Search results for: molecular docking and dynamics

Authors: M. W. Sun, Y. Zhang, L. M. Zhang, Z. H. Wang, Z. Q. Chen

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In the realm of flight control, the Proportional- Derivative (PD) control is still widely used for the attitude control in practice, particularly for the pitch control, and the attitude dynamics using PD controller should be investigated deeply. According to the empirical knowledge about the unstable flight dynamics, the control parameter combination conditions to generate sole or finite number of closed-loop oscillations, which is a quite smooth response and is more preferred by practitioners, are presented in analytical or numerical manners. To analyze the effects of the combination conditions of the control parameters, the roots of several polynomials are sought to obtain feasible solutions. These conditions can also be plotted in a 2-D plane which makes the conditions be more explicit by using multiple interval operations. Finally, numerical examples are used to validate the proposed methods and some comparisons are also performed.

Keywords: attitude control, dynamic performance, numerical solving method, interval, unstable flight dynamics

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Authors: Shuofeng Yuan, Bojian Zheng

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Assembly of the heterotrimeric polymerase complex of influenza virus from the individual subunits PB1, PA, and PB2 is a prerequisite for viral replication, in which the interaction between the N-terminal of PB1 (PB1N) and the C terminal of PA (PAC) may be a desired target for antiviral development. In this study, we first compared the feasibility of high throughput screening by enzyme-linked immunosorbent assay (ELISA) and fluorescence polarization (FP) assay. Among the two, ELISA was demonstrated to own broader dynamic range so that it was used for screening inhibitors, which blocked PA and PB1 interaction. Several binding inhibitors of PAC-PB1N were identified and subsequently tested for the antiviral efficacy. Apparently, 3-(2-chlorophenyl)-6-ethyl-7-methyl[1,2,4]triazolo[4,3-a]pyrimidin-5-ol, designated ANA-1, was found to be a strong inhibitor of PAC-PB1N interaction and act as a potent antiviral agent against the infections of multiple subtypes of influenza A virus, including H1N1, H3N2, H5N1, H7N7, H7N9 and H9N2 subtypes, in cell cultures. Intranasal administration of ANA-1 protected mice from lethal challenge and reduced lung viral loads in H1N1 virus infected BALB/c mice. Docking analyses predicted that ANA-1 bound to an allosteric site of PAC, which would cause conformational changes thereby disrupting the PAC-PB1N interaction. Overall, our study has identified a novel compound with potential to be developed as an anti-influenza drug.

Keywords: influenza, antiviral, viral polymerase, compounds

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Authors: Hao-Wen Chang, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang

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All-solid-state lithium batteries (ASSLBs) are increasingly recognized as a safer and more reliable alternative to conventional lithium-ion batteries due to their non-flammable nature and enhanced safety performance. ASSLBs utilize a range of solid-state electrolytes, including solid polymer electrolytes (SPEs), inorganic solid electrolytes (ISEs), and composite polymer electrolytes (CPEs). SPEs are particularly valued for their flexibility, ease of processing, and excellent interfacial compatibility with electrodes, though their ionic conductivity remains a significant limitation. ISEs, on the other hand, provide high ionic conductivity, broad electrochemical windows, and strong mechanical properties but often face poor interfacial contact with electrodes, impeding performance. CPEs, which merge the strengths of SPEs and ISEs, represent a compelling solution for next-generation ASSLBs by addressing both electrochemical and mechanical challenges. Despite their potential, the mechanisms governing lithium-ion transport within these systems remain insufficiently understood. In this study, we designed CPEs based on argyrodite-type Li₆PS₅Cl (LPSC) combined with two distinct polymer matrices: poly(ethylene oxide) (PEO) with 24.5 wt% lithium bis(trifluoromethane)sulfonimide (LiTFSI) and polycaprolactone (PCL) with 25.7 wt% LiTFSI. Through density functional theory (DFT) calculations, we investigated the interfacial chemistry of these materials, revealing critical insights into their stability and interactions. Additionally, ab initio molecular dynamics (AIMD) simulations of lithium electrodes interfaced with LPSC layers containing polymers and LiTFSI demonstrated that the polymer matrix significantly mitigates LPSC decomposition, compared to systems with only a lithium electrode and LPSC layers. These findings underscore the pivotal role of CPEs in improving the performance and longevity of ASSLBs, offering a promising path forward for next-generation energy storage technologies.

