery victimization experiences, shedding light on the dynamics of the crime over an eight-year period. The paper implored secondary research from newspaper publications, and also content analysis for the research. Routine activity theory was used to explain the phenomenon that exists between the offender and the victim. Consequently, the common method used by offenders is dispossessing victims of their valuables, leading to fear-driven victim experiences, with spikes in incidents observed in June and December, particularly in Vanguard and Punch publications.

Keywords: traffic robbery, victimisation experience, offender, routine activity

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Authors: M. S. M. Yusof, R. Ramli, S. K. C. Soh, N. Ismail, N. Ngah

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This study presents the synthesis of a series of methoxybenzoylthiourea amino acid derivatives. The compounds were obtained from the reactions between 2/3/4-methoxybenzoyl isothiocyanate with threonine. All of the compounds were characterized via mass spectrometry, ¹H and ¹³C NMR spectrometry, UV-Vis spectrophotometer and FT-IR spectroscopy. Mass spectra for all of the compounds showed the presence of molecular ion [M]⁺ peaks at m/z 312, which are in agreement to the calculated molecular weight. For ¹H NMR spectra, the presence of OCH₃, C=S-NH and C=O-NH protons were observed within range of δ_H 3.8-4.0 ppm, 11.1-11.5 ppm and 10.0-11.5 ppm, respectively. ¹³C NMR spectra in all compounds displayed the presence of OCH₃, C=O-NH, C=O-OH and C=S carbon resonances within range of δ_C 55.0-57.0 ppm, 165.0-168.0 ppm, 170.0-171.0 ppm and 180.0-182.0 ppm, respectively. In UV spectra, two absorption bands have been observed and both were assigned to the n-π* and π-π* transitions. Six vibrational modes of v(N-H), v(O-H), v(C=O-OH), v(C=O-NH), v(C=C) aromatic and v(C=S) appeared in the FT-IR spectra within the range of 3241-3467 cm^-1, 2976-3302 cm^-1, 1720-1768 cm^-1, 1655-1672 cm^-1, 1519-1525 cm^-1 and 754-763 cm^-1, respectively. The antibacterial activity for all of the compounds was screened against Staphylococcus aureus, Staphylococcus epidermidis, Salmonella typhimurium and Escherichia coli. However, no activity was observed.

Keywords: methoxybenzoyl isothiocyanate, amino acid, threonine, antibacterial

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Authors: Nishanthi N. S., Srikanth Vedantam

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Intracellular delivery of materials has always proved to be a challenge in research and therapeutic applications. Usually, vector-based methods, such as liposomes and polymeric materials, and physical methods, such as electroporation and sonoporation have been used for introducing nucleic acids or proteins. Reliance on exogenous materials, toxicity, off-target effects was the short-comings of these methods. Microinjection was an alternative process which addressed the above drawbacks. However, its low throughput had hindered its adoption widely. Mechanical deformation of cells by squeezing them through constriction channel can cause the temporary development of pores that would facilitate non-targeted diffusion of materials. Advantages of this method include high efficiency in intracellular delivery, a wide choice of materials, improved viability and high throughput. This cell squeezing process can be studied deeper by employing simple models and efficient computational procedures. In our current work, we present a finite sized dissipative particle dynamics (FDPD) model to simulate the dynamics of the cell flowing through a constricted channel. The cell is modeled as a capsule with FDPD particles connected through a spring network to represent the membrane. The total energy of the capsule is associated with linear and radial springs in addition to constraint of the fixed area. By performing detailed simulations, we studied the strain on the membrane of the capsule for channels with varying constriction heights. The strain on the capsule membrane was found to be similar though the constriction heights vary. When strain on the membrane was correlated to the development of pores, we found higher porosity in capsule flowing in wider channel. This is due to localization of strain to a smaller region in the narrow constriction channel. But the residence time of the capsule increased as the channel constriction narrowed indicating that strain for an increased time will cause less cell viability.

Keywords: capsule, cell squeezing, dissipative particle dynamics, intracellular delivery, microfluidics, numerical simulations

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Authors: Giulio Rosati, Luciano Sappia, Rossana Madrid, Noemi Rozlòsnik

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The addition of PEG of different molecular weights has important effects on the physical, electrical and electrochemical properties of iron(III)-tosylate doped PEDOT. This particular polymer can be easily spin coated over plastic discs, optimizing thickness and uniformity of the PEDOT-PEG films. The conductivity and morphological analysis of the hybrid PEDOT-PEG polymer by 4-point probe (4PP), 12-point probe (12PP), and conductive AFM (C-AFM) show strong effects of the PEG doping. Moreover, the conductive films kinetics at the nanoscale, in response to different bias voltages, change radically depending on the PEG molecular weight. The hybrid conductive films show also interesting electrochemical properties, making the PEDOT PEG doping appealing for biosensing applications both for EIS-based and amperometric affinity/catalytic biosensors.

