Search results for: molecular modelling

Authors: John Onolame Unuofin, Uchechukuw U. Nwodo, Anthony I. Okoh

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Laccase is constantly gaining status as important biocatalyst in biotechnology. The illimitable potential of its industrial applications and the corresponding aggressive need for phenomenal volumes of extracellularly secreted laccases have called for its interminable production from sources which are able to meet this demand within a relatively short period of time, preferably bacteria. In response to this call, this study was designed to source for laccase-producing bacteria from different environmental matrices. Three sampling environments were chosen such as wastewater treatment plants, University of Fort Hare vicinity and the Hogback woodland, all within the Eastern Cape, South Africa. Samples such as effluents, sediments, leaf litters, degrading wood and rock scrapings were selectively enriched with some model aromatic compounds and were further screened qualitatively and quantitatively on five phenolic substrates ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), Guaiacol, 1-Naphthol, Potassium Ferric Cyanide and Syringaldazine). Basis for selection was their ability to elicit a colour change on at least three of the above mentioned agar based assay substrates. The choice isolates were further identified based on 16S rRNA molecular identification techniques. 33 isolates were screened out of the 40 representative distinct colonies during the qualitative plate screens, while quantitative screens selected out 11 bacterial isolates. They were, based on molecular identification, desginated as members of the genera Pseudomonas, Stenotrophomonas and Citrobacter of the gammaproteobacteria and Bordetalla and Achromobacter of the betaproteobacteria respectively. We therefore conclude based on our outcomes that we may have isolated efficient laccase-producing bacteria, which might be of beneficial significance in catalysis and biotechnology.

Keywords: beta proteobacteria, catalysis, gammaproteobacteria, laccase

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Authors: William J. Crowther, Conor Marsh

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

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

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Authors: Aïssa Rezzoug

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This paper is aimed to bring new elements that demonstrate the tide caused the groundwater to rise in the shoreline band, on which the urban areas occurs, especially in the western coastal cities of the Kingdom of Saudi Arabia like Jeddah. The reason for the last events of Jeddah inundation was the groundwater rise in the city coupled at the same time to a strong precipitation event. This paper will illustrate the tide participation in increasing the groundwater level significantly. It shows that the reason for internal groundwater recharge within the urban area is not only the excess of the water supply coming from surrounding areas, due to the human activity, with lack of sufficient and efficient sewage system, but also due to tide effect. The research study follows a quantitative method to assess groundwater level rise risks through many in-situ measurements and mathematical modelling. The proposed approach highlights groundwater level, in the urban areas of the city on the shoreline band, reaching the high tide level without considering any input from precipitation. Despite the small tide in the Red Sea compared to other oceanic coasts, the groundwater level is considerably enhanced by the tide from the seaside and by the freshwater table from the landside of the city. In these conditions, the groundwater level becomes high in the city and prevents the soil to evacuate quickly enough the surface flow caused by the storm event, as it was observed in the last historical flood catastrophe of Jeddah in 2009.

Keywords: flood, groundwater rise, Jeddah, tide

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Authors: Dalal Alghawas, Jetty Lee, Kaisa Poutanen, Hani El-Nezami

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Oat β-glucan a water soluble non starch linear polysaccharide has been approved as a cholesterol lowering agent by various food safety administrations and is commonly used to reduce the risk of heart disease. The molecular weight of oat β-glucan can vary depending on the extraction and fractionation methods. It is not clear whether the molecular weight has a significant impact at reducing the acceleration of atherosclerosis. The aim of this study was to investigate three different oat β-glucan fractionations on the development of atherosclerosis in vivo. With special focus on plaque stability and the intestinal barrier function. To test this, ApoE-/- female mice were fed a high fat diet supplemented with oat bran, high molecular weight (HMW) oat β-glucan fractionate and low molecular weight (LMW) oat β-glucan fractionate for 16 weeks. Atherosclerosis risk markers were measured in the plasma, heart and aortic tree. Plaque size was measured in the aortic root and aortic tree. ICAM-1, VCAM-1, E-Selectin, P-Selectin, protein levels were assessed from the aortic tree to determine plaque stability at 16 weeks. The expression of p22phox at the aortic root was evaluated to study the NADPH oxidase complex involved in nitric oxide bioavailability and vascular elasticity. The tight junction proteins E-cadherin and beta-catenin from western blot analyses were analysed as an intestinal barrier function test. Plasma LPS, intestinal D-lactate levels and hepatic FMO gene expression were carried out to confirm whether the compromised intestinal barrier lead to endotoxemia. The oat bran and HMW oat β-glucan diet groups were more effective than the LMW β-glucan diet group at reducing the plaque size and showed marked improvements in plaque stability. The intestinal barrier was compromised for all the experimental groups however the endotoxemia levels were higher in the LMW β-glucan diet group. The oat bran and HMW oat β-glucan diet groups were more effective at attenuating the development of atherosclerosis. Reasons for this could be due to the LMW oat β-glucan diet group’s low viscosity in the gut and the inability to block the reabsorption of cholesterol. Furthermore the low viscosity may allow more bacterial endotoxin translocation through the impaired intestinal barrier. In future food technologists should carefully consider how to incorporate LMW oat β-glucan as a health promoting food.

