Search results for: molecular modelling

Authors: Olubukayo-Opeyemi Oyetayo, Oscar Mendez-Lucio, Andreas Bender, Hans Kiefer

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The thermal melting curve of a protein provides information on its conformational stability and could provide cues on its aggregation behavior. Naturally-occurring osmolytes have been shown to improve the thermal stability of most proteins in a concentration-dependent manner. They are therefore commonly employed as additives in therapeutic protein purification and formulation. A number of intertwined and seemingly conflicting mechanisms have been put forward to explain the observed stabilizing effects, the most prominent being the preferential exclusion mechanism. We attempted to probe and summarize molecular mechanisms for thermal stabilization of a monoclonal antibody (mAb) by developing quantitative structure-activity relationships using a rationally-selected library of 120 osmolyte-like compounds in the polyhydric alcohols, amino acids and methylamines classes. Thermal stabilization potencies were experimentally determined by thermal shift assays based on differential scanning fluorimetry. The cross-validated QSAR model was developed by partial least squares regression using descriptors generated from Molecular Operating Environment software. Careful evaluation of the results with the use of variable importance in projection parameter (VIP) and regression coefficients guided the selection of the most relevant descriptors influencing mAb thermal stability. For the mAb studied and at pH 7, the thermal stabilization effects of tested compounds correlated positively with their fractional polar surface area and inversely with their fractional hydrophobic surface area. We cannot claim that the observed trends are universal for osmolyte-protein interactions because of protein-specific effects, however this approach should guide the quick selection of (de)stabilizing compounds for a protein from a chemical library. Further work with a large variety of proteins and at different pH values would help the derivation of a solid explanation as to the nature of favorable osmolyte-protein interactions for improved thermal stability. This approach may be beneficial in the design of novel protein stabilizers with optimal property values, especially when the influence of solution conditions like the pH and buffer species and the protein properties are factored in.

Keywords: thermal stability, monoclonal antibodies, quantitative structure-activity relationships, osmolytes

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Authors: Farnaz Fotovvatikhah, Javad Akbari

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Test time of a test architecture is an important factor which depends on the architecture's delay and test patterns. Here a new architecture to store the test results based on network on chip is presented. In addition, simple analytical model is proposed to calculate link test time for built in self-tester (BIST) and external tester (Ext) in multiprocessor systems. The results extracted from the model are verified using FPGA implementation and experimental measurements. Systems consisting 16, 25, and 36 processors are implemented and simulated and test time is calculated. In addition, BIST and Ext are compared in terms of test time at different conditions such as at different number of test patterns and nodes. Using the model the maximum frequency of testing could be calculated and the test structure could be optimized for high speed testing.

Keywords: test, nano on-chip network, JTAG, modelling

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Authors: M. Wigwe, J. G Akpa, E. N Wami

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Mathematical models of the absorber of a glycol dehydration facility was developed using the principles of conservation of mass and energy. Models which predict variation of the water content of gas in mole fraction, variation of gas and liquid temperatures across the parking height were developed. These models contain contributions from bulk and diffusion flows. The effect of diffusion on the process occurring in the absorber was studied in this work. The models were validated using the initial conditions in the plant data from Company W TEG unit in Nigeria. The results obtained showed that the effect of diffusion was noticed between z=0 and z=0.004 m. A deviation from plant data of 0% was observed for the gas water content at a residence time of 20 seconds, at z=0.004 m. Similarly, deviations of 1.584% and 2.844% were observed for the gas and TEG temperatures.

Keywords: separations, absorption, simulation, dehydration, water content, triethylene glycol

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Authors: Tizi Hayet, Berrama Tarek, Bounif Nadia

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Phenol and its derivatives are organic compounds utilized in the chemical industry. They are introduced into the environment by accidental spills and illegal release of industrial and municipal wastewater. Phenols are organic intermediaries that considered as potential pollutants. Adsorption is one of the purification and separation techniques used in this area. Algeria produces annually 131000 tones of fig; therefore, a large amount of fig leaves is generated, and the conversion of this waste into adsorbent allows the valorization of agricultural residue. The main purpose of this present work is to describe an application of the statistical method for modeling and optimization of the conditions of the phenol (Ph) adsorption from agricultural by-product locally available (fig leaves). The best experimental performance of Ph elimination on the adsorbent was obtained with: Adsorbent concentration (X2) = 0.2 g L-1; Initial concentration (X3) = 150 mg L-1; Speed agitation (X1) = 300 rpm.

