Search results for: molecular beam epitaxy

Authors: Radoslav Židek, Veronika Šidlová, Radovan Kasarda, Birgit Fuerst-Waltl

Abstract:

Machine learning represents a set of topics dealing with the creation and evaluation of algorithms that facilitate pattern recognition, classification, and prediction, based on models derived from existing data. The data can present identification patterns which are used to classify into groups. The result of the analysis is the pattern which can be used for identification of data set without the need to obtain input data used for creation of this pattern. An important requirement in this process is careful data preparation validation of model used and its suitable interpretation. For breeders, it is important to know the origin of animals from the point of the genetic diversity. In case of missing pedigree information, other methods can be used for traceability of animal´s origin. Genetic diversity written in genetic data is holding relatively useful information to identify animals originated from individual countries. We can conclude that the application of data mining for molecular genetic data using supervised learning is an appropriate tool for hypothesis testing and identifying an individual.

Keywords: Genetic data, Pinzgau cattle, supervised learning.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2320

Authors: Noor Muzamil Mohamad, Abdul Manaf Ali, Hamzah Mohd Salleh

Abstract:

Phytases (myo-inositol hexakisphosphate phosphohydrolases; EC 3.1.3.8) catalyze the hydrolysis of phytic acid (myoinositol hexakisphosphate) to the mono-, di-, tri-, tetra-, and pentaphosphates of myo-inositol and inorganic phosphate. Therrmophilic bacteria isolated from water sampled from hot spring. About 120 isolates of bacteria were successfully isolated form hot spring water sample and tested for extracellular phytase producing. After 5 passages of the screening on the PSM media, 4 isolates were found stable in producing phytase enzyme. The 16s RDNA sequencing for identification of bacteria using molecular technique revealed that all isolates those positive in phytase producing are belong to Geobacillus spp. And Anoxybacillus spp. Anoxybacillus rupiensis UniSZA-7 were identified for their carbon source utilization using Phenotype Microarray Plate of Biolog and found they utilize several kind of carbon source provided.

Keywords: Phytase, Phytic Acid, Thermophilic Bacteria, PSM Media and Phytase Assay

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2166

Authors: Ruoyang Tang, Jianguo Nie

Abstract:

Lateral-torsional bracing members are critical to the stability of girder systems during the construction phase of steel-concrete composite bridges, and the interaction effect of multiple girders plays an essential role in the determination of buckling load. In this paper, an investigation is conducted on the lateral-torsional buckling behavior of the steel girder system which is composed of three or four I-shaped girders and braced by solid web crossbeams. The buckling load for such girder system is comprehensively analyzed and an analytical solution is developed for uniform pressure loading conditions. Furthermore, post-buckling analysis including initial geometric imperfections is performed and parametric studies in terms of bracing density, stiffness ratio as well as the number and spacing of girders are presented in order to find the optimal bracing plans for an arbitrary girder layout. The theoretical solution of critical load on account of local buckling mode shows good agreement with the numerical results in eigenvalue analysis. In addition, parametric analysis results show that both bracing density and stiffness ratio have a significant impact on the initial stiffness, global stability and failure mode of such girder system. Taking into consideration the effect of initial geometric imperfections, an increase in bracing density between adjacent girders can effectively improve the bearing capacity of the structure, and higher beam-girder stiffness ratio can result in a more ductile failure mode.

Keywords: Bracing member, construction stage, lateral-torsional buckling, steel girder system.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 552

Authors: K. S. Sivakumaran, Bo Chen

Abstract:

The floor beams of steel buildings, cold-formed steel floor joists in particular, often require large web openings, which may affect their shear capacities. A cost effective way to mitigate the detrimental effects of such openings is to weld/fasten reinforcements. A difficulty associated with an experimental investigation to establish suitable reinforcement schemes for openings in shear zone is that moment always coexists with the shear, and thus, it is impossible to create pure shear state in experiments, resulting in moment influenced results. However, Finite Element Method (FEM) based analysis can be conveniently used to investigate the pure shear behaviour of webs including webs with reinforced openings. This paper presents the details associated with the finite element analysis of thick/thin-plates (representing the web of hot-rolled steel beam, and the web of a cold-formed steel member) having a large reinforced opening. The study considered simply-supported rectangular plates subjected to in-plane shear loadings until failure (including post-buckling behaviour). The plate was modelled using geometrically non-linear quadrilateral shell elements, and non-linear stress-strain relationship based on experiments. Total Langrangian with large displacement/small strain formulation was used for such analyses. The model also considered the initial geometric imperfections. This study considered three reinforcement schemes, namely, flat, lip, and angle reinforcements. This paper discusses the modelling considerations and presents the results associated with the various reinforcement schemes under consideration.