Keywords: Atherosclerosis, beta glucan, endotoxemia, intestinal barrier function

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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Authors: N. Harun, E. E. Masiren, W. H. W. Ibrahim, F. Adam

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Amine absorption process is an approach for mitigation of CO2 from flue gas that produces from power plant. This process is the most common system used in chemical and oil industries for gas purification to remove acid gases. On the challenges of this process is high energy requirement for solvent regeneration to release CO2. In the past few years, mixed alkanolamines have received increasing attention. In most cases, the mixtures contain N-methyldiethanolamine (MDEA) as the base amine with the addition of one or two more reactive amines such as PZ. The reason for the application of such blend amine is to take advantage of high reaction rate of CO2 with the activator combined with the advantages of the low heat of regeneration of MDEA. Several experimental and simulation studies have been undertaken to understand this process using blend MDEA/PZ solvent. Despite those studies, the mechanism of CO2 absorption into the aqueous MDEA is not well understood and available knowledge within the open literature is limited. The aim of this study is to investigate the intermolecular interaction of the blend MDEA/PZ using Molecular Dynamics (MD) simulation. MD simulation was run under condition 313K and 1 atm using NVE ensemble at 200ps and NVT ensemble at 1ns. The results were interpreted in term of Radial Distribution Function (RDF) analysis through two system of interest i.e binary and tertiary. The binary system will explain the interaction between amine and water molecule while tertiary system used to determine the interaction between the amine and CO2 molecule. For the binary system, it was observed that the –OH group of MDEA is more attracted to water molecule compared to –NH group of MDEA. The –OH group of MDEA can form the hydrogen bond with water that will assist the solubility of MDEA in water. The intermolecular interaction probability of –OH and –NH group of MDEA with CO2 in blended MDEA/PZ is higher than using single MDEA. This findings show that PZ molecule act as an activator to promote the intermolecular interaction between MDEA and CO2.Thus, blend of MDEA with PZ is expecting to increase the absorption rate of CO2 and reduce the heat regeneration requirement.

Keywords: amine absorption process, blend MDEA/PZ, CO2 capture, molecular dynamic simulation, radial distribution function

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Authors: Ali Karrech, Alberto Puccini, Ben Galvin, Davide Galli

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This paper summarises the laboratory tests, numerical models and statistical approach developed to investigate the behaviour of concrete blocks loaded in shear through metallic anchors. This research is proposed to bridge a gap in the state of the art and practice related to anchors loaded against partially confined concrete surfaces. Eight concrete blocks (420 mm x 500 mm x 1000 mm) with 150 and/or 250 deep anchors were tested. The stainless-steel anchors of diameter 16 mm were bonded with HIT-RE 500 V4 injection epoxy resin and were subjected to shear loading against partially supported edges. In addition, finite element models were constructed to validate the laboratory tests and explore the influence of key parameters such as anchor depth, anchor distance from the edge, and compressive strength on the stability of the block. Upon their validation experimentally, the numerical results were used to populate, develop and interpret a systematic parametric study based on the Design of Experiment approach through the Box-Behnken design and Response Surface Methodology. An empirical model has been derived based on this approach, which predicts the load capacity with the desirable intervals of confidence.