Keywords: low-cost adsorbents, fig leaves, full factorial design, phenol, biosorption

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Authors: Yuhei Kunihiro, Sorin V. Sabau, Kazuhiro Shibuya

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We study the molecular evolution of insulin from the metric geometry point of view. In mathematics, and particularly in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from the geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords: metric geometry, evolution, insulin, C. elegans

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Authors: Juan Manuel Sanchez-Cartas, Gonzalo Leon

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A price competition algorithm for ABMs based on game theory principles is proposed to deal with the simulation of theoretical market models. The algorithm is applied to the classical Hotelling’s model and to a two-sided market model to show it leads to the optimal behavior predicted by theoretical models. However, when theoretical models fail to predict the equilibrium, the algorithm is capable of reaching a feasible outcome. Results highlight that the algorithm can be implemented in other simulation models to guarantee rational users and endogenous optimal behaviors. Also, it can be applied as a tool of verification given that is theoretically based.

Keywords: agent-based models, algorithmic game theory, multi-sided markets, price optimization

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Authors: Dewi Selvia Fardhyanti, Astrilia Damayanti

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Coal tar is a liquid by-product of the process of coal gasification and carbonation, also in some industries such as steel, power plant, cement, and others. This liquid oil mixture contains various kinds of useful compounds such as aromatic compounds and phenolic compounds. These compounds are widely used as raw material for insecticides, dyes, medicines, perfumes, coloring matters, and many others. This research investigates thermodynamic modelling of liquid-liquid equilibria (LLE) in solvent extraction of o-Cresol from the coal tar. The equilibria are modeled by ternary components of Wohl, Van Laar, and Three-Suffix Margules models. The values of the parameters involved are obtained by curve-fitting to the experimental data. Based on the comparison between calculated and experimental data, it turns out that among the three models studied, the Three-Suffix Margules seems to be the best to predict the LLE of o-Cresol for those system.

Keywords: coal tar, o-Cresol, Wohl, Van Laar, three-suffix margules

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Authors: V. Radulescu, S. Dumitru

Abstract:

Introduction: Determination of the temperature field inside a fluid in motion has many practical issues, especially in the case of turbulent flow. The phenomenon is greater when the solid walls have a different temperature than the fluid. The turbulent heat and mass transfer have an essential role in case of the thermal pollution, as it was the recorded during the damage of the Thermoelectric Power-plant Oradea (closed even today). Basic Methods: Solving the theoretical turbulent thermal pollution represents a particularly difficult problem. By using the semi-empirical theories or by simplifying the made assumptions, based on the experimental measurements may be assured the elaboration of the mathematical model for further numerical simulations. The three zones of flow are analyzed separately: the vicinity of the solid wall, the turbulent transition zone, and the turbulent core. For each area are determined the distribution law of temperature. It is determined the dependence of between the Stanton and Prandtl numbers with correction factors, based on measurements experimental. Major Findings/Results: The limitation of the laminar thermal substrate was determined based on the theory of Landau and Levice, using the assumption that the longitudinal component of the velocity pulsation and the pulsation’s frequency varies proportionally with the distance to the wall. For the calculation of the average temperature, the formula is used a similar solution as for the velocity, by an analogous mediation. On these assumptions, the numerical modeling was performed with a gradient of temperature for the turbulent flow in pipes (intact or damaged, with cracks) having 4 different diameters, between 200-500 mm, as there were in the Thermoelectric Power-plant Oradea. Conclusions: It was made a superposition between the molecular viscosity and the turbulent one, followed by addition between the molecular and the turbulent transfer coefficients, necessary to elaborate the theoretical and the numerical modeling. The concept of laminar boundary layer has a different thickness when it is compared the flow with heat transfer and that one without a temperature gradient. The obtained results are within the margin of error of 5%, between the semi-empirical classical theories and the developed model, based on the experimental data. Finally, it is obtained a general correlation between the Stanton number and the Prandtl number, for a specific flow (with associated Reynolds number).