Keywords: Cold-formed steel, finite element analysis, opening, reinforcement, shear resistance.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2021

Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

Abstract:

In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1919

Authors: Comingstarful Marthong, Deba Kumar Sarma

Abstract:

Concrete is strong in compression however weak in tension. The tensile strength as well as ductile property of concrete could be improved by addition of short dispersed fibers. Polyethylene terephthalate (PET) fiber obtained from hand cutting or mechanical slitting of plastic sheets generally used as discrete reinforcement in substitution of steel fiber. PET fiber obtained from the former process is in the form of straight slit sheet pattern that impart weaker mechanical bonding behavior in the concrete matrix. To improve the limitation of straight slit sheet fiber the present study considered two additional geometry of fiber namely (a) flattened end slit sheet and (b) deformed slit sheet. The mix for plain concrete was design for a compressive strength of 25 MPa at 28 days curing time with a watercement ratio of 0.5. Cylindrical and beam specimens with 0.5% fibers volume fraction and without fibers were cast to investigate the influence of geometry on the mechanical properties of concrete. The performance parameters mainly studied include flexural strength, splitting tensile strength, compressive strength and ultrasonic pulse velocity (UPV). Test results show that geometry of fiber has a marginal effect on the workability of concrete. However, it plays a significant role in achieving a good compressive and tensile strength of concrete. Further, significant improvement in term of flexural and energy dissipation capacity were observed from other fibers as compared to the straight slit sheet pattern. Also, the inclusion of PET fiber improved the ability in absorbing energy in the post-cracking state of the specimen as well as no significant porous structures.

Keywords: Concrete matrix, polyethylene terephthalate (PET) fibers, mechanical bonding, mechanical properties, UPV.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2054

Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

Abstract:

The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1633

Authors: Nurhayati Abdullah, Fauziah Sulaiman, Muhamad Azman Miskam, Rahmad Mohd Taib

Abstract:

Banana pseudo-stem and fruit-bunch-stem are agricultural residues that can be used for conversion to bio-char, biooil, and gases by using thermochemical process. The aim of this work is to characterize banana pseudo-stem and banana fruit-bunch-stem through proximate analysis, elemental analysis, chemical analysis, thermo-gravimetric analysis, and heating calorific value. The ash contents of the banana pseudo-stem and banana fruit-bunch-stem are 11.0 mf wt.% and 20.6 mf wt.%; while the carbon content of banana pseudo-stem and fruit-bunch-stem are 37.9 mf wt.% and 35.58 mf wt.% respectively. The molecular formulas for banana stem and banana fruit-bunch-stem are C24H33NO26 and C19H29NO33 respectively. The measured higher heating values of banana pseudostem and banana fruit-bunch-stem are 15.5MJ/kg and 12.7 MJ/kg respectively. By chemical analysis, the lignin, cellulose, and hemicellulose contents in the samples will also be presented. The feasibility of the banana wastes to be a feedstock for thermochemical process in comparison with other biomass will be discussed in this paper.

Keywords: Banana Waste, Biomass, Renewable Energy, Thermo-chemical Characteristics.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 8753

Authors: Jin Xu, Albert Y.S. Lam, Victor O.K. Li

Abstract:

Stock portfolio selection is a classic problem in finance, and it involves deciding how to allocate an institution-s or an individual-s wealth to a number of stocks, with certain investment objectives (return and risk). In this paper, we adopt the classical Markowitz mean-variance model and consider an additional common realistic constraint, namely, the cardinality constraint. Thus, stock portfolio optimization becomes a mixed-integer quadratic programming problem and it is difficult to be solved by exact optimization algorithms. Chemical Reaction Optimization (CRO), which mimics the molecular interactions in a chemical reaction process, is a population-based metaheuristic method. Two different types of CRO, named canonical CRO and Super Molecule-based CRO (S-CRO), are proposed to solve the stock portfolio selection problem. We test both canonical CRO and S-CRO on a benchmark and compare their performance under two criteria: Markowitz efficient frontier (Pareto frontier) and Sharpe ratio. Computational experiments suggest that S-CRO is promising in handling the stock portfolio optimization problem.

