Search results for: molecular dynamics simulations

Authors: Reda Mankbadi

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The current work explores the use of Synthetic Jet Actuators (SJAs) for control of the acoustic radiation of a low-speed transitioning airfoil in a uniform stream. In the adopted numerical procedure, the actuator is modeled without its resonator cavity through imposing a simple fluctuating-velocity boundary condition at the bottom of the actuator's orifice. The orifice cavity, with the properly defined boundary condition, is then embedded into the airfoil surface. High-accuracy viscous simulations are then conducted to study the effects of the actuation on sound radiated by the airfoil. Results show that SJA can considerably suppress the radiated sound of the airfoil in uniform incoming stream.

Keywords: simulations, aeroacoustics, wind turbine noise, synthetic jet actuators (SJAs)

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Authors: Igor B. Sivaev

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Design of molecular machines is an extraordinary growing and very important area of research that it was recognized by awarding Sauvage, Stoddart and Feringa the Nobel Prize in Chemistry in 2016 'for the design and synthesis of molecular machines'. Based on the type of motion being performed, molecular machines can be divided into two main types: molecular motors and molecular switches. Molecular switches are molecules or supramolecular complexes having bistability, i.e., the ability to exist in two or more stable forms, among which may be reversible transitions under external influence (heating, lighting, changing the medium acidity, the action of chemicals, exposure to magnetic or electric field). Molecular switches are the main structural element of any molecular electronics devices. Therefore, the design and the study of molecules and supramolecular systems capable of performing mechanical movement is an important and urgent problem of modern chemistry. There is growing interest in molecular switches and other devices of molecular electronics based on transition metal complexes; therefore choice of suitable stable organometallic unit is of great importance. An example of such unit is bis(dicarbollide) complexes of transition metals [3,3’-M(1,2-C₂B₉H₁₁)₂]ⁿ⁻. The control on the ligand rotation in such complexes can be reached by introducing substituents which could provide stabilization of certain rotamers due to specific interactions between the ligands, on the one hand, and which can participate as Lewis bases in complex formation with external metals resulting in a change in the rotation angle of the ligands, on the other hand. A series of isomeric methyl sulfide derivatives of cobalt bis(dicarbollide) complexes containing methyl sulfide substituents at boron atoms in different positions of the pentagonal face of the dicarbollide ligands [8,8’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻, rac-[4,4’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[4,7’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ were synthesized by the reaction of CoCl₂ with the corresponding methyl sulfide carborane derivatives [10-MeS-7,8-C₂B₉H₁₁)₂]⁻ and [10-MeS-7,8-C₂B₉H₁₁)₂]⁻. In the case of asymmetrically substituted cobalt bis(dicarbollide) complexes the corresponding rac- and meso-isomers were successfully separated by column chromatography as the tetrabutylammonium salts. The compounds obtained were studied by the methods of ¹H, ¹³C, and ¹¹B NMR spectroscopy, single crystal X-ray diffraction, cyclic voltammetry, controlled potential coulometry and quantum chemical calculations. It was found that in the solid state, the transoid- and gauche-conformations of the 8,8’- and 4,4’-isomers are stabilized by four intramolecular CH···S(Me)B hydrogen bonds each one (2.683-2.712 Å and 2.709-2.752 Å, respectively), whereas gauche-conformation of the 4,7’-isomer is stabilized by two intramolecular CH···S hydrogen bonds (2.699-2.711 Å). The existence of the intramolecular CH·S(Me)B hydrogen bonding in solutions was supported by the 1H NMR spectroscopy. These data are in a good agreement with results of the quantum chemical calculations. The corresponding iron and nickel complexes were synthesized as well. The reaction of the methyl sulfide derivatives of cobalt bis(dicarbollide) with various labile transition metal complexes results in rupture of intramolecular hydrogen bonds and complexation of the methyl sulfide groups with external metal. This results in stabilization of other rotational conformation of cobalt bis(dicarbollide) and can be used in design of molecular switches. This work was supported by the Russian Science Foundation (16-13-10331).

