Search results for: Molecular Modeling

Authors: Dileep Kumar, Janhavi Ramchandra Rao Kumar, Rao

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COVID-19 has ravaged the globe, and it is spreading its Spectre day by day. In the absence of established drugs, this disease has created havoc. Some of the infected persons are symptomatic or asymptomatic. The respiratory system, cardiac system, digestive system, etc. in human beings are affected by this virus. In our present investigation, we have undertaken a study of the Indian Ayurvedic herb, Ocimum sanctum against SARS-CoV-2 using molecular docking and dynamics studies. The docking analysis was performed on the Glide module of Schrödinger suite on two different proteins from SARS-CoV-2 viz. NSP15 Endoribonuclease and spike receptor-binding domain. MM-GBSA based binding free energy calculations also suggest the most favorable binding affinities of carvacrol, β elemene, and β caryophyllene with binding energies of −61.61, 58.23, and −54.19 Kcal/mol respectively with spike receptor-binding domain and NSP15 Endoribonuclease. It rekindles our hope for the design and development of new drug candidates for the treatment of COVID19.

Keywords: molecular docking, COVID-19, ocimum sanctum, binding energy

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Authors: Sina Saadati, Mohammadreza Razzazi

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In this article, we have tried to present an agent-based model of human muscle. A suitable model of muscle is necessary for the analysis of mankind's movements. It can be used by clinical researchers who study the influence of motion sicknesses, like Parkinson's disease. It is also useful in the development of a prosthesis that receives the electromyography signals and generates force as a reaction. Since we have focused on computational efficiency in this research, the model can compute the calculations very fast. As far as it concerns prostheses, the model can be known as a charge-efficient method. In this paper, we are about to illustrate an agent-based model. Then, we will use it to simulate the human gait cycle. This method can also be done reversely in the analysis of gait in motion sicknesses.

Keywords: agent-based modeling and simulation, human muscle, gait cycle, motion sickness

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Authors: Mueller Jann, Hoffmann Christian Hugo

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Conventional quantitative risk management in banking is a risk factor of its own, because it rests on assumptions such as independence and availability of data which do not hold when rare events of extreme consequences are involved. There is a growing recognition of the need for alternative risk measures that do not make these assumptions. We propose a novel method for modeling the risk associated with investment products, in particular derivatives, by using a formal language for specifying financial contracts. Expressions in this language are interpreted in the category of values annotated with (a formal representation of) uncertainty. The choice of uncertainty formalism thus becomes a parameter of the model, so it can be adapted to the particular application and it is not constrained to classical probabilities. We demonstrate our approach using a simple logic-based uncertainty model and a case study in which we assess the risk of counter party default in a portfolio of collateralized loans.

Keywords: risk model, uncertainty monad, derivatives, contract algebra

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Authors: Virendra J. Majarikar, Harikrishnan N. Unni

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This paper sets to demonstrate a modeling of electrokinetic mixing employing electroosmotic stationary and time-dependent microchannel using alternate zeta patches on the lower surface of the micromixer in a lab on chip microfluidic device. Electroosmotic flow is amplified using different 2D and 3D model designs with alternate and geometric zeta potential values such as 25, 50, and 100 mV, respectively, to achieve high concentration mixing in the electrokinetically-driven microfluidic system. The enhancement of electrokinetic mixing is studied using Finite Element Modeling, and simulation workflow is accomplished with defined integral steps. It can be observed that the presence of alternate zeta patches can help inducing microvortex flows inside the channel, which in turn can improve mixing efficiency. Fluid flow and concentration fields are simulated by solving Navier-Stokes equation (implying Helmholtz-Smoluchowski slip velocity boundary condition) and Convection-Diffusion equation. The effect of the magnitude of zeta potential, the number of alternate zeta patches, etc. are analysed thoroughly. 2D simulation reveals that there is a cumulative increase in concentration mixing, whereas 3D simulation differs slightly with low zeta potential as that of the 2D model within the T-shaped micromixer for concentration 1 mol/m³ and 0 mol/m³, respectively. Moreover, 2D model results were compared with those of 3D to indicate the importance of the 3D model in a microfluidic design process.