Keywords: Stock portfolio selection, Markowitz model, Chemical Reaction Optimization, Sharpe ratio

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2075

Authors: Hyung T. Kwak, Jun Gao, Yao An, Alfred Kleinhammes, Yue Wu

Abstract:

Surface wettability is a crucial factor in oil recovery. In oil industry, the rock wettability involves the interplay between water, oil, and solid surface. Therefore, studying the interplay between adsorptions of water and hydrocarbon molecules on solid surface would be very informative for understanding rock wettability. Here we use the in-situ Nuclear Magnetic Resonance (NMR) gas isotherm technique to study competitive adsorptions of water and isopropanol, an intermediate step from hydrocarbons. This in-situ NMR technique obtains information on thermodynamic properties such as the isotherm, molecular dynamics via spin relaxation measurements, and adsorption kinetics such as how fast the system can reach thermal equilibrium after changes of vapor pressures. Using surfaces of silica glass beads, which can be modified from hydrophilic to hydrophobic, we obtained information on the influence of surface hydrophilicity on the state of surface water via obtained thermodynamic and dynamic properties.

Keywords: Competitive adsorption, nuclear magnetic resonance, wettability.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 730

Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

Abstract:

To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1365

Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

Abstract:

Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1769

Authors: Ibrahim Abdul Razak, Suhana Arshad, Nur Rafikah Razali, Azhar Abdul Rahman, Mohd Sukeri Mohd Yusof

Abstract:

Theoretical investigations are performed by DFT method of B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p) basis sets for three carbonyl thiourea compounds, namely N-[(2,6-Diethylphenyl)carbamothioyl]-2,2-diphenylacetamide (Compound I), N-[(3-Ethylphenyl)carbamothioyl]-2,2-diphenylacetamide (Compound II) and 2,2-Diphenyl-N-{[2-(trifluoromethyl)phenyl]carbamothioyl}acetamide (Compound III). Theoretical calculations for bond parameters, harmonic vibration frequencies and isotropic chemical shifts are in good agreement with the experimental results. The calculated molecular vibrations show good correlation values, which are 0.998 and 0.999 with the experimental data. The energy gap for compounds I, II and III calculated at B3LYP/6-31G+(2d,p) basis set are 4.455866117, 4.297495791 and 4.313550514 eV respectively, while for B3LYP/6-311G+(2d,p) basis set the energy gap obtained are 4.453689205 (Compound I), 4.311373603 (Compound II) and 4.315727426 (Compound III) eV.

Keywords: Crystallization, DFT studies, Spectroscopic Analysis, Thiourea.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1651

Authors: K. Santacruz-Gomez, E. Silva-Campa, S. Álvarez-García, V. Mata-Haro, D. Soto-Puebla, M. Pedroza-Montero

Abstract:

Blood gamma irradiation is the only available method to prevent transfusion associated graft versus host disease (TAGVHD). However, when blood is irradiated, determine blood shelf time is crucial. Non irradiated blood have a self-time from 21 to 35 days when is preserved with anticoagulated solution and stored at 4°C. During their storage, red blood cells (RBC) undergo a series of biochemical, biomechanical and molecular changes involving what is known as storage lesion (SL). SL include loss of structural integrity of RBC, decrease of 2,3-diphosphatidylglyceric acid levels, and increase of both ion potassium concentration and hemoglobin (Hb). On the other hand, Atomic force Microscopy (AFM) represents a versatile tool for a nano-scale high resolution topographic analysis in biological systems. In order to evaluate SL in irradiated and nonirradiated blood, RBC topography and morphometric parameters were obtained from an AFM XE-BIO system. Cell viability was followed using flow cytometry. Our results showed that early markers as nanoscale roughness, allow us to evaluate blood quality since other perspective.