Keywords: molecular switches, NMR spectroscopy, single crystal X-ray diffraction, transition metal bis(dicarbollide) complexes, quantum chemical calculations

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Authors: Isha Sharawat, R. P. Dahiya, T. R. Sreekrishnan

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One of the environmental challenges in India is urban wastewater management as regulations and infrastructural development has not kept pace with the urbanization and growing population. The quality of life of people is also improving with the rapid growth of the gross domestic product. This has contributed to the enhancement in the per capita water requirement and consumption. More domestic water consumption generates more wastewater. The scarcity of potable water is making the situation quite serious, and water supply has to be regulated in most parts of the country during summer. This requires elaborate and concerted efforts to efficiently manage the water resources and supply systems. In this article, a system dynamics modelling approach is used for estimating the water demand and wastewater generation in a district headquarter city of North India. Projections are made till the year 2035. System dynamics is a software tool used for formulation of policies. On the basis of the estimates, policy scenarios are developed for sustainable development of water resources in conformity with the growing population. Mitigation option curtailing the water demand and wastewater generation include population stabilization, water reuse and recycle and water pricing. The model is validated quantitatively, and sensitivity analysis tests are carried out to examine the robustness of the model.

Keywords: system dynamics, wastewater, water pricing, water recycle

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Authors: Ali M. EL-Soll

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Physical properties of Sarir waxy crude oil was investigated, pour-point was determined using ASTM D-79 procedure, paraffin content and carbon number distribution of the paraffin was determined using gas liquid Chromatography(GLC), polymeric additives were prepared and their structures were confirmed using IR spectrophotometer. The molecular weight and molecular weigh distribution of these additives were determined by gel permeation chromatography (GPC). the performance of the synthesized additives as pour-point depressants was evaluated, for the mentioned crude oil.

Keywords: sarir, waxy, crude, pour point, depressants

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G(d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G(d,p) method show good agreement with experimental X-ray data. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide, polarizability

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Authors: R. R. Mankbadi

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There are several technologically-important flow situations in which there is a need to control the outcome of the fluid flow. This could include flow separation, drag, noise, as well as particulate separations, to list only a few. One possible approach is the passive control, in which the design geometry is changed. An alternative approach is the Active Flow Control (AFC) technology in which an actuator is embedded in the flow field to change the outcome. Examples of AFC are pulsed jets, synthetic jets, plasma actuators, heating, and cooling, etc. In this work will present an overview of the development of this field. Some examples will include Airfoil Noise Suppression: Large-Eddy Simulations (LES) is used to simulate the effect of synthetic jet actuator on controlling the far field sound of a transitional airfoil. The results show considerable suppression of the noise if the synthetic jet is operated at frequencies. Mixing Enhancement and suppression: Results will be presented to show that imposing acoustic excitations at the nozzle exit can lead to enhancement or reduction of the jet plume mixing. In vertical takeoff of Aircrafts or in Space Launch, we will present results on the effects of water injection on reducing noise, and on protecting the structure and payload from fatigue damage. Other applications will include airfoil-gust interaction and propulsion systems optimizations.

Keywords: aeroacoustics, flow control, aerodynamics, large eddy simulations

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić

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The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.

Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR

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Authors: Nini Johana Marín Rodríguez, William Fernando Oquendo Patino

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In this work, we model a coupled system where we explore the effects of steady and random behavior on a linear system like an extension of the classic Strogatz model. This is exemplified by modeling a couple love dynamics as a linear system of two coupled differential equations and studying its stability for four types of lovers chosen as CC='Cautious- Cautious', OO='Only other feelings', OP='Opposites' and RR='Romeo the Robot'. We explore the effects of, first, introducing saturation, and second, adding a random variation to one of the CC-type lover, which will shape his character by trying to model how its variability influences the dynamics between love and hate in couple in a long run relationship. This work could also be useful to model other kind of systems where interactions can be modeled as linear systems with external or internal random influence. We found the final results are not easy to predict and a strong dependence on initial conditions appear, which a signature of chaos.