Keywords: experimental measurements, numerical correlations, thermal pollution through pipelines, turbulent thermal flow

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Authors: Oulad Naoui Noureddine, Cherif ELAmine, Djehiche Abdelkader

Abstract:

Water resources management includes several disciplines; the modeling of rainfall-runoff relationship is the most important discipline to prevent natural risks. There are several models to study rainfall-runoff relationship in watersheds. However, the majority of these models are not applicable in all basins of the world.  In this study, a new stochastic method called The Only Corresponding Competitor method (OCC) was used for the hydrological modeling of M’ZAB   Watershed (South East of Algeria) to adapt a few empirical models for any hydrological regime.  The results obtained allow to authorize a certain number of visions, in which it would be interesting to experiment with hydrological models that improve collectively or separately the data of a catchment by the OCC method.

Keywords: modelling, optimization, rainfall-runoff relationship, empirical model, OCC

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Authors: Deon Bezuidenhout

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Pre-seeding with autologous endothelial cells improves the long-term patency of synthetic vascular grafts levels obtained with autografts, but is limited to a single centre due to resource, time and other constraints. Spontaneous in vivo endothelialization would obviate the need for pre-seeding, but has been shown to be absent in man due to limited transanastomotic and fallout healing, and the lack of transmural ingrowth due to insufficient porosity. Two types of graft scaffolds with increased interconnected porosity for improved tissue ingrowth and healing are thus proposed and described. Foam-type polyurethane (PU) scaffolds with small, medium and large, interconnected pores were made by phase inversion and spherical porogen extraction, with and without additional surface modification with covalently attached heparin and subsequent loading with and delivery of growth factors. Fibrillar scaffolds were made either by standard electrospinning using degradable PU (Degrapol®), or by dual electrospinning using non-degradable PU. The latter process involves sacrificial fibres that are co-spun with structural fibres and subsequently removed to increased porosity and pore size. Degrapol samples were subjected to in vitro degradation, and all scaffold types were evaluated in vivo for tissue ingrowth and vascularization using rat subcutaneous model. The foam scaffolds were additionally evaluated in a circulatory (rat infrarenal aortic interposition) model that allows for the grafts to be anastomotically and/or ablumenally isolated to discern and determine endothelialization mode. Foam-type grafts with large (150 µm) pores showed improved subcutaneous healing in terms of vascularization and inflammatory response over smaller pore sizes (60 and 90µm), and vascularization of the large porosity scaffolds was significantly increased by more than 70% by heparin modification alone, and by 150% to 400% when combined with growth factors. In the circulatory model, extensive transmural endothelialization (95±10% at 12 w) was achieved. Fallout healing was shown to be sporadic and limited in groups that were ablumenally isolated to prevent transmural ingrowth (16±30% wrapped vs. 80±20% control; p<0.002). Heparinization and GF delivery improved both mural vascularization and lumenal endothelialization. Degrapol electrospun scaffolds showed decrease in molecular mass and corresponding tensile strength over the first 2 weeks, but very little decrease in mass over the 4w test period. Studies on the effect of tissue ingrowth with and without concomitant degradation of the scaffolds, are being used to develop material models for the finite element modelling. In the case of the dual-spun scaffolds, the PU fibre fraction could be controlled shown to vary linearly with porosity (P = −0.18FF +93.5, r2=0.91), which in turn showed inverse linear correlation with tensile strength and elastic modulus (r2 > 0.96). Calculated compliance and burst pressures of the scaffolds increased with fibre fraction, and compliances matching the human popliteal artery (5-10 %/100 mmHg), and high burst pressures (> 2000 mmHg) could be achieved. Increasing porosity (76 to 82 and 90%) resulted in increased tissue ingrowth from 33±7 to 77±20 and 98±1% after 28d. Transmural endothelialization of highly porous foamed grafts is achievable in a circulatory model, and the enhancement of porosity and tissue ingrowth may hold the key the development of spontaneously endothelializing electrospun grafts.