Keywords: all-solid-state lithium-ion batteries, composite solid electrolytes, DFT calculations, Li-ion transport

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Authors: Hafiz Md. HasanBabu, Khandaker Mohammad Mohi Uddin, Md. IstiakJaman Ami, Rahat Hossain Faisal

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Computing in biomolecular programming performs through the different types of reactions. Proteins and nucleic acids are used to store the information generated by biomolecular programming. DNA (Deoxyribose Nucleic Acid) can be used to build a molecular computing system and operating system for its predictable molecular behavior property. The DNA device has clear advantages over conventional devices when applied to problems that can be divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in memory and conduct multiple operations at once, thus solving decomposable problems much faster. Programmable Logic Array, abbreviated as PLA is a programmable device having programmable AND operations and OR operations. In this paper, a DNA PLA is designed by different molecular operations using DNA molecules with the proposed algorithms. The molecular PLA could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism, and extraordinary energy efficiency.

Keywords: biological systems, DNA computing, parallel computing, programmable logic array, PLA, DNA

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Authors: Rui Mao, Heming Ji, Xiaoyu Wang

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Keystroke dynamics are widely used in identity recognition. It has the advantage that the individual typing rhythm is difficult to imitate. It also supports continuous authentication through the keyboard without extra devices. The existing keystroke dynamics authentication methods based on machine learning have a drawback in supporting relatively complex scenarios with massive data. There are drawbacks to both feature extraction and model optimization in these methods. To overcome the above weakness, an authentication model of keystroke dynamics based on deep learning is proposed. The model uses feature vectors formed by keystroke content and keystroke time. It ensures efficient continuous authentication by cooperating attention mechanisms with the combination of CNN and Bi-LSTM. The model has been tested with Open Data Buffalo dataset, and the result shows that the FRR is 3.09%, FAR is 3.03%, and EER is 4.23%. This proves that the model is efficient and accurate on continuous authentication.

Keywords: keystroke dynamics, identity authentication, deep learning, CNN, LSTM

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Authors: R. F. B. Gonçalves, E. N. Iwama, J. A. F. F. Rocco, K. Iha

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Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.

Keywords: shelf-life, thermal analysis, Ozawa method, Kissinger method, LAMMPS software, thrust

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Authors: Vigen Barkhudaryan

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The influence of external effects (γ-, UV–radiations, high temperature) in presence of air oxygen on structural transformations of low-density polyethylene (LDPE) have been investigated dependent on the polymers’ thickness, the intensity and the dose of external actions. The methods of viscosimetry, light scattering, turbidimetry and gelation measuring were used for this purpose. The comparison of influence of external effects on LDPE shows, that the destruction and cross-linking processes of macromolecules proceed simultaneously with all kinds of external effects. A remarkable growth of average molecular mass of LDPE along with the irradiation doses and heat treatment exposure growth was established. It was linear for the mass average molecular mass and at the initial doses is mainly the result of the increase of the macromolecular branching. As a result, the macromolecular hydrodynamic volumes have been changed, and therefore the dependence of viscosity average molecular mass on the doses was going through the minimum at initial doses. A significant change of molecular mass, sizes and shape of macromolecules of LDPE occurs under the influence of external effects. The influence is limited only by diffusion of oxygen during -irradiation and heat treatment. At UV–irradiation the influence is limited both by diffusion of oxygen and penetration of radiation. Consequently, the molecular transformations are deeper and evident in case of -irradiation, as soon as the polymer is transformed in a whole volume. It was also established, that the mechanism of molecular transformations in polymers from the surface layer distinctly differs from those of the sample deeper layer. A comparison of the results of these investigations allows us to conclude, that the mechanisms of influence of investigated external effects on polyethylene are similar.