Keywords: COMSOL Multiphysics®, electrokinetic, electroosmotic, microfluidics, zeta potential

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Authors: Mohammadjavad Sotoudeheian

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Heart failure (HF) prevalence, as a global cardiovascular problem, is increasing gradually. A variety of molecular mechanisms contribute to HF. Proteins involved in cardiac contractility regulation, such as ion channels and calcium handling proteins, are altered. Additionally, epigenetic modifications and gene expression can lead to altered cardiac function. Moreover, inflammation and oxidative stress contribute to HF. The progression of HF can be attributed to mitochondrial dysfunction that impairs energy production and increases apoptosis. Molecular mechanisms such as these contribute to the development of cardiomyocyte defects and HF and can be therapeutically targeted. The heart's contractile function is controlled by cardiomyocytes. Calpain, and its related molecules, including Bax, VEGF, and AMPK, are among the proteins involved in regulating cardiomyocyte function. Apoptosis is facilitated by Bax. Cardiomyocyte apoptosis is regulated by this protein. Furthermore, cardiomyocyte survival, contractility, wound healing, and proliferation are all regulated by VEGF, which is produced by cardiomyocytes during inflammation and cytokine stress. Cardiomyocyte proliferation and survival are also influenced by AMPK, an enzyme that plays an active role in energy metabolism. They all play key roles in apoptosis, angiogenesis, hypertrophy, and metabolism during myocardial inflammation. The role of calpains has been linked to several molecular pathways. The calpain pathway plays an important role in signal transduction and apoptosis, as well as autophagy, endocytosis, and exocytosis. Cell death and survival are regulated by these calcium-dependent cysteine proteases that cleave proteins. As a result, protein fragments can be used for various cellular functions. By cleaving adhesion and motility proteins, calcium proteins also contribute to cell migration. HF may be brought about by calpain-mediated pathways. Many physiological processes are mediated by the calpain molecular pathways. Signal transduction, cell death, and cell migration are all regulated by these molecular pathways. Calpain is activated by calcium binding to calmodulin. In the presence of calcium, calmodulin activates calpain. Calpains are stimulated by calcium, which increases matrix metalloproteinases (MMPs). In order to develop novel treatments for these diseases, we must understand how this pathway works. A variety of myocardial remodeling processes involve calpains, including remodeling of the extracellular matrix and hypertrophy of cardiomyocytes. Calpains also play a role in maintaining cardiac homeostasis through apoptosis and autophagy. The development of HF may be in part due to calpain-mediated pathways promoting cardiomyocyte death. Numerous studies have suggested the importance of the Ca2+ -dependent protease calpain in cardiac physiology and pathology. Therefore, it is important to consider this pathway to develop and test therapeutic options in humans that targets calpain in HF. Apoptosis, autophagy, endocytosis, exocytosis, signal transduction, and disease progression all involve calpain molecular pathways. Therefore, it is conceivable that calpain inhibitors might have therapeutic potential as they have been investigated in preclinical models of several conditions in which the enzyme has been implicated that might be treated with them. Ca 2+ - dependent proteases and calpains contribute to adverse ventricular remodeling and HF in multiple experimental models. In this manuscript, we will discuss the calpain molecular pathway's important roles in HF development.

Keywords: calpain, heart failure, autophagy, apoptosis, cardiomyocyte

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Authors: Felix U. Asoiro, Kingsley O. Anyichie, Meshack I. Simeon, Chinenye E. Azuka

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The work was aimed at studying the effects of microwave drying (450 W) and hot air oven drying on the drying kinetics and physico-functional properties of yams and cocoyams species. The yams and cocoyams were cut into chips of thicknesses of 3mm, 5mm, 7mm, 9mm, and 11mm. The drying characteristics of yam and cocoyam chips were investigated under microwave drying and hot air oven temperatures (50oC – 90oC). Drying methods, temperature, and thickness had a significant effect on the drying characteristics and physico-functional properties of yam and cocoyam. The result of the experiment showed that an increase in the temperature increased the drying time. The result also showed that the microwave drying method took lesser time to dry the samples than the hot air oven drying method. The iodine affinity of starch for yam was higher than that of cocoyam for the microwaved dried samples over those of hot air oven-dried samples. The results of the analysis would be useful in modeling the drying behavior of yams and cocoyams under different drying methods. It could also be useful in the improvement of shelf life for yams and cocoyams as well as designs of efficient systems for drying, handling, storage, packaging, processing, and transportation of yams and cocoyams.

Keywords: coco yam, drying, microwave, modeling, energy consumption, iodine affinity, drying ate

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Authors: Joseph E. Estevez, Mahdi Ghazizadeh, James G. Ryan, Ajit D. Kelkar

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Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B10’s large neutron capture cross section. The B10 has an effective neutron capture cross section suitable for low energy neutrons ranging from 10-5 to 104 eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm3. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.