Keywords: atomic force microscopy, biosensors, four-point probe, nano-films, PEDOT

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Authors: Po-Wen Chen, Jin-Yu Wu, Md. Manirul Ali, Yang Peng, Chen-Te Chang, Der-Jun Jan

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Dynamics of cathode spot has become a major part of vacuum arc discharge with its high academic interest and wide application potential. In this article, using a three-dimensional statistical model, we simulate the distribution of the ignition probability of a new cathode spot occurring in different magnetic pressure on old cathode spot surface and at different arcing time. This model for the ignition probability of a new cathode spot was proposed in two typical situations, one by the pure isotropic random walk in the absence of an external magnetic field, other by the retrograde motion in external magnetic field, in parallel with the cathode surface. We mainly focus on developed relationship between the ignition probability density distribution of a new cathode spot and the external magnetic field.

Keywords: cathode spot, vacuum arc discharge, transverse magnetic field, random walk

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Authors: M. H. Alhajeri, Hamad M. Alhajeri, A. H. Alenezi

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Computational fluid dynamics (CFD) investigation of heat transfer in U-duct with turbulators is presented in this paper. The duct passages used to cool internally the blades in gas turbine. The study is focused in the flow behavior and the Nusselt number (Nu) distributions. The model of the u-duct contains two square legs that are connected by 180* turn. Four turbulators are located in each surface of the leg and distributed in a staggered arrangement. The turbulator height and width are equal to 0.1 of the duct width, and the turbulator height is 0.1 of the distance between the turbulators. The Reynolds number (Re) used in this study is 95000 and the inlet velocity is 10 m/s. It was noticed that, after the flow resettles from the interruptions generated by the first turbulator or the turn, the flow construct two eddies, one large and the other is small after and before the turbulator, respectively. The maximum values of the Nu are found at a distance of approximately one turbulator width w before of the flow reattachment point.

Keywords: computational fluid dynamics, CFD, rib, heat transfer, blade

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Authors: Gajanan M. Sonwane

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The computational studies on 2-phenazinamines with their protein targets have been carried out to design compounds with potential anticancer activity. This strategy of designing compounds possessing selectivity over specific tyrosine kinase has been achieved through G-QSAR and molecular docking studies. The objective of this research has been to design newer 2-phenazinamine derivatives as Bcr-Abl tyrosine kinase inhibitors by G-QSAR, molecular docking studies followed by wet-lab studies along with evaluation of their anticancer potential. Computational chemistry was done by using VLife MDS 4.3 and Autodock 4.2 followed by wet-lab experiments for synthesizing 2-phenazinamine derivatives. The chemical structures of ligands in 2D were drawn by employing Chemdraw 2D Ultra 8.0 and were converted into 3D. These were optimized by using a semi-empirical method called MOPAC. The protein structure was retrieved from RCSC protein data bank as a PDB file. The binding interactions of protein and ligands were done by using PYMOL. The molecular properties of the designed compounds were predicted in silico by using Osiris property explorer. The parent compound 2-phenazinamine was synthesized by reduction of 2, 4-dinitro-N-phenyl-benzenamine in the presence of tin chloride followed by cyclization in the presence of nitrobenzene and magnesium sulfate. The derivatization at the amino function of 2-phenazinamine was performed by treating parent compound with various aldehydes in the presence of dicyclohexylcarbodiimide (DCC) and urea to afford 2-(2-chlorophenyl)-3-(phenazine-2-yl) thiazolidine-4-one. Synthesized 39 novel derivatives of 2-phenazinamine and performed antioxidant activity, anti antiproliferative on the bulb of onion and anticancer activity on cell line showing significant competition with marked blockbuster drug imatinib.

Keywords: computer-aided drug design, tyrosin kinases, anticancer, docking

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Authors: Omar Concepcion, Osvaldo De Melo, Arturo Escobosa

Abstract:

Topological insulator (TI) materials are insulating in the bulk and conducting in the surface. The unique electronic properties associated with these surface states make them strong candidates for exploring innovative quantum phenomena and as practical applications for quantum computing, spintronic and nanodevices. Many materials, including Bi₂Te₃, have been proposed as TIs and, in some cases, it has been demonstrated experimentally by angle-resolved photoemission spectroscopy (ARPES), scanning tunneling spectroscopy (STM) and/or magnetotransport measurements. A clean surface is necessary in order to make any of this measurements. Several techniques have been used to produce films and different kinds of nanostructures. Growth and characterization in situ is usually the best option although cleaving the films can be an alternative to have a suitable surface. In the present work, we report a comparison of Bi₂Te₃ grown by physical vapor transport (PVT) and molecular beam epitaxy (MBE). The samples were characterized by X-ray diffraction (XRD), Scanning electron microscopy (SEM), Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and ARPES. The Bi₂Te₃ samples grown by PVT, were cleaved in the ultra-high vacuum in order to obtain a surface free of contaminants. In both cases, the XRD shows a c-axis orientation and the pole diagrams proved the epitaxial relationship between film and substrate. The ARPES image shows the linear dispersion characteristic of the surface states of the TI materials. The samples grown by PVT, a relatively simple and cost-effective technique shows the same high quality and TI properties than the grown by MBE.