Keywords: cross-linking, destruction, high temperature, LDPE, γ-radiations, UV-radiations

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Authors: Sabyasachi Mukhopadhyay, Joseph Ogutu, Hans-Peter Piepho

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We aim to model dynamics of wildlife or pastoral livestock population for understanding of their population change and hence for wildlife conservation and promoting human welfare. The study is motivated by an age-sex structured population counts in different regions of Serengeti-Mara during the period 1989-2003. Developing reliable and realistic models for population dynamics of large herbivore population can be a very complex and challenging exercise. However, the Bayesian statistical domain offers some flexible computational methods that enable the development and efficient implementation of complex population dynamics models. In this work, we have used a novel Bayesian state-space model to analyse the dynamics of topi and hartebeest populations in the Serengeti-Mara Ecosystem of East Africa. The state-space model involves survival probabilities of the animals which further depend on various factors like monthly rainfall, size of habitat, etc. that cause recent declines in numbers of the herbivore populations and potentially threaten their future population viability in the ecosystem. Our study shows that seasonal rainfall is the most important factors shaping the population size of animals and indicates the age-class which most severely affected by any change in weather conditions.

Keywords: bayesian state-space model, Markov Chain Monte Carlo, population dynamics, conservation

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Authors: Yuri V. Kim

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This article presents a new approach to the Functional Testing of Space Systems (SS). It can be considered as a generic test and used for a wide class of SS that from the point of view of System Dynamics and Control may be described by the ordinary differential equations. Suggested methodology is based on using semi-natural experiment- laboratory stand that doesn’t require complicated, precise and expensive technological control-verification equipment. However, it allows for testing system as a whole totally assembled unit during Assembling, Integration and Testing (AIT) activities, involving system hardware (HW) and software (SW). The test physically activates system input (sensors) and output (actuators) and requires recording their outputs in real time. The data is then inserted in laboratory PC where it is post-experiment processed by Matlab/Simulink Identification Toolbox. It allows for estimating system dynamics in form of estimation of system differential equations by the experimental way and comparing them with expected mathematical model prematurely verified by mathematical simulation during the design process.

Keywords: system dynamics, space system ground tests and space qualification, system dynamics identification, satellite attitude control, assembling, integration and testing

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Authors: Salem El-Tohami Ashoor

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A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Shachi Pathak

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We are living in knowledge based economy where firms can gain competitive advantage with the help of managing knowledge within the organization. The purpose the study is to develop a conceptual model to explain the relationship between factors affecting knowledge sharing, called as knowledge enablers, in an organization, knowledge sharing activities and organizational performance, using system dynamics approach. This research is important since it will provide better understandings on what are the key knowledge enablers to support knowledge sharing activities, and how knowledge sharing activities will affect the capability of an organization to enhance the performance of the organization.

Keywords: knowledge management, knowledge sharing, organizational performance, system dynamics

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Authors: T. Rajamäki

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In clean room environment molecular contamination in very small concentrations can cause significant harm for the components and processes. This is commonly referred as airborne molecular contamination (AMC). There is a shortage of high sensitivity continuous measurement data for existence and behavior of several of these contaminants. Accordingly, in most cases correlation between concentration of harmful molecules and their effect on processes is not known. In addition, the formation and distribution of contaminating molecules are unclear. In this work sensitive optical techniques are applied in clean room facilities for investigation of concentrations, forming mechanisms and effects of contaminating molecules. Special emphasis is on reactive acid and base gases ammonia (NH3) and hydrogen fluoride (HF). They are the key chemicals in several operations taking place in clean room processes.

Keywords: AMC, clean room, concentration, reactive gas

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Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

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The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Harish Rajak, Swati Singh

