Search results for: molecular modelling

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: 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: Bojana Horvat, Barbara Karleusa, Goran Volf, Nevenka Ozanic, Ivica Kisic

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Forest fire is a major threat in many regions in Croatia, especially in coastal areas. Although they are often caused by natural processes, the most common cause is the human factor, intentional or unintentional. Forest fires drastically transform landscapes and influence natural processes. The main goal of the presented research is to analyse and quantify the impact of the forest fire on hydrological processes and propose the model that best describes changes in hydrological patterns in the analysed catchments. Keeping in mind the spatial component of the processes, geospatial analysis is performed to gain better insight into the spatial variability of the hydrological response to disastrous events. In that respect, two catchments that experienced severe forest fire were delineated, and various hydrological and meteorological data were collected both attribute and spatial. The major drawback is certainly the lack of hydrological data, common in small torrential karstic streams; hence modelling results should be validated with the data collected in the catchment that has similar characteristics and established hydrological monitoring. The event chosen for the modelling is the forest fire that occurred in July 2019 and burned nearly 10% of the analysed area. Surface (land use/land cover) conditions before and after the event were derived from the two Sentinel-2 images. The mapping of the burnt area is based on a comparison of the Normalized Burn Index (NBR) computed from both images. To estimate and compare hydrological behaviour before and after the event, curve number (CN) values are assigned to the land use/land cover classes derived from the satellite images. Hydrological modelling resulted in surface runoff generation and hence prediction of hydrological responses in the catchments to a forest fire event. The research was supported by the Croatian Science Foundation through the project 'Influence of Open Fires on Water and Soil Quality' (IP-2018-01-1645).

Keywords: Croatia, forest fire, geospatial analysis, hydrological response

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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: Omar Qaftan

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Earthquakes can cause tremendous loss of human life and can result in severe damage to a several of civil engineering structures especially the tall buildings. The response of a multistory structure subjected to earthquake loading is a complex task, and it requires to be studied by physical and numerical modelling. For many circumstances, the scale models on shaking table may be a more economical option than the similar full-scale tests. A shaking table apparatus is a powerful tool that offers a possibility of understanding the actual behaviour of structural systems under earthquake loading. It is required to use a set of scaling relations to predict the behaviour of the full-scale structure. Selecting the scale factors is the most important steps in the simulation of the prototype into the scaled model. In this paper, the principles of scaling modelling procedure are explained in details, and the simulation of scaled multi-storey concrete structure for dynamic studies is investigated. A procedure for a complete dynamic simulation analysis is investigated experimentally and numerically with a scale factor of 1/50. The frequency domain accounting and lateral displacement for both numerical and experimental scaled models are determined. The procedure allows accounting for the actual dynamic behave of actual size porotype structure and scaled model. The procedure is adapted to determine the effects of the tall multi-storey structure on a raft foundation. Four generated accelerograms were used as inputs for the time history motions which are in complying with EC8. The output results of experimental works expressed regarding displacements and accelerations are compared with those obtained from a conventional fixed-base numerical model. Four-time history was applied in both experimental and numerical models, and they concluded that the experimental has an acceptable output accuracy in compare with the numerical model output. Therefore this modelling methodology is valid and qualified for different shaking table experiments tests.

Keywords: structure, raft, soil, interaction

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Authors: Victoria Goodall, Paul Fatti, Norman Owen-Smith

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Hidden Markov Models have become popular for the analysis of animal tracking data. These models are being used to model the movements of a variety of species in many areas around the world. A common assumption of the model is that the observations need to have regular time steps. In many ecological studies, this will not be the case. The objective of the research is to modify the movement model to allow for irregularly spaced locations and investigate the effect on the inferences which can be made about the latent states. A modification of the likelihood function to allow for these irregular spaced locations is investigated, without using interpolation or averaging the movement rate. The suitability of the modification is investigated using GPS tracking data for lion (Panthera leo) in South Africa, with many observations obtained during the night, and few observations during the day. Many nocturnal predator tracking studies are set up in this way, to obtain many locations at night when the animal is most active and is difficult to observe. Few observations are obtained during the day, when the animal is expected to rest and is potentially easier to observe. Modifying the likelihood function allows the popular Hidden Markov Model framework to be used to model these irregular spaced locations, making use of all the observed data.