Keywords: differential equations, dynamical systems, linear system, love dynamics

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Authors: Zakaria Baka, Halima Alem

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Cancer is a major worldwide health problem that has caused around ten million deaths in 2020. In addition, efforts to develop new anti-cancer drugs still face a high failure rate. This is partly due to the lack of preclinical models that recapitulate in-vivo drug responses. Indeed conventional cell culture approach (known as 2D cell culture) is far from reproducing the complex, dynamic and three-dimensional environment of tumors. To set up more in-vivo-like cancer models, 3D bioprinting seems to be a promising technology due to its ability to achieve 3D scaffolds containing different cell types with controlled distribution and precise architecture. Moreover, the introduction of microfluidic technology makes it possible to simulate in-vivo dynamic conditions through the so-called “cancer-on-chip” platforms. Whereas several cancer types have been modeled through the cancer-on-chip approach, such as lung cancer and breast cancer, only a few works describing ovarian cancer models have been described. The aim of this work is to combine 3D bioprinting and microfluidic technics with setting up a 3D dynamic model of ovarian cancer. In the first phase, alginate-gelatin hydrogel containing SKOV3 cells was used to achieve tumor-like structures through an extrusion-based bioprinter. The desired form of the tumor-like mass was first designed on 3D CAD software. The hydrogel composition was then optimized for ensuring good and reproducible printability. Cell viability in the bioprinted structures was assessed using Live/Dead assay and WST1 assay. In the second phase, these bioprinted structures will be included in a microfluidic device that allows simultaneous testing of different drug concentrations. This microfluidic dispositive was first designed through computational fluid dynamics (CFD) simulations for fixing its precise dimensions. It was then be manufactured through a molding method based on a 3D printed template. To confirm the results of CFD simulations, doxorubicin (DOX) solutions were perfused through the dispositive and DOX concentration in each culture chamber was determined. Once completely characterized, this model will be used to assess the efficacy of anti-cancer nanoparticles developed in the Jean Lamour institute.

Keywords: 3D bioprinting, ovarian cancer, cancer-on-chip models, microfluidic techniques

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Authors: M. F. Elzarei, A. M. Alseaf

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Hundred uncorrelated animal and thirty six markers were used in this study to study the molecular characterization of Saudi native Ardi goat (BM18189, ILSTS030, INRA005, OarFCB48, BM2113, ILSTS033, INRA023, RM088, CSRD247, ILSTS034, INRA063, SRCRSP1, ILSTS002, ILSTS044, INRA172, SRCRSP5, ILSTS005, ILSTS049, MAF70, SRCRSP8, ILSTS011, ILSTS058, OarAE54, SRCRSP9, ILSTS019, ILSTS059, OARCP34, TGLA53, ILSTS022, ILSTS082, OARE129, TGLA73, ILSTS029, ILSTS087, OARE193, and RM004). Ardi goat showed high variability. The mean number of alleles per locus ranged from 5 in SRCRSP1 locus to 13.5 in CSRD247 locus. Gene diversities varied within a wide range, from 0.53 in ILSTS002 locus to 0.86 in RM088 locus. Hardy-Weinberg equilibrium was tested in order to evaluate the significance of inbreeding occurring in each locus in Ardi population. Only SRCRSP9, INRA005, ILSTS030 loci showed significance in this way.

Keywords: molecular characterization, microsatellite markers, Ardi goats, Hardy-Weinberg equilibrium

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Authors: Asma Ahmed Aljohani, Mohammed Orif

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The concentration of polycyclic aromatic hydrocarbons (PAH) in clam (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyse the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: bivalves, biomonitoring, hydrocarbons, PAHs

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Authors: Moustafa Osman Mohammed

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This paper introduces topological order in descried social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. Topological order is important in describing the physical systems for exploiting optical systems and improving photonic devices. The stats of topological order have some interesting properties of topological degeneracy and fractional statistics that reveal the entanglement origin of topological order, etc. Topological ideas in photonics form exciting developments in solid-state materials, that being; insulating in the bulk, conducting electricity on their surface without dissipation or back-scattering, even in the presence of large impurities. A specific type of autopoiesis system is interrelated to the main categories amongst existing groups of the ecological phenomena interaction social and medical sciences. The hypothesis, nevertheless, has a nonlinear interaction with its natural environment 'interactional cycle' for exchange photon energy with molecules without changes in topology. The engineering topology of a biosensor is based on the excitation boundary of surface electromagnetic waves in photonic band gap multilayer films. The device operation is similar to surface Plasmonic biosensors in which a photonic band gap film replaces metal film as the medium when surface electromagnetic waves are excited. The use of photonic band gap film offers sharper surface wave resonance leading to the potential of greatly enhanced sensitivity. So, the properties of the photonic band gap material are engineered to operate a sensor at any wavelength and conduct a surface wave resonance that ranges up to 470 nm. The wavelength is not generally accessible with surface Plasmon sensing. Lastly, the photonic band gap films have robust mechanical functions that offer new substrates for surface chemistry to understand the molecular design structure and create sensing chips surface with different concentrations of DNA sequences in the solution to observe and track the surface mode resonance under the influences of processes that take place in the spectroscopic environment. These processes led to the development of several advanced analytical technologies: which are; automated, real-time, reliable, reproducible, and cost-effective. This results in faster and more accurate monitoring and detection of biomolecules on refractive index sensing, antibody-antigen reactions with a DNA or protein binding. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other in order to form unique spatial structure and dynamics of biological molecules for providing the environment mutual contribution in investigation of changes due to the pathogenic archival architecture of cell clusters.