Keywords: finite element modelling, design of experiment, response surface methodology, Box-Behnken design, empirical model, interval of confidence, load capacity

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Authors: Yasmina Houda Bendahma, Tewfik Bouchaour, Meriem Merad, Ulrich Maschke

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The purpose of this work is to study retention of dye dissolved in distilled water, by an hydrophilic acrylic polymer network. The polymer network considered is Poly (2-hydroxyethyl methacrylate) (PHEMA): it is prepared by photo-polymerization under UV irradiation in the presence of a monomer (HEMA), initiator and an agent cross-linker. PHEMA polymer network obtained can be used in the retention of dye molecules present in the wastewater. The results obtained are interesting in the study of the kinetics of swelling and de-swelling of cross linked polymer networks PHEMA in colored aqueous solutions. The dyes used for retention by the PHEMA networks are eosin Y and Malachite Green, dissolved in distilled water. Theoretical conformational study by a simplified molecular model of system cross linked PHEMA / dye (eosin Y and Malachite Green), is used to simulate the retention phenomenon (or Docking) dye molecules in cavities in nano-domains included in the PHEMA polymer network.

Keywords: dye retention, molecular modeling, photochemically crosslinked polymer network, swelling deswelling, PHEMA, HEMA

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Karen C. Olufokunbi, Odetunji A. Odejobi

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The discourse of this paper is the examination of the generation, accumulation and growth of e-waste in a developing country. Images and other data about computer e-waste were collected using a digital camera, 290 copies of questionnaire and three structured interviews using Obafemi Awolowo University (OAU), Ile-Ife, Nigeria environment as a case study. The numerical data were analysed using R data analysis and process tool. Automata-based techniques and Petri net modeling tool were used to design and simulate a computational model for the recovery of saleable materials from e-waste. The R analysis showed that at a 95 percent confidence level, the computer equipment that will be disposed by 2020 will be 417 units. Compared to the 800 units in circulation in 2014, 50 percent of personal computer components will become e-waste. This indicates that personal computer components were in high demand due to their low costs and will be disposed more rapidly when replaced by new computer equipment Also, 57 percent of the respondents discarded their computer e-waste by throwing it into the garbage bin or by dumping it. The simulated model using Coloured Petri net modelling tool for the process showed that the e-waste dynamics is a forward sequential process in the form of a pipeline meaning that an e-waste recovery of saleable materials process occurs in identifiable discrete stages indicating that e-waste will continue to accumulate and grow in volume with time.

Keywords: Coloured Petri net, computational modelling, electronic waste, electronic waste process dynamics

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Authors: Abas Mohsenzadeh, Tariq Bashir, Waseen Tahir, Ulf Stigh, Mikael Skrifvars, Kim Bolton

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The area of artificial muscles has received significant attention from many research domains including soft robotics, biomechanics and smart textiles in recent years. Poly(vinylidene fluoride) (PVDF) has been used to form artificial muscles since it contracts upon heating when under load. In this study, PVDF fibers were produced by melt spinning technique at different solid state draw ratios and then actuation mechanism for PVDF tie molecules within the semicrystalline region of PVDF polymer has been investigated using molecular dynamics simulations. Tie molecules are polymer chains that link two (or more) crystalline regions in semicrystalline polymers. The changes in fiber length upon heating have been investigated using a novel simulation technique. The results show that conformational changes of the tie molecules from the longer all-trans conformation at low temperature (β structure) to the shorter conformation (α structure) at higher temperature accrue by increasing the temperature. These results may be applied to understand the actuation observed for PVDF upon heating.

Keywords: poly(vinylidene fluoride), molecular dynamics, simulation, actuators, tie molecules, semicrystalline

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Authors: Iram Batool, Aamer Saeed, Irfan Zia Qureshi, Ayesha Razzaq, Saima Kalsoom

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Heterocyclic compounds analogues and their derivatives have attracted strong interest in medicinal chemistry due to their biological and pharmacological properties. A series of new thiazolopyrimidine carboxylates were conveniently synthesized by one-pot three-component reaction of ethyl acetoacetate, 2-aminothiazole and benzaldehyde substituted with electron-donating and electron-withdrawing groups in order to find some more potent antidiabetic and antibacterial drugs. The structures of synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopy. An in vitro antidiabetic effect was evaluated in adult male BALB/c mice and antibacterial activities were tested against Micrococcus luteus, Salmonella typhimurium, Bacillus subtilis, Bordetella bronchiseptica and Escherichia coli. Some of the tested compounds proved to possess good to excellent activities more than the reference drugs. An in silico molecular docking was also performed on synthesized compounds. The current study is expected to provide useful insights into the design of antidiabetic and antibacterial drugs and understanding the mechanism by which such drugs interact with RNA and diabetes target and exert their biochemical action.