Keywords: Bismuth telluride, molecular beam epitaxy, physical vapor transport, topological insulator

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Authors: Sourav Ray, Christoph Stein, Marcus Weber

Abstract:

A new class of drug candidates, initially derived from mathematical modeling of ligand-receptor interactions, activate the μ-opioid receptor (MOR) preferentially at acidic extracellular pH-levels, as present in injured tissues. This is of commercial interest because it may preclude the adverse effects of conventional MOR agonists like fentanyl, which include but are not limited to addiction, constipation, sedation, and apnea. Animal studies indicate the importance of taking the pH value of the chemical environment of MOR into account when designing new drugs. Hydrogen bonds (HBs) play a crucial role in stabilizing protein secondary structure and molecular interaction, such as ligand-protein interaction. These bonds may depend on the pH value of the chemical environment. For the MOR, antagonist naloxone and agonist [D-Ala2,N-Me-Phe4,Gly5-ol]-enkephalin (DAMGO) form HBs with ionizable residue HIS 297 at physiological pH to modulate signaling. However, such interactions were markedly reduced at acidic pH. Although fentanyl-induced signaling is also diminished at acidic pH, HBs with HIS 297 residue are not observed at either acidic or physiological pH for this strong agonist of the MOR. Molecular dynamics (MD) simulations can provide greater insight into the interaction between the ligand of interest and the HIS 297 residue. Amino acid protonation states are adjusted to the model difference in system acidity. Unbiased and unrestrained MD simulations were performed, with the ligand in the proximity of the HIS 297 residue. Ligand-receptor complexes were embedded in 1-palmitoyl-2-oleoyl-sn glycero-3-phosphatidylcholine (POPC) bilayer to mimic the membrane environment. The occurrence of HBs between the different ligands and the HIS 297 residue of MOR at acidic and physiological pH values were tracked across the various simulation trajectories. No HB formation was observed between fentanyl and HIS 297 residue at either acidic or physiological pH. Naloxone formed some HBs with HIS 297 at pH 5, but no such HBs were noted at pH 7. Interestingly, DAMGO displayed an opposite yet more pronounced HB formation trend compared to naloxone. Whereas a marginal number of HBs could be observed at even pH 5, HBs with HIS 297 were more stable and widely present at pH 7. The HB formation plays no and marginal role in the interaction of fentanyl and naloxone, respectively, with the HIS 297 residue of MOR. However, HBs play a significant role in the DAMGO and HIS 297 interaction. Post DAMGO administration, these HBs might be crucial for the remediation of opioid tolerance and restoration of opioid sensitivity. Although experimental studies concur with our observations regarding the influence of HB formation on the fentanyl and DAMGO interaction with HIS 297, the same could not be conclusively stated for naloxone. Therefore, some other supplementary interactions might be responsible for the modulation of the MOR activity by naloxone binding at pH 7 but not at pH 5. Further elucidation of the mechanism of naloxone action on the MOR could assist in the formulation of cost-effective naloxone-based treatment of opioid overdose or opioid-induced side effects.

Keywords: effect of system acidity, hydrogen bond formation, opioid action, receptor activation

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Authors: Abouzar Kaboudian, Ravi Chaithanya Mysa, Boo Cheong Khoo, Rajeev Kumar Jaiman

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The vortex structures observed in the wake of a flexible cylinder can be significantly different from those of a traditional vibrating, spring mounted, rigid cylinder. These differences can significantly affect the VIV characteristics of the flow and subsequently the VIV response of the cylindrical structures. In this work, we present how the aspect ratio of a flexible cylinder can change the vortex structures in its wake. We will discuss different vortex dynamics which can be observed in the wake of the vibrating flexible cylinder, and how they can affect the vibrational response of the cylinder. Moreover, we will study the transition of these structures versus the aspect ratio of the flexible cylinder. We will discuss how these transitions affect the in-line and transverse forces on the structure. In the end, we will provide general guidelines on the minimum acceptable aspect ratio for the offshore riser studies which may have grave implications for future numerical and experimental works.