Keywords: boron nitride nanotube, radiation shielding, young modulus, atomistic modeling

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Authors: Csaba Tóth, Éva Lakatos, László Pethő, Seoyoung Cho

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The temperature effect on asphalt pavement structure is a crucial factor at the design stage. In this paper, by applying the German guidelines for temperature along the asphalt depth is estimated. The aim is to consider temperature profiles in different seasons in numerical modelling. The model is built with an elastic and isotropic solid element with 19 subdivisions of asphalt layers to reflect the temperature variation. Comparison with the simple three-layer pavement system (asphalt layers, base, and subgrade layers) will be followed to see the difference in result without temperature variation along with the depth. Finally, the fatigue life calculation was checked to prove the validity of the methodology of considering the temperature in the numerical modelling.

Keywords: temperature profile, flexible pavement modeling, finite element method, temperature modeling

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Authors: Sergey M. Karabanov, Dmitry V. Suvorov, Dmitry Yu. Tarabrin

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The operating principle of magnetically controlled microelectromechanical system (MEMS) switches is based on controlling the beam movement under the influence of a magnetic field. Currently, there is a MEMS switch design with a flexible ferromagnetic electrode in the form of a fixed-terminal beam, with an electrode fastened on a straight or cranked anchor. The basic performance characteristics of magnetically controlled MEMS switches (service life, sensitivity, contact resistance, fast response) are largely determined by the flexible electrode design. To ensure the stable and controlled motion of the flexible electrode, it is necessary to provide the optimal design of a flexible electrode.

Keywords: flexible electrode, magnetically controlled MEMS, mathematical modeling, mechanical stress

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Authors: Ahmed S. Eissa

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Whey represents about 85-95% of the milk volume and about 55% of milk nutrients. Whey proteins are of special importance in formulated foods due to their rich nutritional and functional benefits. Whey proteins form large polymers upon heating to a temperature greater than the denaturation temperature. Hydrophobic interactions play an important role in building whey protein polymers. In this study, dissociation of hydrophobic interactions of whey protein polymers was done by adding Sodium Dodecyl Sulphonate (SDS). At low SDS concentrations, protein polymers were dissociated to smaller chains, as revealed by dilution solution viscometry (DSV). Interestingly, at higher SDS concentrations, polymer molecules got larger in size. Intrinsic viscosity was increased to many folds when raising the SDS concentration from 0.5% to 2%. Complex molecular arrangement leads to the formation of larger macromolecules, due to micelle formation. The study opens a venue for manipulating and enhancing whey protein functional properties by manipulating the hydrophobic interactions.

Keywords: whey proteins, hydrophobic interactions, SDS

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Authors: P. Charvin, R. Bourrou, F. Lemont, C. Lafon, A. Russello

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For nuclear waste treatment and confinement, a specific IN-CAN melting module based on low-frequency induction heating have been designed. The frequency of 50Hz has been chosen to improve penetration length through metal. In this design, the liquid metal, strongly stirred by electromagnetic effects, presents shape of a dome caused by strong Laplace forces developing in the bulk of bath. Because of a lower density, the glass phase is located above the metal phase and is heated and stirred by metal through interface. Electric parameters (Intensity, frequency) give precious information about metal load and composition (resistivity of alloy) through impedance modification. Then, power supply can be adapted to energy transfer efficiency for suitable process supervision. Modeling of this system allows prediction of metal dome shape (in agreement with experimental measurement with a specific device), glass and metal velocity, heat and motion transfer through interface. MHD modeling is achieved with COMSOL and Fluent. First, a simplified model is used to obtain the shape of the metal dome. Then the shape is fixed to calculate the fluid flow and the thermal part.

Keywords: electromagnetic stirring, induction heating, interface modeling, metal load

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Authors: Nour El Houda Bensiradj, Nafila Zouaghi, Taha Bensiradj

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The pollution of water resources is characterized by the presence of microorganisms, chemicals, or industrial waste. Generally, this waste generates effluents containing large quantities of heavy metals, making the water unsuitable for consumption and causing the death of aquatic life and associated biodiversity. Currently, it is very important to assess the impact of heavy metals in water pollution as well as the processes for treating and reducing them. Among the methods of water treatment and disinfection, we mention the complexation of metal ions using ligands which serve to precipitate and subsequently eliminate these ions. In this context, we are interested in the study of complexes containing heavy metals such as zinc, nickel, and cadmium, which are present in several industrial discharges and are discharged into water sources. We will use the ligands of triethanolamine (TEA) and nitrilotriacetic acid (NTA). The theoretical study is based on molecular modeling, using the density functional theory (DFT) implemented in the Gaussian 09 program. The geometric and energetic properties of the above complexes will be calculated. Spectral properties such as infrared, as well as reactivity descriptors, and thermodynamic properties such as enthalpy and free enthalpy will also be determined.