Keywords: antidiabetic, antibacterial, MOE docking, thiazolopyrimidine

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Authors: Ngoc Trung Ngo, Buddhima Indraratna, Cholachat Rujikiathmakjornr

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For several hundred years, the design of railway tracks has practically remained unchanged. Traditionally, rail tracks are placed on a ballast layer due to several reasons, including economy, rapid drainage, and high load bearing capacity. The primary function of ballast is to distributing dynamic track loads to sub-ballast and subgrade layers, while also providing lateral resistance and allowing for rapid drainage. Upon repeated trainloads, the ballast becomes fouled due to ballast degradation and the intrusion of fines which adversely affects the strength and deformation behaviour of ballast. This paper presents the use of three-dimensional discrete element method (DEM) in studying the shear behaviour of the fouled ballast subjected to direct shear loading. Irregularly shaped particles of ballast were modelled by grouping many spherical balls together in appropriate sizes to simulate representative ballast aggregates. Fouled ballast was modelled by injecting a specified number of miniature spherical particles into the void spaces. The DEM simulation highlights that the peak shear stress of the ballast assembly decreases and the dilation of fouled ballast increases with an increase level of fouling. Additionally, the distributions of contact force chain and particle displacement vectors were captured during shearing progress, explaining the formation of shear band and the evolutions of volumetric change of fouled ballast.

Keywords: railway ballast, coal fouling, discrete element modelling, discrete element method

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Authors: Olaf Visker, Arnout De Vries, Lambert Schomaker

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Predictive policing refers to the usage of analytical techniques to identify potential criminal activity. It has been widely implemented by various police departments. Being a relatively new area of research, there are, to the author’s knowledge, no absolute tried, and true methods and they still exhibit a variety of potential problems. One of those problems is closely related to the lack of understanding of how acting on these prediction influence crime itself. The goal of law enforcement is ultimately crime reduction. As such, a policy needs to be established that best facilitates this goal. This research aims to find such a policy by using adversarial agent-based modeling in combination with modern reinforcement learning techniques. It is presented here that a baseline model for both law enforcement and criminal agents and compare their performance to their respective reinforcement models. The experiments show that our smart law enforcement model is capable of reducing crime by making more deliberate choices regarding the locations of potential criminal activity. Furthermore, it is shown that the smart criminal model presents behavior consistent with popular crime theories and outperforms the baseline model in terms of crimes committed and time to capture. It does, however, still suffer from the difficulties of capturing long term rewards and learning how to handle multiple opposing goals.

Keywords: adversarial, agent based modelling, predictive policing, reinforcement learning

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Authors: Drashti G. Daraji, Rosa E. Moo-Puc, Hitesh D. Patel

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Substituted 2-Thioimidazole analogues have been synthesized and confirmed by advanced spectroscopic techniques. Among them, ten compounds have been selected and evaluated for their in vitro anti-cancer activity at the National Cancer Institute (NCI) for testing against a panel of 60 different human tumor cell lines derived from nine neoplastic cancer types. Furthermore, synthesized compounds were tested for their in vitro antiprotozoal activity, and none of them exhibited significant potency against antiprotozoans. It was observed that the tested all compounds seem effective on the UACC-62 melanoma cancer cell line as compared to other cancer cell lines and also exhibited the least potent in the Non-Small Cell Lung Cancer cell line in one-dose screening. In silico studies of these derivatives were carried out by molecular docking techniques and Absorption, Distribution, Metabolism, and Excretion (ADME) using Schrödinger software to find potent B-Raf kinase inhibitor (PDB ID: 3OG7). All the compounds have been performed for docking study; Compound D4 has a good docking score for melanoma cancer as compared with other.

Keywords: anticancer activity, cancer cell line, 2-thio imidazole, one-dose assay, molecular docking

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Authors: Ertuğ Yıldırım, Dile Kara, Salih Zeki Yıldız