Keywords: autopoiesis, photonics systems, quantum topology, molecular structure, biosensing

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Authors: Jagdish Prasad Maurya, Sanjay Kumar Pandey

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Inadequate understanding of the complex nature of flow features in tornado vortex is a major problem in modelling tornadoes. Tornadoes are violent atmospheric phenomenon that appear all over the world. Modelling tornadoes aim to reduce the loss of the human lives and material damage caused by the tornadoes. Dynamics of tornado is investigated by a numerical technique, the improved version of the projection method. In this paper, authors solve the problem for axisymmetric tornado vortex by the said method that uses a finite difference approach for getting an accurate and stable solution. The conclusions drawn are that large radial inflow velocity occurs near the ground that leads to increase the tangential velocity. The increased velocity phenomenon occurs close to the boundary and absolute maximum wind is obtained near the vortex core. The results validate previous numerical and theoretical models.

Keywords: computational fluid dynamics, mathematical model, Navier-Stokes equations, tornado

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Authors: A. Douka, S. Vouyiouka, L. M. Papaspyridi, D. Korres, C. Papaspyrides

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A "green" process was studied for the preparation of partially renewable aliphatic polyesters based on 1,4-butanediol and 1,8-octanediol with various diacids and derivatives, namely diethyl succinate, adipic acid, sebacic acid, 1,12-dodecanedioic acid and 1,14-tetradecanedioic acid. A first step of enzymatic prepolymerization was carried out in the presence of two different solvents, toluene and diphenylether, applying molecular sieves and vacuum, respectively, to remove polycondensation by-products. Poly(octylene adipate) (PE 8.6), poly(octylene dodecanate)(PE 8.12) and poly(octylene tetradecanate) (PE 8.14) were firstly enzymatically produced in toluene using molecular sieves giving however, low-molecular-weight products. Thereafter, the synthesis of PE 8.12 and PE 8.14 was examined under optimized conditions using diphenylether as solvent and a more vigorous by-product removal step, such as application of vacuum. Apart from these polyesters, the optimized process was also implemented for the production of another long-chain polyester-poly(octylene sebacate) (PE 8.10) and a short-chain polyester-poly(butylene succinate) (PE 4.4). Subsequently, bulk post-polymerization in the melt or solid state was performed. SSP runs involved absence of biocatalyst and reaction temperatures (T) in the vicinity of the prepolymer melting point (Tm-T varied between 15.5 up to 4oC). Focusing on PE 4.4 and PE 8.12, SSP took place under vacuum or flowing nitrogen leading to increase of the molecular weight and improvement of the end product physical appearance and thermal properties.

Keywords: aliphatic polyester, enzymatic polymerization, solid state polymerization, Novozym 435

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Authors: Samah Laalej, Abdelfattah Bouatem

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In the field of wind turbine blades, it is complicated to evaluate the aerodynamic performances through experimental measurements as it requires a lot of computing time and resources. Therefore, in this paper, a hybrid BEM-CFD numerical technique is developed to predict power and aerodynamic forces acting on the blades. Computational fluid dynamics (CFD) simulation was conducted to calculate the drag and lift forces through Ansys software using the K-w model. Then an enhanced BEM code was created to predict the power outputs generated by the wind turbine using the aerodynamic properties extracted from the CFD approach. The numerical approach was compared and validated with experimental data. The power curves calculated from this hybrid method were in good agreement with experimental measurements for all velocity ranges.