Keywords: heavy metals, NTA, TEA, DFT, IR, reactivity descriptors

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Authors: Mohamed Rabhi, Kouider Halim Benrahou

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The rheological properties of the carbonyl-methylcellulose (CMC), of different concentrations (25000, 50000, 60000, 80000 and 100000 ppm) and different temperatures were studied. We found that the rheological behavior of all CMC solutions presents a pseudo-plastic behavior, it follows the model of Ostwald-de Waele. The objective of this work is the modeling of flow by the CMC Cross model. The Cross model gives us the variation of the viscosity according to the shear rate. This model allowed us to adjust more clearly the rheological characteristics of CMC solutions. A comparison between the Cross model and the model of Ostwald was made. Cross the model fitting parameters were determined by a numerical simulation to make an approach between the experimental curve and those given by the two models. Our study has shown that the model of Cross, describes well the flow of "CMC" for low concentrations.

Keywords: CMC, rheological modeling, Ostwald model, cross model, viscosity

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Authors: Aneesh Joshi, Sagil James

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Cold Spray (CS) process is deposition of solid particles over a substrate above a certain critical impact velocity. Unlike thermal spray processes, CS process does not melt the particles thus retaining their original physical and chemical properties. These characteristics make CS process ideal for various engineering applications involving metals, polymers, ceramics and composites. The bonding mechanism involved in CS process is extremely complex considering the dynamic nature of the process. Though CS process offers great promise for several engineering applications, the realization of its full potential is limited by the lack of understanding of the complex mechanisms involved in this process and the effect of critical process parameters on the deposition efficiency. The goal of this research is to understand the complex nanoscale mechanisms involved in CS process. The study uses Molecular Dynamics (MD) simulation technique to understand the material deposition phenomenon during the CS process. Impact of a single crystalline copper nanoparticle on copper substrate is modelled under varying process conditions. The quantitative results of the impacts at different velocities, impact angle and size of the particles are evaluated using flattening ratio, von Mises stress distribution and local shear strain. The study finds that the flattening ratio and hence the quality of deposition was highest for an impact velocity of 700 m/s, particle size of 20 Å and an impact angle of 90°. The stress and strain analysis revealed regions of shear instabilities in the periphery of impact and also revealed plastic deformation of the particles after the impact. The results of this study can be used to augment our existing knowledge in the field of CS processes.

Keywords: cold spray process, molecular dynamics simulation, nanoparticles, particle impact

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Authors: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Karla Cautivo, Thomas Riley, Daniel Knight

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Clostridium difficile infection (CDI) is the most common cause of infectious diarrhea in hospitalised humans. C. difficile colonises the gastrointestinal tract, causes disease in a variety of animal species and can persist as a spore in diverse environments. Genetic overlap between C. difficile strains from human, animal and environmental sources suggests CDI has a zoonotic or foodborne aetiology. In Australia, C. difficile PCR ribotype RT014 (MLST clade 1) and several ST11 (MLST clade 5) RTs are found commonly in livestock. The high prevalence and diversity of ST11 strains in Australian production animals indicates Australia might be the ancestral home for this lineage. This project describes for the first time the ecology of C. difficile in Australian native animals, providing insights into the prevalence, molecular epidemiology and evolution of C. difficile in this unique environment and a possible role in CDI in humans and animals in Australia. Faecal samples were collected from wild/captive reptiles (n=37), mammals (n=104) and birds (n=102) in Western Australia in 2020/21. Anaerobic enrichment culture was performed, and C. difficile isolates were characterised by PCR ribotyping and toxin gene profiling. Seventy isolates of C. difficile were recovered (prevalence of C. difficile in faecal samples 28%, n=68/243); 27 unique RTs were identified, 5 were novel. The prevalence of C. difficile was similar for reptiles and mammals, 46% (n=17/37) and 43%(n=45/104), respectively, but significantly lower in birds (7.8%, n=8/102; p<0.00001 for both reptiles and mammals). Of the 57 isolates available for typing, RT237 (clade 5) and RT002 (clade 2) were the most prevalent, 15.8% (n=9/57) and 14% (n=8/57), respectively. The high prevalence of C. difficile in reptiles and mammals, particularly clade 5 strains, supported by previous studies of C. difficile in Australian soils, suggest that Australia might be the ancestral home of MLST clade 5.

Keywords: Clostridium difficile, zoonosis, molecular epidemiology, ecology and evolution

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Authors: H. Meddah, M. Berediaf-Bourahla, B. El-Djouzi, N. Bourahla

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Shear walls made of cold formed steel are used as lateral force resisting components in residential and low-rise commercial and industrial constructions. The seismic design analysis of such structures is often complex due to the slenderness of members and their instability prevalence. In this context, a simplified modeling technique across the panel is proposed by using the finite element method. The approach is based on idealizing the whole panel by a nonlinear shear link element which reflects its shear behavior connected to rigid body elements which transmit the forces to the end elements (studs) that resist the tension and the compression. The numerical model of the shear wall panel was subjected to cyclic loads in order to evaluate the seismic performance of the structure in terms of lateral displacement and energy dissipation capacity. In order to validate this model, the numerical results were compared with those from literature tests. This modeling technique is particularly useful for the design of cold formed steel structures where the shear forces in each panel and the axial forces in the studs can be obtained using spectrum analysis.