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Metal containing polymers (MCPs) are macro molecules usually containing metal-ligand coordination units and are a multidisciplinary research field mainly based at the interface between coordination chemistry and polymer science. The progress of this area has also been reinforced by the growth of several other closely related disciplines including macro molecular engineering, crystal engineering, organic synthesis, supra molecular chemistry and colloidal and material science. Schiff base ligands are very effective in constructing supra molecular architectures such as coordination polymers, double helical and triple helical complexes. In addition, Schiff base derivatives incorporating a fluorescent moiety are appealing tools for optical sensing of metal ions. MCPs are well-known systems in which the combinations of local parameters are possible by means of fluoro metric techniques. Generally, without incorporation of the fluorescent groups with polymers is unspecific, and it is not useful to analyze their fluorescent properties. Therefore, it is necessary to prepare a new type epoxy polymers with fluorescent groups in terms of metal sensing prop and the other photo chemical applications. In the present study metal containing polymers were prepared via poly functional monomeric Schiff base metal chelate complexes in the presence of dis functional monomers such as diglycidyl ether Bisphenol A (DGEBA). The synthesized complexes and polymers were characterized by FTIR, UV-VIS and mass spectroscopies. The preparations of epoxy polymers have been carried out at 185 °C. The prepared composites having sharp and narrow excitation/emission properties are expected to be applicable in various systems such as heat-resistant polymers and photo voltaic devices. The prepared composite is also ideal for various applications, easily prepared, safe, and maintain good fluorescence properties.

Keywords: Schiff base ligands, crystal engineering, fluorescence properties, Metal Containing Polymers (MCPs)

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Authors: K. Żak, S. Przetocka, R. Kitel, K. Guzik, B. Musielak, S. Malicki, G. Dubin, T. A. Holak

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Studies on tumor genesis revealed a number of factors that may potentially serve as molecular targets for immunotherapies. One of such promising targets are PD1 and PDL1 proteins. PD1 (Programmed cell death protein 1) is expressed by activated T cells and plays a critical role in modulation of the host's immune response. One of the PD1 ligands -PDL1- is expressed by macrophages, monocytes and cancer cells which exploit it to avoid immune attack. The notion of the mechanisms used by cancer cells to block the immune system response was utilized in the development of therapies blocking PD1-PDL1 interaction. Up to date, human PD1-PDL1 complex has not been crystallized and structure of the mouse-human complex does not provide a complete view of the molecular basis of PD1-PDL1 interactions. The purpose of this study is to obtain crystal structure of the human PD1-PDL1 complex which shall allow rational design of small molecule inhibitors of the interaction. In addition, the study presents results of binding small-molecules to PD1 and fragment docking towards PD1 protein which will facilitate the design and development of small–molecule inhibitors of PD1-PDL1 interaction.

Keywords: PD1, PDL1, cancer, small molecule, drug discovery

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Authors: B. Almassri, F. Almahmoud, R. Francois

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Near surface mounted reinforcement (NSM) technique is one of the promising techniques used nowadays to strengthen reinforced concrete (RC) structures. In the NSM technique, the Carbon Fibre Reinforced Polymer (CFRP) rods are placed inside pre-cut grooves and are bonded to the concrete with epoxy adhesive. This paper studies the non-classical mode of failure ‘the separation of concrete cover’ according to experimental and numerical FE modelling results. Experimental results and numerical modelling results of a 3D finite element (FE) model using the commercial software Abaqus and 2D FE model FEMIX were obtained on two beams, one corroded (25 years of corrosion procedure) and one control (A1CL3-R and A1T-R) were each repaired in bending using NSM CFRP rod and were then tested up to failure. The results showed that the NSM technique increased the overall capacity of control and corroded beams despite a non-classical mode of failure with separation of the concrete cover occurring in the corroded beam due to damage induced by corrosion. Another FE model used external steel stirrups around the repaired corroded beam A1CL3-R which failed with the separation of concrete cover, this model showed a change in the mode of failure form a non-classical mode of failure by the separation of concrete cover to the same mode of failure of the repaired control beam by the crushing of compressed concrete.

Keywords: corrosion, repair, Reinforced Concrete, FEM, CFRP, FEMIX

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Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

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Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