Keywords: hidden Markov Models, irregular observations, animal movement modelling, nocturnal predator

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Authors: Jiun-Horng Tsai, Shi-Jie, Nieh

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Fine particulate matter (PM₂.₅) has become an important issue all over the world over the last decade. Annual mean PM₂.₅ concentration has been over the ambient air quality standard of PM₂.₅ (annual average concentration as 15μg/m³) which adapted by Taiwan Environmental Protection Administration (TEPA). TEPA, therefore, has developed a number of air pollution control measures to improve the ambient concentration by reducing the emissions of primary fine particulate matter and the precursors of secondary PM₂.₅. This study investigated the potential improvement of ambient PM₂.₅ concentration by the TEPA program and the other scenario for further emission reduction on various sources. Four scenarios had been evaluated in this study, including a basic case and three reduction scenarios (A to C). The ambient PM₂.₅ concentration was evaluated by Community Multi-scale Air Quality modelling system (CMAQ) ver. 4.7.1 along with the Weather Research and Forecasting Model (WRF) ver. 3.4.1. The grid resolutions in the modelling work are 81 km × 81 km for domain 1 (covers East Asia), 27 km × 27 km for domain 2 (covers Southeast China and Taiwan), and 9 km × 9 km for domain 3 (covers Taiwan). The result of PM₂.₅ concentration simulation in different regions of Taiwan shows that the annual average concentration of basic case is 24.9 μg/m³, and are 22.6, 18.8, and 11.3 μg/m³, respectively, for scenarios A to C. The annual average concentration of PM₂.₅ would be reduced by 9-55 % for those control scenarios. The result of scenario C (the emissions of precursors reduce to allowance levels) could improve effectively the airborne PM₂.₅ concentration to attain the air quality standard. According to the results of unit precursor reduction contribution, the allowance emissions of PM₂.₅, SOₓ, and NOₓ are 16.8, 39, and 62 thousand tons per year, respectively. In the Kao-Ping air basin, the priority for reducing precursor emissions is PM₂.₅ > NOₓ > SOₓ, whereas the priority for reducing precursor emissions is PM₂.₅ > SOₓ > NOₓ in others area. The result indicates that the target pollutants that need to be reduced in different air basin are different, and the control measures need to be adapted to local conditions.

Keywords: airborne PM₂.₅, community multi-scale air quality modelling system, control measures, weather research and forecasting model

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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: 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: Wassana Naiyapo, Atichat Sangtong

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The processes in software development by Object Oriented methodology have many stages those take time and high cost. The inconceivable error in system analysis process will affect to the design and the implementation process. The unexpected output causes the reason why we need to revise the previous process. The more rollback of each process takes more expense and delayed time. Therefore, the good test process from the early phase, the implemented software is efficient, reliable and also meet the user’s requirement. Unified Modelling Language (UML) is the tool which uses symbols to describe the work process in Object Oriented Analysis (OOA). This paper presents the approach for automatically generated UML use case diagram and test cases. UML use case diagram is generated from the event table and test cases are generated from use case specifications and Graphic User Interfaces (GUI). Test cases are derived from the Classification Tree Method (CTM) that classify data to a node present in the hierarchy structure. Moreover, this paper refers to the program that generates use case diagram and test cases. As the result, it can reduce work time and increase efficiency work.

Keywords: classification tree method, test case, UML use case diagram, use case specification

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Authors: Mohammed Salahat, Steve Wade

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This paper presents and compares the SSDDD “Systematic Soft Domain Driven Design Framework” to DDD “Domain Driven Design Framework” as a soft system approach of information systems development. The framework use SSM as a guiding methodology within which we have embedded a sequence of design tasks based on the UML leading to the implementation of a software system using the Naked Objects framework. This framework has been used in action research projects that have involved the investigation and modelling of business processes using object-oriented domain models and the implementation of software systems based on those domain models. Within this framework, Soft Systems Methodology (SSM) is used as a guiding methodology to explore the problem situation and to develop the domain model using UML for the given business domain. The framework is proposed and evaluated in our previous works, a comparison between SSDDD and DDD is presented in this paper, to show how SSDDD improved DDD as an approach to modelling and implementing business domain perspectives for Information Systems Development. The comparison process, the results, and the improvements are presented in the following sections of this paper.