Keywords: blade element momentum, aerodynamic forces, wind turbine blades, computational fluid dynamics approach

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Authors: Nwachukwu Ifeanyi

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Wind energy is a vital component of the global renewable energy portfolio, with wind turbines serving as the primary means of harnessing this abundant resource. However, the efficiency and stability of wind turbines remain critical challenges in maximizing energy output and ensuring long-term operational viability. This study proposes a comprehensive approach utilizing computational aerodynamics and aeromechanics to optimize wind turbine performance across multiple objectives. The proposed research aims to integrate advanced computational fluid dynamics (CFD) simulations with structural analysis techniques to enhance the aerodynamic efficiency and mechanical stability of wind turbine blades. By leveraging multi-objective optimization algorithms, the study seeks to simultaneously optimize aerodynamic performance metrics such as lift-to-drag ratio and power coefficient while ensuring structural integrity and minimizing fatigue loads on the turbine components. Furthermore, the investigation will explore the influence of various design parameters, including blade geometry, airfoil profiles, and turbine operating conditions, on the overall performance and stability of wind turbines. Through detailed parametric studies and sensitivity analyses, valuable insights into the complex interplay between aerodynamics and structural dynamics will be gained, facilitating the development of next-generation wind turbine designs. Ultimately, this research endeavours to contribute to the advancement of sustainable energy technologies by providing innovative solutions to enhance the efficiency, reliability, and economic viability of wind power generation systems. The findings have the potential to inform the design and optimization of wind turbines, leading to increased energy output, reduced maintenance costs, and greater environmental benefits in the transition towards a cleaner and more sustainable energy future.

Keywords: computation, robotics, mathematics, simulation

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Cristina Prandi, Piermichele Kobauri

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The present study is based on molecular modeling of a series of twelve 5-(4-substituent-phenoxy)-3-methylfuran-2(5H)-one derivatives which have potential of strigolactones mimics toward Striga hermonthica. The first step of the analysis included the calculation of molecular descriptors which numerically describe the structures of the analyzed compounds. The descriptors ALOGP (lipophilicity), AClogS (water solubility) and BBB (blood-brain barrier penetration), served as the input variables in multiple linear regression (MLR) modeling of germination activity toward S. hermonthica. Two MLR models were obtained. The first MLR model contains ALOGP and AClogS descriptors, while the second one is based on these two descriptors plus BBB descriptor. Despite the braking Topliss-Costello rule in the second MLR model, it has much better statistical and cross-validation characteristics than the first one. The ALOGP and AClogS descriptors are often very suitable predictors of the biological activity of many compounds. They are very important descriptors of the biological behavior and availability of a compound in any biological system (i.e. the ability to pass through the cell membranes). BBB descriptor defines the ability of a molecule to pass through the blood-brain barrier. Besides the lipophilicity of a compound, this descriptor carries the information of the molecular bulkiness (its value strongly depends on molecular bulkiness). According to the obtained results of MLR modeling, these three descriptors are considered as very good predictors of germination activity of the analyzed compounds toward S. hermonthica seeds. This article is based upon work from COST Action (FA1206), supported by COST (European Cooperation in Science and Technology).

Keywords: chemometrics, germination activity, molecular modeling, QSAR analysis, strigolactones

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Authors: R. Chouatah, E. G. Filali, B. Zouzou

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It has been well established that there are no differences between microscale and macroscale flows of incompressible liquids. However, surface roughness has been known to impact the transport phenomena. The effect of structured roughness on the dynamics and heat transfer of water flowing through minichannel was numerically investigated in this study. Our study consists in characterizing the dynamic field and heat transfer aspect of a flow in circular minichannel equipped with structured roughness using CFD software, CFX. The study is performed to understand the effect of various roughness elements (rectangular, triangular), roughness height and roughness pitch on the friction factor and heat transfer coefficient. Our work focuses on a water flow inside a circular mini-channel of 1 mm in diameter and 10 cm in length. The speed entry into the mini-channel varies from 0.1 m/s to 25 m/s. The wall of the mini-channel is submitted to a constant heat flux; q=100,000 W/m². The simulations results are compared to those obtained with smooth minichannel and the existing experimental and numerical results in the literature.