Keywords: electrospinning, endothelialization, porosity, scaffold, vascular graft

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Authors: Akash K. Walunj, Dipendu Bhunia, Samarth Gupta, Prabhat Gupta

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Coupled shear walls consist of two shear walls connected intermittently by beams along the height. The behavior of coupled shear walls is mainly governed by the coupling beams. The coupling beams are designed for ductile inelastic behavior in order to dissipate energy. The base of the shear walls may be designed for elastic or ductile inelastic behavior. The amount of energy dissipation depends on the yield moment capacity and plastic rotation capacity of the coupling beams. In this paper, an analytical model of coupling beam was developed to calculate the rotations and moment capacities of coupling beam with conventional reinforcement.

Keywords: design studies, computational model(s), case study/studies, modelling, coupling beam

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Authors: Bruno Baptista, Andreia S. R. Oliveira, Patricia V. Mendonca, Jorge F. J. Coelho, Fani Sousa

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Drug delivery systems are designed to allow adequate protection and controlled delivery of drugs to specific locations. These systems aim to reduce side effects and control the biodistribution profile of drugs, thus improving therapeutic efficacy. This study involved the synthesis of polymeric nanoparticles, based on amphiphilic diblock copolymers, comprising a biocompatible, poly (oligo (ethylene oxide) methyl ether methacrylate (POEOMA) as hydrophilic segment and a pH-sensitive block, the poly (2-diisopropylamino)ethyl methacrylate) (PDPA). The objective of this work was the development of polymeric pH-responsive nanoparticles to encapsulate and carry small RNAs as a model to further develop non-coding RNAs delivery systems with therapeutic value. The responsiveness of PDPA to pH allows the electrostatic interaction of these copolymers with nucleic acids at acidic pH, as a result of the protonation of the tertiary amine groups of this polymer at pH values below its pKa (around 6.2). Initially, the molecular weight parameters and chemical structure of the block copolymers were determined by size exclusion chromatography (SEC) and nuclear magnetic resonance (1H-NMR) spectroscopy, respectively. Then, the complexation with small RNAs was verified, generating polyplexes with sizes ranging from 300 to 600 nm and with encapsulation efficiencies around 80%, depending on the molecular weight of the polymers, their composition, and concentration used. The effect of pH on the morphology of nanoparticles was evaluated by scanning electron microscopy (SEM) being verified that at higher pH values, particles tend to lose their spherical shape. Since this work aims to develop systems for the delivery of non-coding RNAs, studies on RNA protection (contact with RNase, FBS, and Trypsin) and cell viability were also carried out. It was found that they induce some protection against constituents of the cellular environment and have no cellular toxicity. In summary, this research work contributes to the development of pH-sensitive polymers, capable of protecting and encapsulating RNA, in a relatively simple and efficient manner, to further be applied on drug delivery to specific sites where pH may have a critical role, as it can occur in several cancer environments.

Keywords: drug delivery systems, pH-responsive polymers, POEOMA-b-PDPA, small RNAs

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Authors: Babatunde J. Falaye

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In this study, we obtain the approximate analytical solutions of the radial Schrödinger equation for the Deng-Fan diatomic molecular potential by using exact quantization rule approach. The wave functions have been expressed by hypergeometric functions via the functional analysis approach. An extension to rotational-vibrational energy eigenvalues of some diatomic molecules are also presented. It is shown that the calculated energy levels are in good agreement with the ones obtained previously E_nl-D (shifted Deng-Fan).

Keywords: Schrödinger equation, exact quantization rule, functional analysis, Deng-Fan potential

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Authors: M. Mosaad, J. H. Almutairi, A. S. Almutairi

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In this paper, saturated-vapour film condensation on a vertical wall with the backside cooled by forced convection is analyzed as a conjugate problem. In the analysis, the temperature and heat flux at the wall sides are assumed unknown and determined from the solution. The model is presented in a dimensionless form to take a broad view of the solution. The dimensionless variables controlling this coupled heat transfer process are discovered from the analysis. These variables explain the relative impact of the interactive heat transfer mechanisms of forced convection and film condensation. The study shows that the conjugate treatment of film condensation process yields results different from that predicted by a non-conjugate Nusselt-type solution, wherein the effect of the cooling fluid is neglected.