Keywords: domain-driven design, soft domain-driven design, naked objects, soft language

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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: Cheng Zhang, James Marco, Walid Allafi, Truong Q. Dinh, W. D. Widanage

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Equivalent circuit models (ECMs) are widely used in battery management systems in electric vehicles and other battery energy storage systems. The battery dynamics and the model parameters vary under different working conditions, such as different temperature and state of charge (SOC) levels, and therefore online parameter identification can improve the modelling accuracy. This paper presents a way of online ECM parameter identification using a continuous time (CT) estimation method. The CT estimation method has several advantages over discrete time (DT) estimation methods for ECM parameter identification due to the widely separated battery dynamic modes and fast sampling. The presented method can be used for online SOC estimation. Test data are collected using a lithium ion cell, and the experimental results show that the presented CT method achieves better modelling accuracy compared with the conventional DT recursive least square method. The effectiveness of the presented method for online SOC estimation is also verified on test data.

Keywords: electric circuit model, continuous time domain estimation, linear integral filter method, parameter and SOC estimation, recursive least square

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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: 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: 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: Nor Mazlin Zahari, Lian Gan, Xuerui Mao

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The power production in wind farms and the mechanical loads on the turbines are strongly impacted by the wake of the wind turbine. Thus, there is a need for understanding and modelling the turbine wake dynamic in the wind farm and the layout optimization. Having a good wake model is important in predicting plant performance and understanding fatigue loads. In this paper, the Dynamic Mode Decomposition (DMD) was applied to the simulation data generated by a Direct Numerical Simulation (DNS) of flow around a turbine, perturbed by upstream inflow noise. This technique is useful in analyzing the wake flow, to predict its future states and to reflect flow dynamics associated with the coherent structures behind wind turbine wake flow. DMD was employed to describe the dynamic of the flow around turbine from the DNS data. Since the DNS data comes with the unstructured meshes and non-uniform grid, the interpolation of each occurring within each element in the data to obtain an evenly spaced mesh was performed before the DMD was applied. DMD analyses were able to tell us characteristics of the travelling waves behind the turbine, e.g. the dominant helical flow structures and the corresponding frequencies. As the result, the dominant frequency will be detected, and the associated spatial structure will be identified. The dynamic mode which represented the coherent structure will be presented.

Keywords: coherent structure, Direct Numerical Simulation (DNS), dominant frequency, Dynamic Mode Decomposition (DMD)

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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

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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: Nikola Tomasevic, Marko Batic, Sanja Vranes

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Emerging Semantic Web technologies can be seen as the next step in evolution of the intelligent facility management systems. Particularly, this considers increased usage of open source and/or standardized concepts for data classification and semantic interpretation. To deliver such facility management systems, providing the comprehensive integration and interoperability platform in from of the facility data model is a prerequisite. In this paper, one of the possible modelling approaches to provide such integrative facility data model which was based on the ontology modelling concept was presented. Complete ontology development process, starting from the input data acquisition, ontology concepts definition and finally ontology concepts population, was described. At the beginning, the core facility ontology was developed representing the generic facility infrastructure comprised of the common facility concepts relevant from the facility management perspective. To develop the data model of a specific facility infrastructure, first extension and then population of the core facility ontology was performed. For the development of the full-blown facility data models, Malpensa and Fiumicino airports in Italy, two major European air-traffic hubs, were chosen as a test-bed platform. Furthermore, the way how these ontology models supported the integration and interoperability of the overall airport energy management system was analyzed as well.