Keywords: heat transfer, laminar and turbulent flow, minichannel, structured roughness

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Authors: Haowei Chen, Kaiqi Xiong

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This paper aims to answer how malware will propagate in Wireless Mesh Networks (WMNs) and how communication radius and distributed density of nodes affects the process of spreading. The above analysis is essential for devising network-wide strategies to counter malware. We answer these questions by developing an improved dynamical system that models malware propagation in the area where nodes were uniformly distributed. The proposed model captures both the spatial and temporal dynamics regarding the malware spreading process. Equilibrium and stability are also discussed based on the threshold of the system. If the threshold is less than one, the infected nodes disappear, and if the threshold is greater than one, the infected nodes asymptotically stabilize at the endemic equilibrium. Numerical simulations are investigated about communication radius and distributed density of nodes in WMNs, which allows us to draw various insights that can be used to guide security defense.

Keywords: Bluetooth security, malware propagation, wireless mesh networks, stability analysis

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Authors: Sundus Mona, Atif Adnan, Babar Ali, Fareeha Arshad, Allah Rakha

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Molecular diversity is the variation in the abundance of species. Forensic entomology is a neglected field in Pakistan. Insects collected from the crime scene should be handled by forensic entomologists who are currently virtually non-existent in Pakistan. Correct identification of insect specimen along with knowledge of their biodiversity can aid in solving many problems related to complicated forensic cases. Inadequate morphological identification and insufficient thermal biological studies limit the entomological utility in Forensic Medicine. Recently molecular identification of entomological evidence has gained attention globally. DNA barcoding is the latest and established method for species identification. Only proper identification can provide a precise estimation of postmortem intervals. Arthropods are known to be the first tourists scavenging on decomposing dead matter. The objective of the proposed study was to identify species by molecular techniques and analyze their phylogenetic importance with barcoded necrophagous insect species of early succession on human cadavers. Based upon this identification, the study outcomes will be the utilization of established DNA bar codes to identify carrion feeding insect species for concordant estimation of post mortem interval. A molecular identification method involving sequencing of a 658bp ‘barcode’ fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene from collected specimens of unknown dipteral species from cadavers of Lahore was evaluated. Nucleotide sequence divergences were calculated using MEGA 7 and Arlequin, and a neighbor-joining phylogenetic tree was generated. Three species were identified, Chrysomya megacephala, Chrysomya saffranea, and Chrysomya rufifacies with low genetic diversity. The fixation index was 0.83992 that suggests a need for further studies to identify and classify forensically relevant insects in Pakistan. There is an exigency demand for further research especially when immature forms of arthropods are recovered from the crime scene.

Keywords: molecular diversity, DNA barcoding, species identification, forensically relevant

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Authors: A. Chouaih, N. Benhalima, N. Boukabcha, R. Rahmani, F. Hamzaoui

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Zwitterionic compounds have received the interest of chemists and physicists due to their applications as nonlinear optical materials. Recently, zwitterionic compounds exhibiting high nonlinear optical activity have been investigated. In this context, the molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment have been determined in order to understand the nature of inter- and intramolecular charge transfer. The study reveals the nature of intermolecular interactions including charge transfer and hydrogen bonds in the title compound. In this crystal, the molecules form dimers via intermolecular hydrogen bonds. The dimers are further linked by C–H...O hydrogen bonds into chains along the c crystallographic axis. This study has also allowed us to determine various nonlinear optical properties such as molecular electrostatic potential, polarizability, and hyperpolarizability of the title compound.

Keywords: organic compounds, polarizability, hyperpolarizability, dipole moment

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

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Authors: Vishnu Asokan, Zaid M. Paloba