Keywords: cold-formed steel, cyclic loading, modeling technique, nonlinear analysis, shear wall panel

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Authors: Barzin Rajabloo, Martin Desilets

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First, an electrochemical model for the reduction of CO₂ into CH₃OH is developed in which mass and charge transfer, reactions at the surface of the electrodes and fluid flow of the electrolyte are considered. This mathematical model is developed in COMSOL Multiphysics® where both secondary and tertiary current distribution interfaces are coupled to consider concentrations and potentials inside different parts of the cell. Constant reaction rates are assumed as the fitted parameters to minimize the error between experimental data and modeling results. The model is validated through a comparison with experimental data in terms of faradaic efficiency for production of CH₃OH, the current density in different applied cathode potentials as well as current density in different electrolyte flow rates. The comparison between model outputs and experimental measurements shows a good agreement. The model indicates the higher hydrogen evolution in comparison with CH₃OH production as well as mass transfer limitation caused by CO₂ concentration, which are consistent with findings in the literature. After validating the model, in the second part of the study, some design parameters of the cell, such as cathode geometry and catholyte/anolyte channel widths, are modified to reach better performance and higher faradaic efficiency of methanol production.

Keywords: carbon dioxide, electrochemical reduction, methanol, modeling

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Authors: Katerina H. Takova, Ivan N. Minkov, Gergana G. Zahmanova

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Molecular farming is the production of recombinant proteins in plants with the aim to use the protein as a purified product, crude extract or directly in the planta. Plants gain more attention as expression systems compared to other ones due to the cost effective production of pharmaceutically important proteins, appropriate post-translational modifications, assembly of complex proteins, absence of human pathogens to name a few. In addition, transient expression in plant leaves enables production of recombinant proteins within few weeks. Hepatitis E virus (HEV) is a causative agent of acute hepatitis. HEV causes epidemics in developing countries and is primarily transmitted through the fecal-oral route. Presently, all efforts for development of Hepatitis E vaccine are focused on the Open Read Frame 2 (ORF2) capsid protein as it contains epitopes that can induce neutralizing antibodies. For our purpose, we used the CMPV-based vector-pEAQ-HT for transient expression of HEV ORF2 in Nicotiana benthamina. Different molecular analysis (Western blot and ELISA) showed that HEV ORF2 capsid protein was expressed in plant tissue in high-yield up to 1g/kg of fresh leaf tissue. Electron microscopy showed that the capsid protein spontaneously assembled in low abundance virus-like particles (VLPs), which are highly immunogenic structures and suitable for vaccine development. The expressed protein was recognized by both human and swine HEV positive sera and can be used as a diagnostic reagent for the detection of HEV infection. Production of HEV capsid protein in plants is a promising technology for further HEV vaccine investigations. Here, we reported for a rapid high-yield transient expression of a recombinant protein in plants suitable for vaccine production as well as a diagnostic reagent. Acknowledgments -The authors’ research on HEV is supported with grants from the Project PlantaSYST under the Widening Program, H2020 as well as under the UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’ (BB/J004596/1). The authors want to thank Prof. George Lomonossoff (JIC, Norwich, UK) for his contribution.

Keywords: hepatitis E virus, plant molecular farming, transient expression, vaccines

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Authors: Mini P. Singh, Jagat Ram, Archit Kumar, Tripti Rungta, Jasmine Khurana, Amit Gupta, R. K. Ratho