Keywords: AFM, Blood γ-irradiation, roughness, Storage lesion.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2697

Authors: Phakamas Rachamontree, Theerawut Phusantisampan, Natthakorn Woravutthikul, Peerapong Pornwongthong, Malinee Sriariyanun

Abstract:

A total of 115 yeast strains isolated from local cassava processing wastes were measured for crude protein content. Among these strains, the strain MSY-2 possessed the highest protein concentration (>3.5 mg protein/mL). By using molecular identification tools, it was identified to be a strain of Pichia kudriavzevii based on similarity of D1/D2 domain of 26S rDNA region. In this study, to optimize the protein production by MSY-2 strain, Response Surface Methodology (RSM) was applied. The tested parameters were the carbon content, nitrogen content, and incubation time. Here, the value of regression coefficient (R2) = 0.7194 could be explained by the model which is high to support the significance of the model. Under the optimal condition, the protein content was produced up to 3.77 g per L of the culture and MSY-2 strain contains 66.8 g protein per 100 g of cell dry weight. These results revealed the plausibility of applying the novel strain of yeast in single-cell protein production.

Keywords: Single cell protein, response surface methodology, yeast, cassava processing waste.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2682

Authors: Nazli Darkhal

Abstract:

The use of gems and ornaments has been common in Iran since the beginning of history. The prosperity of the country, the wealth, and the interest of the people of this land in a luxurious and glorious life, combined with beauty, have always attracted the attention of Iranian people to gems and jewelry. Iranians are famous in the world for having a long history of collecting and recognizing precious stones. In this case, we can use the unique treasure of national jewelry. Raman spectroscopy method is one of the oscillating spectroscopy methods that is classified in the group of nondestructive study methods, and like other methods, in addition to several advantages, it also has disadvantages and problems. Micro Raman spectroscopy is one of the different types of Raman spectroscopy in which an optical microscope is combined with a Raman device to provide more capabilities and advantages than its original method. In this way, with the help of Raman spectroscopy and a light microscope, while observing more details from different parts of the historical sample, natural or artificial pigments can be identified in a small part of it. The EDX (Energy Dispersive X ray) electron microscope also functions as the basis for the interaction of the electron beam with the matter. The beams emitted from this interaction can be used to examine samples. In this article, in addition to introducing the micro-Raman spectroscopy method, studies have been conducted on the structure of three samples of existing stones in the historic citadel of Bam. Using this method of study on precious and semi-precious stones, in addition to requiring a short time, can provide us with complete information about the structure and theme of these samples. The results of experiments and gemology of the stones showed that the selected beads are agate and jasper, and they can be placed in the chalcedony group.

Keywords: Bam citadel, precious stones, semi-precious stones, Raman spectroscopy, scanning electron microscope.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 416

Authors: Yuekun Chen, Yousef Sardahi, Salam Hajjar, Christopher Greer

Abstract:

This paper presents a multi-objective optimal design of a cascade control system for an underactuated mechanical system. Cascade control structures usually include two control algorithms (inner and outer). To design such a control system properly, the following conflicting objectives should be considered at the same time: 1) the inner closed-loop control must be faster than the outer one, 2) the inner loop should fast reject any disturbance and prevent it from propagating to the outer loop, 3) the controlled system should be insensitive to measurement noise, and 4) the controlled system should be driven by optimal energy. Such a control problem can be formulated as a multi-objective optimization problem such that the optimal trade-offs among these design goals are found. To authors best knowledge, such a problem has not been studied in multi-objective settings so far. In this work, an underactuated mechanical system consisting of a rotary servo motor and a ball and beam is used for the computer simulations, the setup parameters of the inner and outer control systems are tuned by NSGA-II (Non-dominated Sorting Genetic Algorithm), and the dominancy concept is used to find the optimal design points. The solution of this problem is not a single optimal cascade control, but rather a set of optimal cascade controllers (called Pareto set) which represent the optimal trade-offs among the selected design criteria. The function evaluation of the Pareto set is called the Pareto front. The solution set is introduced to the decision-maker who can choose any point to implement. The simulation results in terms of Pareto front and time responses to external signals show the competing nature among the design objectives. The presented study may become the basis for multi-objective optimal design of multi-loop control systems.