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Authors: Jiahui Song

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The use of electric fields with high intensity (~ 100kV/cm or higher) and ultra short pulse durations (nanosecond range) has been a recent development. Most of the studies of electroporation have ignored possible thermal effects because of the small duration of the applied voltage pulses. However, it has been predicted membrane temperature gradients ranging from 0.2×109 to 109 K/m. This research focuses on thermal effects that drive for electroporative enhancements, even though the actual temperature values might not have changed appreciably from their equilibrium levels. The dynamics of pore formation with the application of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations of a lipid layer with constant electric field strength of 0.5 V/nm at 25 °C and 47 °C are implemented to simulate the appropriate thermal effects. The GROMACS provides the force fields for the lipid membranes, which is taken to comprise of dipalmitoyl-phosphatidyl-choline (DPPC) molecules. The water model mimicks the aqueous environment surrounding the membrane. Velocities of water and membrane molecules are generated randomly at each simulation run according to a Maxwellian distribution. The high background electric field is typically used in MD simulations to probe electroporation. It serves as an accelerated test of the pore formation process since low electric fields would take inordinately long simulation time. MD simulation shows no pore is formed in a 1-ns snapshot for a DPPC membrane set at a temperature of 25°C after a 0.5 V/nm electric field is applied. A nano-sized pore is clearly seen in a 0.75-ns snapshot on the same geometry, but with the membrane surfaces kept at temperatures of 47°C. And the pore increases at 1 ns. The MD simulation results suggest the possibility that the increase in temperature can result in different degrees of electrically stimulated bio-effects. The results points to the role of thermal effects in facilitating and accelerating the electroporation process.

Keywords: high-intensity, ultra-short, electroporation, thermal effects, molecular dynamics

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Authors: Gómez R. Marta, Martín M. Jesús María

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The general aim of this paper identifies the areas of highest concentration of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) around the incinerator through the use of dispersion models. Atmospheric dispersion models are useful tools for estimating and prevent the impact of emissions from a particular source in air quality. These models allow considering different factors that influence in air pollution: source characteristics, the topography of the receiving environment and weather conditions to predict the pollutants concentration. The PCDD/Fs, after its emission into the atmosphere, are deposited on water or land, near or far from emission source depending on the size of the associated particles and climatology. In this way, they are transferred and mobilized through environmental compartments. The modelling of PCDD/Fs was carried out with following tools: Atmospheric Dispersion Model Software (ADMS) and Surfer. ADMS is a dispersion model Gaussian plume, used to model the impact of air quality industrial facilities. And Surfer is a program of surfaces which is used to represent the dispersion of pollutants on a map. For the modelling of emissions, ADMS software requires the following input parameters: characterization of emission sources (source type, height, diameter, the temperature of the release, flow rate, etc.) meteorological and topographical data (coordinate system), mainly. The study area was set at 5 Km around the incinerator and the first population center nearest to focus PCDD/Fs emission is about 2.5 Km, approximately. Data were collected during one year (2013) both PCDD/Fs emissions of the incinerator as meteorology in the study area. The study has been carried out during period's average that legislation establishes, that is to say, the output parameters are taking into account the current legislation. Once all data required by software ADMS, described previously, are entered, and in order to make the representation of the spatial distribution of PCDD/Fs concentration and the areas affecting them, the modelling was proceeded. In general, the dispersion plume is in the direction of the predominant winds (Southwest and Northeast). Total levels of PCDD/Fs usually found in air samples, are from <2 pg/m3 for remote rural areas, from 2-15 pg/m3 in urban areas and from 15-200 pg/m3 for areas near to important sources, as can be an incinerator. The results of dispersion maps show that maximum concentrations are the order of 10-8 ng/m3, well below the values considered for areas close to an incinerator, as in this case.

Keywords: atmospheric dispersion, dioxin, furan, incinerator

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

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The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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Authors: M. Baldini, H. K. Jacobsen, M. Jaccard

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In light of the international efforts to comply with the Paris agreement and emission targets for future energy systems, Denmark and Canada are among the front-runner countries dealing with climate change. The experiences in the energy sector have seen both countries coping with trade-offs between investments in renewable energy technologies and energy efficiency, thus tackling the climate issue from the supply and demand side respectively. On the demand side, the industrial sector is going through a remarkable transformation, with implementation of energy efficiency measures, change of input fuel for end-use processes and forecasted electrification as main features under the spotlight. By looking at Canada and Denmark's experiences as pathfinders on the demand and supply approach to climate change, it is possible to obtain valuable experience that may be applied to other countries aiming at the same goal. This paper presents a comparative study on industrial energy efficiency between Canada and Denmark. The study focuses on technologies and system options, policy design and implementation and modelling methodologies when implementing industrial energy savings in optimization models in comparison to simulation models. The study identifies gaps and junctures in the approach towards climate change actions and, learning from each other, lessen the differences to further foster the adoption of energy efficiency measurements in the industrial sector, aiming at reducing energy consumption and, consequently, CO₂ emissions.