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A series of novel pyrimidine based semicarbazone were designed and synthesized on the basis of semicarbazone based pharmacophoric model to satisfy the structural prerequisite crucial for antiepileptic activity. The semicarbazones based pharmacophoric model consists of following four essential binding sites: (i) An aryl hydrophobic binding site with halo substituent; (ii) A hydrogen bonding domain; (iii) An electron donor group and (iv) Another hydrophobic-hydrophilic site controlling the pharmacokinetic features of the anticonvulsant. The aryl semicarbazones has been recognized as a structurally novel class of compounds with remarkable anticonvulsant activity. In the present study, all the test semicarbazones were subjected to molecular docking using Glide v5.8. Some of the compounds were found to interact with ARG192, GLU270 and THR353 residues of 1OHV protein, present in GABA-AT receptor. The chemical structures of the synthesized molecules were characterized by elemental and spectral (IR, 1H NMR, 13C NMR and MS) analysis. The anticonvulsant activities of the compounds were investigated using maximal electroshock seizure (MES) and subcutaneous pentylenetrtrazole (scPTZ) models. The neurotoxicity was evaluated in mice by the rotorod test. The attempts were also made to establish structure-activity relationships among synthesized compounds. The results of the present study confirmed that the pharmacophore model with four binding sites is essential for antiepileptic activity.

Keywords: pyrimidine, semicarbazones, anticonvulsant activity, neurotoxicity

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Authors: Etsuo Morishita

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This paper presents the project and experiment-based fluid dynamics education in Meisei University, a private institution in Tokyo, Japan. We pay attention not only to the basic engineering courses but also to the practical aspect of engineering experience. So, we prepare courses called the Projects from I to VI. The Projects I and II are designed for the first year, III and IV are designated for the second year, V and VI are prepared for the third year, respectively. Each supervisor is responsible for two of these projects every year. When students take the Project V and VI at the third year, we automatically assume that these students will join the lab of the project for the graduation thesis. We would like to show our experience in the Project I in the summer term, 2016. In this project, we introduce a traction flight vehicle called Cat Flyer. This is a kind of a kite towed by a car for example. This is very similar to parasailing, but flight is possible even on the roads. Experiments in mechanical engineering education are also very important, and we would like to explain our course on centrifugal pump, venture, and orifice. Although these are described in detail in the text books of fluid dynamics, it is still crucial to have practical experiments as a student.

Keywords: aerodynamics, experiment, fluid dynamics, project

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Authors: T. G. Kassem, A. K. Adunchezor, J. P. Chollom

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This paper describes a mathematical model developed to predict the dynamics of Hepatitis B virus (HBV) infection and to evaluate the potential impact of vaccination and treatment on its dynamics. We used a compartmental model expressed by a set of differential equations based on the characteristic of HBV transmission. With these, we find the threshold quantity R0, then find the local asymptotic stability of disease free equilibrium and endemic equilibrium. Furthermore, we find the global stability of the disease free and endemic equilibrium.

Keywords: hepatitis B virus, epidemiology, vaccination, mathematical model

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Authors: Giovanni Meloni

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Recent results are presented from experiments carried out at the Advanced Light Source (ALS) at the Chemical Dynamics Beamline of Lawrence Berkeley National Laboratory using multiplexed synchrotron photoionization mass spectrometry. The reaction mixture and a buffer gas (He) are introduced through individually calibrated mass flow controllers into a quartz slow flow reactor held at constant pressure and temperature. The gaseous mixture effuses through a 650 μm pinhole into a 1.5 mm skimmer, forming a molecular beam that enters a differentially pumped ionizing chamber. The molecular beam is orthogonally intersected by a tunable synchrotron radiation produced by the ALS in the 8-11 eV energy range. Resultant ions are accelerated, collimated, and focused into an orthogonal time-of-flight mass spectrometer. Reaction species are identified by their mass-to-charge ratios and photoionization (PI) spectra. Comparison of experimental PI spectra with literature and/or simulated curves is routinely done to assure the identity of a given species. With the aid of electronic structure calculations, potential energy surface scans are performed, and Franck-Condon spectral simulations are obtained. Examples of these experiments are discussed, ranging from new intermediates characterization to reaction mechanisms elucidation and biofuels oxidation pathways identification.