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Flow over cavities is an important area of research due to the significant change in flow physics caused by cavity aspect ratio, free stream Mach number and the nature of upstream boundary layer approaching the cavity leading edge. Cavity flow finds application in aircraft wheel well, weapons bay, combustion chamber of scramjet engines, etc. These flows are highly unsteady, compressible and turbulent and it involves mass entrainment coupled with acoustics phenomenon. Variation of flow dynamics in an angled cavity with a heated and cooled pylon upstream to the cavity with spatial combinations of heat flux addition and removal to the wall studied numerically. The goal of study is to investigate the effect of energy addition, removal to the cavity walls and pylon cavity flow dynamics. Preliminary steady state numerical simulations on inclined cavities with heat addition have shown that wall pressure profiles, as well as the recirculation, are influenced by heat transfer to the compressible fluid medium. Such a hybrid control of cavity flow dynamics in the form of heat transfer and pylon geometry can open out greater opportunities in enhancement of mixing and flame holding requirements of supersonic combustors. Addition of pylon upstream to the cavity reduces the acoustic oscillations emanating from the geometry. A numerical unsteady analysis of supersonic flow past cavities exposed to cavity wall heating and cooling with heated and cooled pylon helps to get a clear idea about the oscillation suppression in the cavity. A Cavity of L/D 4 and aft wall angle 22 degree with an upstream pylon of h/D=1.5 mm with a wall angle 29 degree exposed to supersonic flow of Mach number 2 and heat flux of 40 W/cm² and -40 W/cm² modeled for the above study. In the preliminary study, the domain is modeled and validated numerically with a turbulence model of SST k-ω using an HLLC implicit scheme. Both qualitative and quantitative flow data extracted and analyzed using advanced CFD tools. Flow visualization is done using numerical Schlieren method as the fluid medium gives the density variation. The heat flux addition to the wall increases the secondary vortex size of the cavity and removal of energy leads to the reduction in vortex size. The flow field turbulence seems to be increasing at higher heat flux. The shear layer thickness increases as heat flux increases. The steady state analysis of wall pressure shows that there is variation on wall pressure as heat flux increases. Shift in frequency of unsteady wall pressure analysis is an interesting observation for the above study. The time averaged skin friction seems to be reducing at higher heat flux due to the variation in viscosity of fluid inside the cavity.

Keywords: energy addition, frequency shift, Numerical Schlieren, shear layer, vortex evolution

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Authors: Basavaraj Vadavadagi, Satishkumar Shekhawat

Abstract:

Interstitial free steels posses better formability and have many applications in automotive industries. Forming limit diagrams (FLDs) indicate the formability of materials which can be determined by experimental and finite element (FE) simulations. FLDs were determined experimentally by LDH test, utilizing optical strain measurement system for measuring the strains in different width specimens and by FE simulations in Interstitial Free (IF) and Interstitial Free High Strength (IFHS) steels. In this study, the experimental and FE simulated FLDs are compared and also the stress based FLDs were investigated.

Keywords: forming limit diagram, limiting dome height, optical strain measurement, interstitial

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Authors: Shield B. Lin, Sameer Abdali

Abstract:

Computer simulations were performed using MATLAB/Simulink for a vibration isolation system for astronaut’s exercise platform. Simulation parameters initially were based on an on-going experiment in a laboratory at NASA Johnson Space Center. The authors expanded later simulations to include other parameters. A discrete proportional-integral-derivative controller with a low-pass filter commanding a linear actuator served as the active control unit to push and pull a counterweight in balancing the disturbance forces. A spring-damper device is used as an optional passive control unit. Simulation results indicated such design could achieve near complete vibration isolation with small displacements of the exercise platform.

Keywords: control, counterweight, isolation, vibration

Procedia PDF Downloads 134

Authors: Karla Sanchez-Ortiz, Yunuen Tapia-Torres, John Larsen, Felipe Garcia-Oliva

Abstract:

Due to food demand production, the use of synthetic nitrogenous fertilizer has increased in agricultural soils to replace the N losses. Nevertheless, the intensive use of synthetic nitrogenous fertilizer in conventional agriculture negatively affects the soil and therefore the environment, so alternatives such as organic agriculture have been proposed for being more environmentally friendly. However, further research in soil is needed to see how agricultural management affects the dynamics of C and N. The objective of this research was to evaluate the C and N dynamics in the soil with three different agricultural management: an agricultural plot with intensive inorganic fertilization, a plot with semi-organic management and an agricultural plot with recent abandonment (2 years). For each plot, the soil C and N dynamics and the enzymatic activity of NAG and β-Glucosidase were characterized. Total C and N concentration of the plant biomass of each site was measured as well. Dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) was higher in abandoned plot, as well as this plot had higher total carbon (TC) and total nitrogen (TN), besides microbial N and microbial C. While the enzymatic activity of NAG and β-Glucosidase was greater in the agricultural plot with inorganic fertilization, as well as nitrate (NO₃) was higher in fertilized plot, in comparison with the other two plots. The aboveground biomass (AB) of maize in the plot with inorganic fertilization presented higher TC and TN concentrations than the maize AB growing in the semiorganic plot, but the C:N ratio was highest in the grass AB in the abandoned plot. The C:N ration in the maize grain was greater in the semi-organic agricultural plot. These results show that the plot under intensive agricultural management favors the loss of soil organic matter and N, degrading the dynamics of soil organic compounds, promoting its fertility depletion.