Keywords: industrial energy efficiency, comparative study, CO₂ reduction, energy system modelling

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Authors: Varun Dongre, Stefan Pirker, Stefan Heinrich

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Over the last decades, the numerical modelling of fluidized bed processes has become feasible even for industrial processes. Commonly, continuous two-fluid models are applied to describe large-scale fluidization. In order to allow for coarse grids novel two-fluid models account for unresolved sub-grid heterogeneities. However, computational efforts remain high – in the order of several hours of compute-time for a few seconds of real-time – thus preventing the representation of long-term phenomena such as heating or particle conversion processes. In order to overcome this limitation, data-based recurrence computational fluid dynamics (rCFD) has been put forward in recent years. rCFD can be regarded as a data-based method that relies on the numerical predictions of a conventional short-term simulation. This data is stored in a database and then used by rCFD to efficiently time-extrapolate the flow behavior in high spatial resolution. This study will compare the numerical predictions of rCFD simulations with those of corresponding full CFD reference simulations for lab-scale and pilot-scale fluidized beds. In assessing the predictive capabilities of rCFD simulations, we focus on solid mixing and secondary gas holdup. We observed that predictions made by rCFD simulations are highly sensitive to numerical parameters such as diffusivity associated with face swaps. We achieved a computational speed-up of four orders of magnitude (10,000 time faster than classical TFM simulation) eventually allowing for real-time simulations of fluidized beds. In the next step, we apply the checkerboarding technique by introducing gas tracers subjected to convection and diffusion. We then analyze the concentration profiles by observing mixing, transport of gas tracers, insights about the convective and diffusive pattern of the gas tracers, and further towards heat and mass transfer methods. Finally, we run rCFD simulations and calibrate them with numerical and physical parameters compared with convectional Two-fluid model (full CFD) simulation. As a result, this study gives a clear indication of the applicability, predictive capabilities, and existing limitations of rCFD in the realm of fluidization modelling.

Keywords: multiphase flow, recurrence CFD, two-fluid model, industrial processes

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Authors: Amira Abdelhafez, Rufus Brunt

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Geothermal energy in Egypt represents a significant untapped renewable resource that can reduce reliance on conventional power generation. Exploiting these geothermal resources depends on depth, temperature range, and geological characteristics. The intracontinental rift setting of the Gulf of Suez (GoS)-Red Sea rift is a favourable tectonic setting for convection-dominated geothermal plays. The geothermal gradient across the GoS ranges from 24.9 to 86.66 °C/km, with a heat flow of 31-127.2 mW/m². Surface expressions of convective heat loss emerge along the gulf flanks as hot springs (e.g., Hammam Faraun) accompanying deeper geothermal resources. These thermal anomalies are driven mainly by the local tectonic configuration. Characterizing the structural framework of major faults and their control on reservoir properties and subsurface hydrothermal fluid circulation is vital for geothermal applications in the gulf. The geothermal play systems of the GoS depend on structural and lithological properties that contribute to heat storage and vertical transport. Potential geothermal reservoirs include the Nubia sandstones, which, due to their thickness, continuity, and contact with hot basement rocks at a mean depth of 3 km, create an extensive reservoir for geothermal fluids. To develop these geothermal resources for energy production, defining the permeability anisotropy of the reservoir due to faults and facies variation is a crucial step in our study, particularly the evaluation of influence on thermal breakthrough and production rates.

Keywords: geothermal, October field, site specific study, reservoir modelling

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Authors: L. Al Ahmad, C. Latrille, D. Hainos, D. Blanc, M. Clausse

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A two-dimensional finite volume axisymmetric model is developed to predict the simultaneous heat and mass transfers during the drying of industrial sludge. The simulations were run using COMSOL-Multiphysics 3.5a. The input parameters of the numerical model were acquired from a preliminary experimental work. Results permit to establish correlations describing the evolution of the various parameters as a function of the drying temperature and the sludge water content. The selection and coupling of the equation are validated based on the drying kinetics acquired experimentally at a temperature range of 45-65 °C and absolute pressure range of 200-1000 mbar. The model, incorporating the heat and mass transfer mechanisms at different operating conditions, shows simulated values of temperature and water content. Simulated results are found concordant with the experimental values, only at the first and last drying stages where sludge shrinkage is insignificant. Simulated and experimental results show that sludge drying is favored at high temperatures and low pressure. As experimentally observed, the drying time is reduced by 68% for drying at 65 °C compared to 45 °C under 1 atm. At 65 °C, a 200-mbar absolute pressure vacuum leads to an additional reduction in drying time estimated by 61%. However, the drying rate is underestimated in the intermediate stage. This rate underestimation could be improved in the model by considering the shrinkage phenomena that occurs during sludge drying.