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Introduction: Human adenovirus is the most common agent involved in viral conjunctivitis. The clinical manifestations vary with different serotypes. The identification of the circulating strains followed by phylogenetic analysis can be helpful in understanding the origin and transmission of the disease. The present study aimed to carry out molecular epidemiology of the adenovirus types in the patients with conjunctivitis presenting to the eye centre of a tertiary care hospital in North India. Materials and Methods: The conjunctival swabs were collected from 23 suspected adenoviral conjunctivitis patients between April-August, 2014 and transported in viral transport media. The samples were subjected to nested PCR targeting hexon gene of human adenovirus. The band size of 956bp was eluted and 8 representative positive samples were subjected to sequencing. The sequences were analyzed by using CLUSTALX2.1 and MEGA 5.1 software. Results: The male: female ratio was found to be 3.6:1. The mean age of presenting patients was 43.95 years (+17.2). Approximately 52.1% (12/23) of patients presented with bilateral involvement while 47.8% (11/23) with unilateral involvement of the eye. Human adenovirus DNA could be detected in 65.2% (15/23) of the patients. The phylogenetic analysis revealed presence of serotype 8 in 7 patients and serotype 4 in one patient. The serotype 8 sequences showed 99-100% identity with Tunisian, Indian and Japanese strains. The adenovirus serotype 4 strains had 100% identity with strains from Tunisia, China and USA. Conclusion: Human adenovirus was found be an important etiological agent for conjunctivitis in our set up. The phylogenetic analysis showed that the predominant circulating strains in our epidemic keratoconjunctivitis were serotypes 8 and 4.

Keywords: conjunctivitis, human adenovirus, molecular epidemiology, phylogenetics

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Authors: S. N. Harun, H. Ahmad

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A series of ruthenium(II) complexes, including two novel compounds [Ru(dppz)2(L)]2+ where dppz = dipyrido-[3,2-a:2’,3’-c]phenazine, and L = 2-phenylimidazo[4,5-f][1,10]phenanthroline (PIP) or 2-(4-hydroxyphenyl)imidazo[4,5-f][1,10]phenanthroline (p-HPIP) have been synthesized and characterized. The previously reported complexes [Ru(bpy)2L]2+ and [Ru(phen)2L]2+ were also prepared. All complexes were characterized by elemental analysis, 1H-NMR spectroscopy, ESI-Mass spectroscopy and FT-IR spectroscopy. The photophysical properties were analyzed by UV-Visible spectroscopy and fluorescence spectroscopy. [Ru(dppz)2(PIP)]2+ and [Ru(dppz)2(p-HPIP)]2+ displayed ‘molecular light-switch’ effect as they have high emission in acetonitrile but no emission in water. The cytotoxicity of all complexes against cancer cell lines Hela and MCF-7 were investigated through standard MTT assay. [Ru(dppz)2(PIP)]2+ showed moderate toxicity on both MCF-7 and Hela with IC50 of 37.64 µM and 28.02 µM, respectively. Interestingly, [Ru(dppz)2(p-HPIP)]2+ exhibited remarkable cytotoxicity results with IC50 of 13.52 µM on Hela and 11.63 µM on MCF-7 cell lines which are comparable to the infamous anti-cancer drug, cisplatin. The cytotoxicity of this complex series increased as the ligands size extended in order of [Ru(bpy)2(L)]2+ < [Ru(phen)2(L)]2+ < [Ru(dppz)2(L)]2+.

Keywords: ruthenium, cytotoxicity, molecular light-switch, anticancer

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Authors: Nataša Kalajdžija, Strahinja Kovačević, Davor Lončar, Sanja Podunavac Kuzmanović, Lidija Jevrić

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In order to investigate the relationship between retention and structure, a quantitative Structure Retention Relationships (QSRRs) study was applied for the prediction of retention times of a set of 23 secoestrane derivatives in a reversed-phase thin-layer chromatography. After the calculation of molecular descriptors, a suitable set of molecular descriptors was selected by using step-wise multiple linear regressions. Artificial Neural Network (ANN) method was employed to model the nonlinear structure-activity relationships. The ANN technique resulted in 5-6-1 ANN model with the correlation coefficient of 0.98. We found that the following descriptors: Critical pressure, total energy, protease inhibition, distribution coefficient (LogD) and parameter of lipophilicity (miLogP) have a significant effect on the retention times. The prediction results are in very good agreement with the experimental ones. This approach provided a new and effective method for predicting the chromatographic retention index for the secoestrane derivatives investigated.

Keywords: lipophilicity, QSRR, RP TLC retention, secoestranes

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Authors: Sofiane Bendoukha, Daniel Moldt, Hayat Bendoukha

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Workflow concepts are essential for the development of remote sensing applications. They can help users to manage and process satellite data and execute scientific experiments on distributed resources. The objective of this paper is to introduce an approach for the specification and the execution of complex scientific workflows in Cloud-like environments. The approach strives to support scientists during the modeling, the deployment and the monitoring of their workflows. This work takes advantage from Petri nets and more pointedly the so-called reference nets formalism, which provides a robust modeling/implementation technique. RENEWGRASS is a tool that we implemented and integrated into the Petri nets editor and simulator RENEW. It provides an easy way to support not experienced scientists during the specification of their workflows. It allows both modeling and enactment of image processing workflows from the remote sensing domain. Our case study is related to the implementation of vegetation indecies. We have implemented the Normalized Differences Vegetation Index (NDVI) workflow. Additionally, we explore the integration possibilities of the Cloud technology as a supplementary layer for the deployment of the current implementation. For this purpose, we discuss migration patterns of data and applications and propose an architecture.