Keywords: mineralization, nitrogen cycle, soil degradation, soil nutrients

Procedia PDF Downloads 167

Authors: Anita Jäger, Andrew Salazar, Jörg von Hagen, Harald Kolmar

Abstract:

In the treatment of individuals with sensitive and psoriatic skin, several inflammation and itch-related molecular and cellular targets have been identified, but many of these have yet to be characterized. In this study, we present two potential targets in the skin that can be linked to the inflammation and itch cycle. 11ßHSD1 is the enzyme responsible for converting inactive cortisone to active cortisol used to transmit signals downstream. The activation of the receptor NK1R correlates with promoting inflammation and the perception of itch and pain in the skin. In this study, both targets have been investigated based on their involvement in inflammation. The role of both identified targets was characterized based on the secretion of inflammation cytokine- IL6, IL-8, and CCL2, as well as phosphorylation and signaling pathways. It was found that treating skin cells with molecules able to inhibit inflammatory pathways results in the reduction of inflammatory signaling molecules secreted by skin cells and increases their proliferative capacity. Therefore, these molecular targets and their associated pathways show therapeutic potential and can be mitigated via small molecules. This research can be used for further studies in inflammation and itch pathways and can help to treat pathological symptoms.

Keywords: inflammation, itch, signaling pathway, skin

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Authors: Abdelhafid Zenati, Mohamed Tadjine

Abstract:

The mathematical formulation of biomedical problems is an important phase to understand and predict the dynamic of the controlled population. In this paper we perform a stability analysis of a coupled model for healthy and cancerous cells dynamics in Acute Myeloid Leukemia, this represents our first aim. Second, we illustrate the effect of the interconnection between healthy and cancer cells. The PDE-based model is transformed to a nonlinear distributed state space model (delay system). For an equilibrium point of interest, necessary and sufficient conditions of global asymptotic stability are given. Thus, we came up to give necessary and sufficient conditions of global asymptotic stability of the origin and the healthy situation and control of the dynamics of normal hematopoietic stem cells and cancerous during myelode Acute leukemia. Simulation studies are given to illustrate the developed results.

Keywords: distributed delay, global stability, modelling, nonlinear models, PDE, state space

Procedia PDF Downloads 242

Authors: Ik–Tae Im, H. M. Abdelmotalib, M. A. Youssef, S. B. Young

Abstract:

In this study the flow characteristics and bed-to-wall heat transfer in a gas-solid conical fluidized bed combustor were investigated using both experimental and numerical methods. The computational fluid dynamic (CFD) simulations were carried out using a commercial software, Fluent V6.3. A two-fluid Eulerian-Eulerian model was applied in order to simulate the gas–solid flow and heat transfer in a conical sand-air bed with 30o con angle and 22 cm static bed height. Effect of different fluidizing number varying in the range of 1.5 - 2.3, drag models namely (Syamlal-O’Brien and Gidaspow), and friction viscosity on flow and bed-to-wall heat transfer were analyzed. Both bed pressure drop and heat transfer coefficient increased with increasing inlet gas velocity. The Gidaspow drag model showed a better agreement with experimental results than other drag model. The friction viscosity had no clear effect on both hydrodynamics and heat transfer.

Keywords: computational fluid dynamics, heat transfer coefficient, hydrodynamics, renewable energy

Procedia PDF Downloads 390

Authors: Carla E. O. de Moraes, Gladson O. Antunes, Mauro A. Rincon

Abstract:

The aim of this paper is to study the internal stabilization of the Bernoulli-Euler equation numerically. For this, we consider a square plate subjected to a feedback/damping force distributed only in a subdomain. An algorithm for obtaining an approximate solution to this problem was proposed and implemented. The numerical method used was the Finite Difference Method. Numerical simulations were performed and showed the behavior of the solution, confirming the theoretical results that have already been proved in the literature. In addition, we studied the validation of the numerical scheme proposed, followed by an analysis of the numerical error; and we conducted a study on the decay of the energy associated.

Keywords: Bernoulli-Euler plate equation, numerical simulations, stability, energy decay, finite difference method

Procedia PDF Downloads 395