Keywords: industrial sludge drying, heat transfer, mass transfer, mathematical modelling

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Authors: Sorin Muraru

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Computational generation of carbon nanostructures is still a very demanding process. This work provides an alternative to manual molecular modeling through an algorithm meant to automate the design of such structures. Specifically, carbon nanochimneys are obtained through the bonding of a carbon nanotube with the smaller edge of an open carbon nanocone. The methods of connection rely on mathematical, geometrical and chemical properties. Non-hexagonal rings are used in order to perform the correct bonding of dangling bonds. Once obtained, they are useful for thermal transport, gas storage or other applications such as gas separation. The carbon nanochimneys are meant to produce a less steep connection between structures such as the carbon nanotube and graphene sheet, as in the pillared graphene, but can also provide functionality on its own. The method relies on connecting dangling bonds at the edges of the two carbon nanostructures, employing the use of two different types of auxiliary structures on a case-by-case basis. The code is implemented in Python 3.7 and generates an output file in the .pdb format containing all the system’s coordinates. Acknowledgment: This work was supported by a grant of the Executive Agency for Higher Education, Research, Development and innovation funding (UEFISCDI), project number PN-III-P1-1.1-TE-2016-24-2, contract TE 122/2018.

Keywords: carbon nanochimneys, computational, carbon nanotube, carbon nanocone, molecular modeling, carbon nanostructures

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Authors: C. Castro-Egler, A. Durán-Escalante, A. García-González

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This paper presents a method to generate a finite element model of the human auditory inner ear system. The geometric model has been realized using 2D images from a virtual model of temporal bones. A point cloud has been gotten manually from those images to construct a whole mesh with hexahedral elements. The main difference with the predecessor models is the spiral shape of the cochlea with its three scales completely defined: scala tympani, scala media and scala vestibuli; which are separate by basilar membrane and Reissner membrane. To validate this model, numerical simulations have been realised with two models: an isolated inner ear and a whole model of human auditory system. Ideal conditions of displacement are applied over the oval window in the isolated Inner Ear model. The whole model is made up of the outer auditory channel, the tympani, the ossicular chain, and the inner ear. The boundary condition for the whole model is 1Pa over the auditory channel entrance. The numerical simulations by FEM have been done using a harmonic analysis with a frequency range between 100-10.000 Hz with an interval of 100Hz. The following results have been carried out: basilar membrane displacement; the scala media pressure according to the cochlea length and the transfer function of the middle ear normalized with the pressure in the tympanic membrane. The basilar membrane displacements and the pressure in the scala media make it possible to validate the response in frequency of the basilar membrane.

Keywords: finite elements method, human auditory system model, numerical analysis, 3D modelling cochlea

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Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

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Authors: Mathieu Le Cam, Tejaswinee Darure, Mateusz Pawlucki

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Climate control of cabin aircraft is traditionally conditioned as a single unit by the environmental control system. Cabin temperature is controlled by the crew while passengers of the aircraft have control on the gaspers providing fresh air from the above head area. The small nozzles are difficult to reach and adjust to meet the passenger’s needs in terms of flow and direction. More dedicated control over the near environment of each passenger can be beneficial in many situations. The European project COCOON, funded under Clean Sky 2, aims at developing and demonstrating a microclimate conditioning module (MCM) integrated into a standard economy 3-seat row. The system developed will lead to improved passenger comfort with more control on their personal thermal area. This study focuses on the assessment of thermal comfort of passengers in the cabin aircraft through simulation on the TAITherm modelling platform. A first analysis investigates thermal comfort and sensation of passengers in varying cabin environmental conditions: from cold to very hot scenarios, with and without MCM installed in the seats. The modelling platform is also used to evaluate the impact of different physiologies of passengers on their thermal comfort as well as different seat locations. Under the current cabin conditions, a passenger of a 50th percentile body size is feeling uncomfortably cool due to the high velocity cabin air ventilation. The simulation shows that the in-seat MCM developed in COCOON project improves the thermal comfort of the passenger.

Keywords: cabin aircraft, in-seat HVAC, microclimate conditioning module, thermal comfort

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