Keywords: Cascade control, multi-loop control systems, multi-objective optimization, optimal control.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 925

Authors: Zeynep R. Ege, Aydin Akan, Faik N. Oktar, Betul Karademir, Oguzhan Gunduz

Abstract:

Early detection of cancer could save human life and quality in insidious cases by advanced biomedical imaging techniques. Designing targeted detection system is necessary in order to protect of healthy cells. Electrospun nanofibers are efficient and targetable nanocarriers which have important properties such as nanometric diameter, mechanical properties, elasticity, porosity and surface area to volume ratio. In the present study, indocyanine green (ICG) organic dye was stabilized and encapsulated in polymer matrix which polyethylene oxide (PEO) and chitosan (CHI) multilayer nanofibers via co-axial electrospinning method at one step. The co-axial electrospun nanofibers were characterized as morphological (SEM), molecular (FT-IR), and entrapment efficiency of Indocyanine Green (ICG) (confocal imaging). Controlled release profile of PEO/CHI/ICG nanofiber was also evaluated up to 40 hours.

Keywords: Chitosan, coaxial electrospinning, controlled releasing, indocyanine green, nanoprobe, polyethylene oxide.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 765

Authors: M. Inmaculada Alvarez-Fernández, Celestino González-Nicieza, M. Belén Prendes-Gero, Fernando López-Gayarre

Abstract:

Among many factors affecting the stability of mining excavations, rock-bursts and tremors play a special role. These dynamic loads occur practically always and have different sources of generation. The most important of them is the commonly used mining technique, which disintegrates a certain area of the rock mass not only in the area of the planned mining, but also creates waves that significantly exceed this area affecting the structural elements. In this work it is analysed the consequences of dynamic loads over the structural elements in an underground room and pillar mine to avoid roof instabilities. With this end, dynamic loads were evaluated through in situ and laboratory tests and simulated with numerical modelling. Initially, the geotechnical characterization of all materials was carried out by mean of large-scale tests. Then, drill holes were done on the roof of the mine and were monitored to determine possible discontinuities in it. Three seismic stations and a triaxial accelerometer were employed to measure the vibrations from blasting tests, establish the dynamic behaviour of roof and pillars and develop the transmission laws. At last, computer simulations by FLAC3D software were done to check the effect of vibrations on the stability of the roofs. The study shows that in-situ tests have a greater reliability than laboratory samples because of eliminating the effect of heterogeneities, that the pillars work decreasing the amplitude of the vibration around them, and that the tensile strength of a beam and depending on its span is overcome with waves in phase and delayed. The obtained transmission law allows designing a blasting which guarantees safety and prevents the risk of future failures.

Keywords: Dynamic modelling, long term instability risks, room and pillar, seismic collapse.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 485

Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 804

Authors: Mehdi Shamshiri, Mahmud Ashrafizaadeh

Abstract:

The significant effects of the interactions between the system boundaries and the near wall molecules in miniaturized gaseous devices lead to the formation of the Knudsen layer in which the Navier-Stokes-Fourier (NSF) equations fail to predict the correct associated phenomena. In this paper, the well-known lattice Boltzmann method (LBM) is employed to simulate the fluid flow and heat transfer processes in rarefied gaseous micro media. Persuaded by the problematic deficiency of the LBM in capturing the Knudsen layer phenomena, present study tends to concentrate on the effective molecular mean free path concept the main essence of which is to compensate the incapability of this mesoscopic method in dealing with the momentum and energy transport within the above mentioned kinetic boundary layer. The results show qualitative and quantitative accuracy comparable to the solutions of the linearized Boltzmann equation or the DSMC data for the Knudsen numbers of O (1) .

Keywords: Fluid flow and Heat transfer, Knudsen layer, Lattice Boltzmann method (LBM), Micro-scale numerical simulation, Transition regime.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1763

Authors: Binnur Sagbas

Abstract:

Artificial joint replacements such as total knee and total hip prosthesis have been applied to the patients who affected by osteoarthritis. Although different material combinations are used for these joints, biopolymers are most commonly preferred materials especially for acetabular cup and tibial component of hip and knee joints respectively. The main limitation that shortens the service life of these prostheses is wear. Wear is complicated phenomena and it must be considered with friction and lubrication. In this study, micro wave (MW) induced argon+oxygen plasma surface modification were applied on ultra-high molecular weight polyethylene (UHMWPE) and vitamin E blended UHMWPE (VE-UHMWPE) biopolymer surfaces to improve surface wettability and wear resistance of the surfaces. Contact angel measurement method was used for determination of wettability. Ball-on-disc wear test was applied under 25% bovine serum lubrication conditions. The results show that surface wettability and wear resistance of both material samples were increased by plasma surface modification.