Keywords: airport ontology, energy management, facility data model, ontology modeling

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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: Mazharuddin Syed Ahmed

Abstract:

This research presents a framework used to develop The Ara Polytechnic College of Architecture Studies building “Kahukura” which is Green Building certified. This framework integrates the development of a smart building digital twin by utilizing Building Information Modelling (BIM) and its BIM maturity levels, including Levels of Development (LOD), eight dimensions of BIM, Heritage-BIM (H-BIM) and Facility Management BIM (FM BIM). The research also outlines a structured approach to building performance analysis and integration with the circular economy, encapsulated within a five-level digital twin framework. Starting with Level 1, the Descriptive Twin provides a live, editable visual replica of the built asset, allowing for specific data inclusion and extraction. Advancing to Level 2, the Informative Twin integrates operational and sensory data, enhancing data verification and system integration. At Level 3, the Predictive Twin utilizes operational data to generate insights and proactive management suggestions. Progressing to Level 4, the Comprehensive Twin simulates future scenarios, enabling robust “what-if” analyses. Finally, Level 5, the Autonomous Twin, represents the pinnacle of digital twin evolution, capable of learning and autonomously acting on behalf of users.

Keywords: building information modelling, circular economy integration, digital twin, predictive analytics

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Authors: Karim Hamidi Machekposhti, Hossein Sedghi, Abdolrasoul Telvari, Hossein Babazadeh

Abstract:

Floods have huge environmental and economic impact. Therefore, flood prediction is given a lot of attention due to its importance. This study analysed the annual maximum streamflow (discharge) (AMS or AMD) of Karkheh River in Karkheh River Basin for flood predicting using ARIMA model. For this purpose, we use the Box-Jenkins approach, which contains four-stage method model identification, parameter estimation, diagnostic checking and forecasting (predicting). The main tool used in ARIMA modelling was the SAS and SPSS software. Model identification was done by visual inspection on the ACF and PACF. SAS software computed the model parameters using the ML, CLS and ULS methods. The diagnostic checking tests, AIC criterion, RACF graph and RPACF graphs, were used for selected model verification. In this study, the best ARIMA models for Annual Maximum Discharge (AMD) time series was (4,1,1) with their AIC value of 88.87. The RACF and RPACF showed residuals’ independence. To forecast AMD for 10 future years, this model showed the ability of the model to predict floods of the river under study in the Karkheh River Basin. Model accuracy was checked by comparing the predicted and observation series by using coefficient of determination (R²).

Keywords: time series modelling, stochastic processes, ARIMA model, Karkheh river

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Authors: Aboubakr Gambo, Adama Diaw, Tobias Wunscher

Abstract:

This study attempts to identify factors affecting rural households’ resilience to food insecurity in Niger. For this, we first create a resilience index by using Principal Component Analysis on the following five variables at the household level: income, food expenditure, duration of grain held in stock, livestock in Tropical Livestock Units and number of farms exploited and second apply Structural Equation Modelling to identify the determinants. Data from the 2010 National Survey on Households’ Vulnerability to Food Insecurity done by the National Institute of Statistics is used. The study shows that asset and social safety nets indicators are significant and have a positive impact on households’ resilience. Climate change approximated by long-term mean rainfall has a negative and significant effect on households’ resilience to food insecurity. The results indicate that to strengthen households’ resilience to food insecurity, there is a need to increase assistance to households through social safety nets and to help them gather more resources in order to acquire more assets. Furthermore, early warning of climatic events could alert households especially farmers to be prepared and avoid important losses that they experience anytime an uneven climatic event occur.

Keywords: food insecurity, principal component analysis, structural equation modelling, resilience

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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: Zuhaina Zakaria, Noraliza Hamzah, Siti Halijjah Shariff, Noor Aizah Abdul Karim

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The residential sector in Malaysia has become the single largest energy sector accounting for 21% of the entire energy usage of the country. In the past 10 years, a number of energy efficiency initiatives in the residential sector had been undertaken by the government including. However, there is no clear evidence that the total residential energy consumption has been reduced substantially via these strategies. Household electrical appliances such as air conditioners, refrigerators, lighting and televisions are used depending on the consumers’ activities. The behavior of household occupants played an important role in energy consumption and influenced the operation of the physical devices. Therefore, in order to ensure success in energy efficiency program, it requires not only the technological aspect but also the consumers’ behaviors component. This paper focuses on the challenges and opportunities in modelling residential consumer behavior in Malaysia. A field survey to residential consumers was carried out and responses from the survey were analyzed to determine the consumers’ level of knowledge and awareness on energy efficiency. The analyses will be used in determining a right framework to explain household energy use intentions and behavior. These findings will be beneficial to power utility company and energy regulator in addressing energy efficiency related issues.