Keywords: cloud computing, scientific workflows, petri nets, RENEWGRASS

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Authors: Farhad Alizadeh, Alireza Faregh Gharamaleki, Mojtaba Jalilzadeh, Houshang Gholami, Ali Akhoundzadeh

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This study presented hybrid pre-processing approach along with a conceptual model to enhance the accuracy of river discharge prediction. In order to achieve this goal, Ensemble Empirical Mode Decomposition algorithm (EEMD), Discrete Wavelet Transform (DWT) and Mutual Information (MI) were employed as a hybrid pre-processing approach conjugated to Least Square Support Vector Machine (LSSVM). A conceptual strategy namely multi-station model was developed to forecast the Souris River discharge more accurately. The strategy used herein was capable of covering uncertainties and complexities of river discharge modeling. DWT and EEMD was coupled, and the feature selection was performed for decomposed sub-series using MI to be employed in multi-station model. In the proposed feature selection method, some useless sub-series were omitted to achieve better performance. Results approved efficiency of the proposed DWT-EEMD-MI approach to improve accuracy of multi-station modeling strategies.

Keywords: river stage-discharge process, LSSVM, discrete wavelet transform, Ensemble Empirical Decomposition Mode, multi-station modeling

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Authors: Shahrokh Barati

Abstract:

In this paper, we introduced AIDS disease at first, then proposed dynamic model illustrate its progress, after expression of a short history of nonlinear modeling by polynomial phasing systems, we considered the stability conditions of the systems, which contained a huge amount of researches in order to modeling and control of AIDS in dynamic nonlinear form, in this approach using a frame work of control any polynomial phasing modeling system which have been generalized by part of phasing model of T-S, in order to control the system in better way, the stability conditions were achieved based on polynomial functions, then we focused to design the appropriate controller, firstly we considered the equilibrium points of system and their conditions and in order to examine changes in the parameters, we presented polynomial phase model that was the generalized approach rather than previous Takagi Sugeno models, then with using case we evaluated the equations in both open loop and close loop and with helping the controlling feedback, the close loop equations of system were calculated, to simulate nonlinear model of AIDS disease, we used polynomial phasing controller output that was capable to make the parameters of a nonlinear system to follow a sustainable reference model properly.

Keywords: polynomial fuzzy, AIDS, nonlinear AIDS model, fuzzy control systems

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Authors: Samantha Shallop, Hakinya Karra, Tytus Bernas, Gladys Shaw, Gretchen Neigh, Jeffrey Dupree, Mathula Thangarajh

Abstract:

Abnormal neuronal homeostasis is considered a structural correlate of cognitive deficits in Duchenne Muscular Dystrophy. Neurons are highly polarized cells with multiple dendrites but a single axon. Trafficking of cellular organelles are highly regulated, with the cargo in the somatodendritic region of the neuron not permitted to enter the axonal compartment. We investigated the molecular mechanisms that regular organelle trafficking in neurons using a multimodal approach, including high-resolution structural illumination, proteomics, immunohistochemistry, and computational modeling. We investigated the expression of ankyrin-G, the master regulator controlling neuronal polarity. The expression of ankyrin G and the morphology of the axon initial segment was profoundly abnormal in the CA1 hippocampal neurons in the mdx52 animal model of DMD. Ankyrin-G colocalized with kinesin KIF5a, the anterograde protein transporter, with higher levels in older mdx52 mice than younger mdx52 mice. These results suggest that the functional trafficking from the somatodendritic compartment is abnormal. Our data suggests that dystrophin deficiency compromised neuronal homeostasis via ankyrin-G-based mechanisms.

Keywords: neurons, axonal transport, duchenne muscular dystrophy, organelle transport

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Authors: Rafal Sochaczewski, Ksenia Siadkowska, Tytus Tulwin

Abstract:

The paper describes the modeling of a fuel injector for common rail systems. A one-dimensional model of a solenoid-valve-controlled injector with Valve Closes Orifice (VCO) spray was modelled in the AVL Hydsim. This model shows the dynamic phenomena that occur in the injector. The accuracy of the calibration, based on a regulation of the parameters of the control valve and the nozzle needle lift, was verified by comparing the numerical results of injector flow rate. Our model is capable of a precise simulation of injector operating parameters in relation to injection time and fuel pressure in a fuel rail. As a result, there were made characteristics of the injector flow rate and backflow.