Keywords: Artificial joints, plasma surface modification, UHMWPE, vitamin E, wear.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1630

Authors: Suman Bala, Sunil Kamboj, Vipin Saini

Abstract:

Quantitative Structure Activity Relationship (QSAR) analysis has been developed to relate antifungal activity of novel substituted 1,3,4-oxadiazole against Candida albicans and Aspergillus niger using computer assisted multiple regression analysis. The study has shown the better relationship between antifungal activities with respect to various descriptors established by multiple regression analysis. The analysis has shown statistically significant correlation with R² values 0.932 and 0.782 against Candida albicans and Aspergillus niger respectively. These derivatives were further subjected to molecular docking studies to investigate the interactions between the target compounds and amino acid residues present in the active site of glucosamine-6-phosphate synthase. All the synthesized compounds have better docking score as compared to standard fluconazole. Our results could be used for the further design as well as development of optimal and potential antifungal agents.

Keywords: 1, 3, 4-Oxadiazole, QSAR, Multiple linear regression, Docking, Glucosamine-6-Phosphate Synthase.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1597

Authors: Pravin S. Bodke, Shradha S. Binani, Ravi V. Joat

Abstract:

Science and technology of ultrasonic is widely used in recent years for industrial and medicinal application. The acoustical properties of 2-mercapto substituted pyrimidines viz.,2- Mercapto-4- (2’,4’ –dichloro phenyl) – 6-(2’ – hydroxyl -4’ –methyl-5’ – chlorophenyl) pyrimidine and 2 –Mercapto – 4-(4’ –chloro phenyl) – 6-(2’ – hydroxyl -4’ –methyl-5’ –chlorophenyl) pyrimidine have been investigated from the ultrasonic velocity and density measurements at different concentration and different % in dioxane-water mixture at 305K. The adiabatic compressibility (βs), acoustic impedance (Z), intermolecular free length (Lf), apparent molar volume(ϕv) and relative association (RA) values have been calculated from the experimental data of velocity and density measurement at concentration range of 0.01- 0.000625 mol/lit and 70%,75% and 80% dioxane water mixture. These above parameters are used to discuss the structural and molecular interactions.

Keywords: Acoustical parameters, Density, Dioxane-water mixture, Ultrasonic velocity.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1647

Authors: M. Hashemi, R. Madani, N. Razmi

Abstract:

M. paratuberculosis is a slow growing mycobactin dependent mycobacterial species known to be the causative agent of Johne’s disease in all species of domestic ruminants worldwide. JD is characterized by gradual weight loss; decreased milk production. Excretion of the organism may occur for prolonged periods (1 to 2.5 years) before the onset of clinical disease. In recent years researchers focus on identification a specific antigen of MAP to use in diagnosis test and preparation of effective vaccine. In this paper, for production of polyclonal antibody against proteins of Mycobacterium avium paratuberculosis cell well a rabbit immunization at a certain time period with antigen. After immunization of the animal, rabbit was bleeded for producing enriched serum. Antibodies were purification with ion exchange chromatography. For exact measurement of interaction, western blotting test was used that this study demonstrated sharp bands appears in nitrocellulose paper and specific bands were 50 and 150 KD molecular weight. These were indicating immunodominant proteins.

Keywords: Paratuberculosis, Immunodominant, Western blotting, Ion exchange choromatography.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1758

Authors: L. V. Ignatova, Y. V. Brazhnikova, T. D. Mukasheva, A. A. Omirbekova, R. Zh. Berzhanova, R. K. Sydykbekova, T. A. Karpenyuk, A. V. Goncharova

Abstract:

The comparative analysis of different taxonomic groups of microorganisms isolated from dark chernozem soils under different agricultures (alfalfa, melilot, sainfoin, soybean, rapeseed) at Almaty region of Kazakhstan was conducted. It was shown that the greatest number of micromycetes was typical to the soil planted with alfalfa and canola. Species diversity of micromycetes markedly decreases as it approaches the surface of the root, so that the species composition in the rhizosphere is much more uniform than in the virgin soil. Promising strains of microscopic fungi and yeast with plant growth-promoting activity to agricultures were selected. Among the selected fungi there are representatives of Penicillium bilaiae, Trichoderma koningii, Fusarium equiseti, Aspergillus ustus. The highest rates of growth and development of seedlings of plants observed under the influence of yeasts Aureobasidium pullulans, Rhodotorula mucilaginosa, Metschnikovia pulcherrima. Using molecular - genetic techniques confirmation of the identification results of selected micromycetes was conducted.