Keywords: consumer behavior theories, energy efficiency, household occupants, residential consumer

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Authors: Maria Teresa Signes Pont, Jose Juan Cortes Plana

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Our proposal provides suitable modelling to the spread of plant pest and particularly to the propagation of Xylella fastidiosa in the almond trees. We compared the impact of temperature and humidity on the propagation of Xylella fastidiosa in various subspecies. Comparison between Balearic Islands and Alicante (Spain). Most sharpshooter and spittlebug species showed peaks in population density during the month of higher mean temperature and relative humidity (April-October), except for the splittlebug Clastoptera sp.1, whose adult population peaked from September-October (late summer and early autumn). The critical season is from when they hatch from the eggs until they are in the pre-reproductive season (January -April) to expand. We focused on winters in the egg state, which normally hatches in early March. The nymphs secrete a foam (mucilage) in which they live and that protects them from natural enemies of temperature changes and prevents dry as long as the humidity is above 75%. The interaction between the life cycles of vectors and vegetation influences the food preferences of vectors and is responsible for the general seasonal shift of the population from vegetation to trees and vice versa, In addition to the temperature maps, we have observed humidity as it affects the spread of the pest Xylella fastidiosa (Xf).

Keywords: xylella fastidiosa, almod tree, temperature, humidity, environmental model

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Authors: Shank Kulkarni, Alireza Tabarraei

Abstract:

The fantastic properties of polyurea such as flexibility, durability, and chemical resistance have brought it a wide range of application in various industries. Effective prediction of the response of polyurea under different loading and environmental conditions necessitates the development of an accurate constitutive model. Similar to most polymers, the behavior of polyurea depends on both strain and strain rate. Therefore, the constitutive model should be able to capture both these effects on the response of polyurea. To achieve this objective, in this paper, a nonlinear hyper-viscoelastic constitutive model is developed by the superposition of a hyperelastic and a viscoelastic model. The proposed constitutive model can capture the behavior of polyurea under compressive loading conditions at various strain rates. Four parameter Ogden model and Mooney Rivlin model are used to modeling the hyperelastic behavior of polyurea. The viscoelastic behavior is modeled using both a three-parameter standard linear solid (SLS) model and a K-BKZ model. Comparison of the modeling results with experiments shows that Odgen and SLS model can more accurately predict the behavior of polyurea. The material parameters of the model are found by curve fitting of the proposed model to the uniaxial compression test data. The proposed model can closely reproduce the stress-strain behavior of polyurea for strain rates up to 6500 /s.

Keywords: constitutive modelling, ogden model, polyurea, SLS model, uniaxial compression test

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Authors: Karlijn Van Den Broek, Ian Walker, Christian Klöckner

Abstract:

Campaigns aiming to induce energy-saving behaviour among householders use a wide range of approaches that address many different drivers thought to underpin this behaviour. However, little research has compared the relative importance of the different factors that influence energy behaviour, meaning campaigns are not informed about where best to focus resources. Therefore, this study applies the Comprehensive Action Determination Model (CADM) to compare the role of normative, intentional, habitual, and situational processes on energy-saving behaviour. An online survey on a sample of households (N = 247) measured the CADM variables and the data was analysed using structural equation modelling. Results showed that situational and habitual processes were best able to account for energy saving behaviour while normative and intentional processes had little predictive power. These findings suggest that policymakers should move away from motivating householders to save energy and should instead focus their efforts on changing energy habits and creating environments that facilitate energy saving behaviour. These findings add to the wider development in social and environmental psychology that emphasizes the importance of extra-personal variables such as the physical environment in shaping behaviour.

Keywords: energy consumption, behavioural modelling, environmental psychology theory, habits, values

Procedia PDF Downloads 233