Keywords: aspect ratio, flexible cylinder, vortex-shedding, VIV

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Authors: Jixiang Zhang

Abstract:

A dynamic of Bertrand duopoly game is analyzed, where players use different production methods and choose their prices with bounded rationality. The equilibriums of the corresponding discrete dynamical systems are investigated. The stability conditions of Nash equilibrium under a local adjustment process are studied. The stability conditions of Nash equilibrium under a local adjustment process are studied. The stability of Nash equilibrium, as some parameters of the model are varied, gives rise to complex dynamics such as cycles of higher order and chaos. On this basis, we discover that an increase of adjustment speed of bounded rational player can make Bertrand market sink into the chaotic state. Finally, the complex dynamics, bifurcations and chaos are displayed by numerical simulation.

Keywords: Bertrand duopoly model, discrete dynamical system, heterogeneous expectations, nash equilibrium

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Authors: Omar Hussein El Ayadi, EmadY. El-Mansouri, Mohamed B. Dozan

Abstract:

Production oil process require specific details i.e. oil composition. Generally, types of oil or differentiation between reservoir fluids depend specifically on composition. The main purpose of this study is to correlate and predict the Libyan oil (reservoir fluid and residual) composition utilizing tri-angle-coordinate plots discovered and tasked with Excel. The reservoir fluid data (61 old + 47 new), the residual oil data (33 new) collected from most of Libyan reservoirs were correlated with each others. Moreover, find a relation between stock tank molecular weight and stock tank oil gravity (oAPI), the molecular weight oh (C7+) versus residual oil gravity (oAPI). The average value of every oil composition was estimated including non-hydrocarbon (H2S, CO2, and N2). Nevertheless, the isomers (i-…) and normal (n-…) structure of (C4) and (C5) were also obtained. The summary of the conclusion is; utilizing excel Microsoft office to draw triangle coordinates to find two unknown component if only one is known. However, it is recommended to use the obtained oil composition plots and equations for any oil composition dependents i.e. optimum separator pressure.

Keywords: PVT, phase behavior, petroleum, chemical engineering

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Authors: Niloufar Ghoreishi, Ali Nekouzadeh

Abstract:

The stability of the flight during maneuvering and in response to probable perturbations is one of the most essential features of an aircraft that should be analyzed and designed for. In this study, we derived the non-linear governing equations of aircraft dynamics during the climb/descend phase and simulated a model aircraft. The corresponding force and moment dimensionless coefficients of the model and their variations with elevator angle and other relevant aerodynamic parameters were measured experimentally. The short-period mode and phugoid mode response were simulated by solving the governing equations numerically and then compared with the desired stability parameters for the particular level, category, and class of the aircraft model. To meet the target stability, a controller was designed and used. This resulted in significant improvement in the stability parameters of the flight.

Keywords: flight stability, phugoid mode, short period mode, climb phase, damping coefficient

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Authors: Mohammed Auwal Ibrahim, Aminu Mohammed

Abstract:

Stigmasterol has previously been reported to possess antitrypanosomal activity using in vitro and in vivo models. However, the mechanism of antitrypanosomal activity is yet to be elucidated. In the present study, molecular docking was used to decipher the mode of interaction and binding affinity of stigmasterol to three known antitrypanosomal drug targets viz; adenosine kinase, ornithine decarboxylase and triose phosphate isomerase. Stigmasterol was found to bind to the selected trypanosomal enzymes with minimum binding energy of -4.2, -6.5 and -6.6 kcal/mol for adenosine kinase, ornithine decarboxylase, and triose phosphate isomerase respectively. However, hydrogen bond was not involved in the interaction of stigmasterol with all the three enzymes, but hydrophobic interaction seemed to play a vital role in the binding phenomenon which was predicted to be non-competitive like type of inhibition. It was concluded that binding to the three selected enzymes, especially triose phosphate isomerase, might be involved in the antitrypanosomal activity of stigmasterol but not mediated via a hydrogen bond interaction.

Keywords: antitrypanosomal, in silico, molecular docking, stigmasterol

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Authors: Sunsoo Kim, Niladri Das, Raktim Bhattacharya

Abstract:

This paper addresses modeling and control of a six-degree-of-freedom unmanned aerial vehicle capable of vertical take-off and landing in the presence of wind disturbances. We design a hybrid vehicle that combines the benefits of both the fixed-wing and the rotary-wing UAVs. A non-linear model for the hybrid vehicle is rapidly built, combining rigid body dynamics, aerodynamics of wing, and dynamics of the motor and propeller. Further, we design a H₂ optimal controller to make the UAV robust to wind disturbances. We compare its results against that of proportional-integral-derivative and linear-quadratic regulator based control. Our proposed controller results in better performance in terms of root mean squared errors and time responses during two scenarios: hover and level- flight.

Keywords: hybrid UAVs, VTOL, aircraft modeling, H2 optimal control, wind disturbances

Procedia PDF Downloads 156