Keywords: common rail, diesel engine, fuel injector, modeling

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Authors: Rong Li, Brian D. Wirth, Bing Liu

Abstract:

Graphite is the matrix, and structural material in the high temperature gas-cooled reactor exhibits an irradiation response. It is of significant importance to analyze the defect production and evaluate the role of graphite under irradiation. A vast experimental literature exists for graphite on the dimensional change, mechanical properties, and thermal behavior. However, simulations have not been applied to the atomistic perspective. Remarkably few molecular dynamics simulations have been performed to study the irradiation response in graphite. In this paper, irradiation-induced damage cascades in graphite were investigated with molecular dynamics simulation. Statistical results of the graphite defects were obtained by sampling a wide energy range (1–30 KeV) and 10 different runs for every cascade simulation with different random number generator seeds to the velocity scaling thermostat function. The chemical bonding in carbon was described using the adaptive intermolecular reactive empirical bond-order potential (AIREBO) potential coupled with the standard Ziegler–Biersack–Littmack (ZBL) potential to describe close-range pair interactions. This study focused on analyzing the number of defects, the final cascade morphology and the distribution of defect clusters in space, the length-scale cascade properties such as the cascade length and the range of primary knock-on atom (PKA), and graphite mechanical properties’ variation. It can be concluded that the number of surviving Frenkel pairs increased remarkably with the increasing initial PKA energy but did not exhibit a thermal spike at slightly lower energies in this paper. The PKA range and cascade length approximately linearly with energy which indicated that increasing the PKA initial energy will come at expensive computation cost such as 30KeV in this study. The cascade morphology and the distribution of defect clusters in space mainly related to the PKA energy meanwhile the temperature effect was relatively negligible. The simulations are in agreement with known experimental results and the Kinchin-Pease model, which can help to understand the graphite damage cascades and lifetime span under irradiation and provide a direction to the designs of these kinds of structural materials in the future reactors.

Keywords: graphite damage cascade, molecular dynamics, cascade morphology, cascade distribution

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Authors: S. Srinivasan, E. Cretu

Abstract:

The information flow (e.g. block-diagram or signal flow graph) paradigm for the design and simulation of Microelectromechanical (MEMS)-based systems allows to model MEMS devices using causal transfer functions easily, and interface them with electronic subsystems for fast system-level explorations of design alternatives and optimization. Nevertheless, the physical bi-directional coupling between different energy domains is not easily captured in causal signal flow modeling. Moreover, models of fundamental components acting as building blocks (e.g. gap-varying MEMS capacitor structures) depend not only on the component, but also on the specific excitation mode (e.g. voltage or charge-actuation). In contrast, the energy flow modeling paradigm in terms of generalized across-through variables offers an acausal perspective, separating clearly the physical model from the boundary conditions. This promotes reusability and the use of primitive physical models for assembling MEMS devices from primitive structures, based on the interconnection topology in generalized circuits. The physical modeling capabilities of Simscape have been used in the present work in order to develop a MEMS library containing parameterized fundamental building blocks (area and gap-varying MEMS capacitors, nonlinear springs, displacement stoppers, etc.) for the design, simulation and optimization of MEMS inertial sensors. The models capture both the nonlinear electromechanical interactions and geometrical nonlinearities and can be used for both small and large signal analyses, including the numerical computation of pull-in voltages (stability loss). Simscape behavioral modeling language was used for the implementation of reduced-order macro models, that present the advantage of a seamless interface with Simulink blocks, for creating hybrid information/energy flow system models. Test bench simulations of the library models compare favorably with both analytical results and with more in-depth finite element simulations performed in ANSYS. Separate MEMS-electronic integration tests were done on closed-loop MEMS accelerometers, where Simscape was used for modeling the MEMS device and Simulink for the electronic subsystem.

Keywords: across-through variables, electromechanical coupling, energy flow, information flow, Matlab/Simulink, MEMS, nonlinear, pull-in instability, reduced order macro models, Simscape

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Authors: Abdelatif Gadoum, Djilali Benyoucef, Mouloudj Hadj, Alla Eddine Toubal Maamar, Mohamed Habib Allah Lahoual

Abstract:

Hydrogen occurs naturally in the form of chemical compounds, most often in water and hydrocarbons. The main objective of this study is 2D modeling of hydrogen production in inductively coupled plasma in methane at low pressure. In the present model, we include the motions and the collisions of both neutral and charged particles by considering 19 species (i.e in total ; neutrals, radicals, ions, and electrons), and more than 120 reactions (electron impact with methane, neutral-neutral, neutral-ions and surface reactions). The results show that the rate conversion of methane reach 90% and the hydrogen production is about 30%.

Keywords: hydrogen production, inductively coupled plasma, fluid model, methane plasma

Procedia PDF Downloads 153