Keywords: mass spectrometry, reaction intermediates, synchrotron photoionization, oxidation reactions

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Authors: Khaled Suleiman Mohammed Al-Mashrafi

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A compositional plume is a fluid flow in a directional channel of finite width in another fluid of different material composition. The study of the dynamics of compositional plumes plays an essential role in many real-life applications like industrial applications (e.g., iron casting), environmental applications (e.g., salt fingers and sea ice), and geophysical applications (e.g., solidification at the inner core boundary (ICB) of the Earth, and mantle plumes). The dynamics of compositional plumes have been investigated experimentally and theoretically. The experimental works observed that the plume flow seems to be stable, although some experiments showed that it can be unstable. At the same time, the theoretical investigations showed that the plume flow is unstable. This is found to be true even if the plume is subject to rotation or/and in the presence of a magnetic field and even if another plume of different composition is also present. It is noticeable that all the theoretical studies on the dynamics of compositional plumes are conducted in unbounded domains. The present work is to investigate theoretically the influence of vertical walls (boundaries) on the dynamics of compositional plumes in the absence/presence of a rotation field. The mathematical model of the dynamics of compositional plumes used the equations of continuity, motion, heat, concentration of light material, and state. It is found that the presence of boundaries has a strong influence on the basic state solution as well as the stability of the plume, particularly when the plume is close to the boundary, but the compositional plume remains unstable.

Keywords: compositional plumes, stability, bounded domain, vertical boundaries

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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

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

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

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Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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Authors: Carlos F. Sanz-Navarro, Sonia Fereres

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Binary and ternary mixtures of molten salts are excellent thermal energy storage systems and have been widely used in commercial tanks both in nuclear and solar thermal applications. However, the energy density of the commercially used mixtures is still insufficient, and therefore, new systems based on latent heat storage (or phase change materials, PCM) are currently being investigated. In order to shed some light on the macroscopic physical properties of the molten salt phases, knowledge of the microscopic structure and dynamics is required. Several molecular dynamics (MD) simulations have been performed to model the thermal behavior of (Li,K)2CO3 mixtures. Up to this date, this particular molten salt mixture has not been extensively studied but it is of fundamental interest for understanding the behavior of other commercial salts. Molten salt diffusivities, the internal electrical ion mobility, and the physical properties of the solid-liquid phase transition have been calculated and compared to available data from literature. The effect of anion polarization and the application of a strong external electric field have also been investigated. The influence of electrical ion mobility on local composition is explained through the Chemla effect, well known in electrochemistry. These results open a new way to design optimal high temperature energy storage materials.

Keywords: atomistic simulations, thermal storage, latent heat, molten salt, ion mobility

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Authors: Misagh Faezipour

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System dynamics is a systems engineering approach that can help address the complex challenges in different systems. Little is known about how the brain represents people to predict behavior. This work is based on how the brain simulates different personal behavior and responds to them in the case of young children ages one to five. As we know, children’s minds/brains are just as clean as a crystal, and throughout time, in their surroundings, families, and education center, they grow to develop and have different kinds of behavior towards the world and the society they live in. Hence, this work aims to identify how young children respond to various personality behavior and observes their reactions towards them from a system dynamics perspective. We will be exploring the Big Five personality traits in young children. A causal model is developed in support of the system dynamics approach. These models graphically present the factors and factor relationships that contribute to the big five personality traits and provide a better understanding of the entire behavior model. A simulator will be developed that includes a set of causal model factors and factor relationships. The simulator models the behavior of different factors related to personality traits and their impacts and can help make more informed decisions in a risk-free environment.

Keywords: personality traits, systems engineering, system dynamics, causal model, behavior model

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Paul Bayron, Richard Kelso, Rey Chin

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Wind tunnel experiments were performed in the KC closed-circuit wind tunnel in the University of Adelaide to study the influence of tip-speed-ratio (

Keywords: hotwire anemometry, wake dynamics, wind tunnel, wind turbines

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Authors: Callistus I. Iheme, Kenneth E. Asika, Emmanuel I. Ugwor, Chukwuka U. Ogbonna, Ugonna H. Uzoka, Nneamaka A. Chiegboka, Chinwe S. Alisi, Obinna S. Nwabueze, Amanda U. Ezirim, Judeanthony N. Ogbulie

Abstract:

Antimicrobial resistance (AMR) is a major threat to the global health sector. Zinc oxide nanocomposites (ZnONCs), composed of zinc oxide nanoparticles and phytochemicals from Azadirachta indica aqueous leaf extract, were assessed for their physico-chemicals, in silico and in vitro antimicrobial properties on multidrug-resistant Escherichia coli enzymes. Gas chromatography coupled with mass spectroscope (GC-MS) analysis on the ZnONCs revealed the presence of twenty volatile phytochemical compounds, among which is scoparone. Characterization of the ZnONCs was done using ultraviolet-visible spectroscopy (UV-vis), energy dispersive spectroscopy (EDX), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and x-ray diffractometer (XRD). Dehydrogenase enzyme converts colorless 2,3,5-triphenyltetrazolium chloride to the red triphenyl formazan (TPF). The rate of formazan formation in the presence of ZnONCs is proportional to the enzyme activities. The color formation is extracted and determined at 500 nm, and the percentage of enzyme activity is calculated. To determine the bioactive components of the ZnONCs, characterize their binding to enzymes, and evaluate the enzyme-ligand complex stability, respectively Discrete Fourier Transform (DFT) analysis, docking, and molecular dynamics simulations will be employed. The results showed arrays of ZnONCs nanorods with maximal absorption wavelengths of 320 nm and 350 nm and thermally stable at the temperature range of 423.77 to 889.69 ℃. In vitro study assessed the dehydrogenase inhibitory properties of the ZnONCs, conjugate of ZnONCs and ampicillin (ZnONCs-amp), the aqueous leaf extract of A. indica, and ampicillin (standard drug). The findings revealed that at the concentration of 500 μm/mL, 57.89 % of the enzyme activities were inhibited by ZnONCs compared to 33.33% and 21.05% of the standard drug (Ampicillin), and the aqueous leaf extract of the A. indica respectively. The inhibition of the enzyme activities by the ZnONCs at 500 μm/mL was further enhanced to 89.74 % by conjugating with Ampicillin. In silico study on the ZnONCs revealed scoparone as the most viable competitor of nicotinamide adenine dinucleotide (NAD⁺) for the coenzyme binding pocket on E. coli malate and histidinol dehydrogenase. From the findings, it can be concluded that the scoparone components of the nanocomposites in synergy with the zinc oxide nanoparticles inhibited E. coli malate and histidinol dehydrogenase by competitively binding to the NAD⁺ pocket and that the conjugation of the ZnONCs with ampicillin further enhanced the antimicrobial efficiency of the nanocomposite against multidrug resistant E. coli.

Keywords: antimicrobial resistance, dehydrogenase activities, E. coli, zinc oxide nanocomposites

Procedia PDF Downloads 49

Authors: A. K. Visnuprasad, P. J. Jojo, Reshma Bhaskaran

Abstract:

Computational fluid dynamics (CFD) is used to simulate the distribution of indoor radon concentration in a living room with elevated levels of radon concentration which varies from 22 Bqm-3 to 1533 Bqm-3 in 24 hours. Finite volume method (FVM) was used for the simulation. The simulation results were experimentally validated at 16 points in two horizontal planes (y=1.4m & y=2.0m) using pin-hole dosimeters and at 3 points using scintillation radon monitor (SRM). Passive measurement using pin-hole dosimeters were performed in all seasons. Another simulation was done to find a suitable position for a passive ventilation system for the effective mitigation of radon.

Keywords: indoor radon, computational fluid dynamics, radon flux, ventilation rate, pin-hole dosimeter

Procedia PDF Downloads 413

Authors: Micheale Yifter Weldemichael

Abstract:

Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

Procedia PDF Downloads 35

Authors: David Nagy

Abstract:

This paper exemplifies the influence of the purpose of an aircraft on the aerodynamic properties of its airfoil. In particular, the research takes into consideration two types of aircraft, namely cargo aircraft and military high-speed aircraft and compares their airfoil characteristics using their NACA airfoils as well as computational fluid dynamics. The results show that airfoils of aircraft designed for cargo have a heavier focus on maintaining a large lift force whereas speed-oriented airplanes focus on minimizing the drag force.

Keywords: aerodynamic simulation, aircraft, airfoil, computational fluid dynamics, lift to drag ratio, NACA 64-206, NACA 65-415

Procedia PDF Downloads 388