Keywords: Agricultures, biodiversity, micromycetes, plant growth-promoting microorganisms.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2652

Authors: Juliana V. Pereira, Adriana S. M. Batista, Jefferson P. Nascimento, Clascídia A. Furtado, Luiz O. Faria

Abstract:

The combination of the properties of graphene oxide (OG) and PVDF homopolymer makes their combined composite materials as multifunctional systems with great potential. Knowledge of the molecular structure is essential for better use. In this work, the degradation of PVDF polymer exposed to gamma irradiation in oxygen atmosphere in high dose rate has been studied and compared to degradation of PVDF/OG composites. The samples were irradiated with a Co-60 source at constant dose rate, with doses ranging from 100 kGy to 1,000 kGy. In FTIR data shown that the formation of oxidation products was at the both samples with formation of carbonyl and hydroxyl groups amongst the most prevalent products in the pure PVDF samples. In the other hand, the composites samples exhibit less presence of degradation products with predominant formation of carbonyl groups, these results also seen in the UV-Vis analysis. The results show that the samples of composites may have greater resistance to the irradiation process, since they have less degradation products than pure PVDF samples seen by spectroscopic techniques.

Keywords: Gamma irradiation, PVDF, PVDF/OG composites, spectroscopic techniques.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2139

Authors: Ahmed, M., Yasser A., Mahmoud H., Ahmed, A., Abdulla M. S., Nazar, S.

Abstract:

Strut-and-Tie Models (STM) for the design of concrete beams, comprising of struts, ties, nodes as the basic tools, is conceptually simple, but its realization for complex concrete structure is not straightforward and depends on flow of internal forces in the structure. STM technique has won wide acceptance for deep member and shear design. STM technique is a unified approach that considers all load effects (bending, axial, shear, and torsion) simultaneously, not just applicable to shear loading only. The present study is to portray Strut-and-Tie Modeling based on Load-Transfer-Mechanisms as a unified method to analyze, design and detailing for deep and slender concrete beams. Three shear span- effective depth ratio (a/ d) are recommended for the modeling of STM elements corresponding to dominant load paths. The study also discusses the research work conduct on effective stress of concrete, tie end anchorage, and transverse reinforcement demand under different load transfer mechanism. It is also highlighted that to make the STM versatile tool for design of beams applicable to all shear spans, the effective stress of concrete and, transverse reinforcement demand, inclined angle of strut, and anchorage requirements of tie bars is required to be correlated with respect to load transfer mechanism. The country code provisions are to be modified and updated to apply for generalized design of concrete deep and slender member using load transfer mechanism based STM technique. Examples available in literature are reanalyzed with refined STM based on load transfer mechanisms and results are compared. It is concluded from the results that proposed approach will require true reinforcement demand depending on dominant force transfer action in concrete beam.

Keywords: Deep member, Load transfer mechanism, Strut-and-Tie Model, Strut, Truss.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 5991

Authors: Puntipar Sonthiphand, Tawan Limpiyakorn

Abstract:

In this study, communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrifying activated sludge (NAS) prepared by enriching sludge from a municipal wastewater treatment plant in three continuous-flow reactors receiving an inorganic medium containing different ammonium concentrations of 2, 10, and 30 mM NH4 +-N (NAS2, NAS10, and NAS30, respectively) were investigated using molecular analysis. Results suggested that almost all AOA clones from NAS2, NAS10, and NAS30 fell into the same AOA cluster and AOA communities in NAS2 and NAS10 were more diverse than those of NAS30. In contrast to AOA, AOB communities obviously shifted from the seed sludge to enriched NASs and in each enriched NAS, communities of AOB varied particularly. The seed sludge contained members of N. communis cluster and N. oligotropha cluster. After it was enriched under various ammonium loads, members of N. communis cluster disappeared from all enriched NASs. AOB with high affinity to ammonia presented in NAS 2, AOB with low affinity to ammonia presented in NAS 30, and both types of AOB survived in NAS 10. These demonstrated that ammonium load significantly influenced AOB communities, but not AOA communities in enriched NASs.

Keywords: ammonia-oxidizing bacteria, ammonia-oxidizingarchaea, nitrifying activated sludge.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1588

Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

Abstract:

Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1895