Keywords: film condensation, forced convection, coupled heat transfer, analytical modelling

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Authors: Gowtham Kalkere Jayanna, Mohamad Nazri Husin

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Graph theory, chemistry, and technology are all combined in cheminformatics. The structure and physiochemical properties of organic substances are linked using some useful graph invariants and the corresponding molecular graph. In this paper, we study specific reverse topological indices such as the reverse sum-connectivity index, the reverse Zagreb index, the reverse arithmetic-geometric, and the geometric-arithmetic, the reverse Sombor, the reverse Nirmala indices for the bistar graphs B (n: m) and the corona product Kₘ∘Kₙ', where Kₙ' Represent the complement of a complete graph Kₙ.

Keywords: reverse topological indices, bistar graph, the corona product, graph

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Authors: Mohammadjavad Sotoudeheian

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COVID-19, which began in December 2019, uses the angiotensin-converting enzyme 2 (ACE2) receptor to enter and spread through the cells. ACE2 mRNA is present in almost every organ, including nasopharynx, lung, as well as the brain. Ports of entry of SARS-CoV-2 into the central nervous system (CNS) may include arterial circulation, while viremia is remarkable. However, it is imperious to develop neurological symptoms evaluation CSF analysis in patients with COVID-19, but theoretically, ACE2 receptors are expressed in cerebellar cells and may be a target for SARS-CoV-2 infection in the brain. Recent evidence agrees that SARS-CoV-2 can impact the brain through direct and indirect injury. Two biomarkers for CNS injury, glial fibrillary acidic protein (GFAP) and neurofilament light chain (NFL) detected in the plasma of patients with COVID-19. NFL, an axonal protein expressed in neurons, is related to axonal neurodegeneration, and GFAP is over-expressed in CNS inflammation. GFAP cytoplasmic accumulation causes Schwan cells to misfunction, so affects myelin generation, reduces neuroskeletal support over NfLs during CNS inflammation, and leads to axonal degeneration. Interleukin-6 (IL-6), which extensively over-express due to interleukin storm during COVID-19 inflammation, regulates gene expression, as well as GFAP through STAT molecular pathway. IL-6 also impresses the phosphoinositide 3-kinase (PI3K)/STAT/smads pathway. The PI3K/ protein kinase B (Akt) pathway is the main modulator upstream of the mammalian target of rapamycin (mTOR), and alterations in this pathway are common in neurodegenerative diseases. Most neurodegenerative diseases show a disruption of autophagic function and display an abnormal increase in protein aggregation that promotes cellular death. Therefore, induction of autophagy has been recommended as a rational approach to help neurons clear abnormal protein aggregates and survive. The mTOR is a major regulator of the autophagic process and is regulated by cellular stressors. The mTORC1 pathway and mTORC2, as complementary and important elements in mTORC1 signaling, have become relevant in the regulation of the autophagic process and cellular survival through the extracellular signal-regulated kinase (ERK) pathway.

Keywords: mTORC1, COVID-19, PI3K, autophagy, neurodegeneration

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Authors: S. Jakšić, B. Žmuk

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The paper investigates the key factors of export dynamics for a set of Central and Southeast European (CSEE) countries in the context of current economic and financial crisis. In order to model the export dynamics a Global Vector Auto Regressive (GVAR) model is defined. As opposed to models which model each country separately, the GVAR combines all country models in a global model which enables obtaining important information on spill-over effects in the context of globalization and rising international linkages. The results of the study indicate that for most of the CSEE countries, exports are mainly driven by domestic shocks, both in the short run and in the long run. This study is the first application of the GVAR model to studying the export dynamics in the CSEE countries and therefore the results of the study present an important empirical contribution.

Keywords: export, GFEVD, global VAR, international trade, weak exogeneity

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Authors: Jadwiga Królikowska, Andrzej Królikowski, Jarosław Bajer

Abstract:

The work delineates the threats of maladjustment of the capacity of rain canals, designed and built in the early 20th century, in connection to heavy rainfall, especially in summer. This is the cause of the so called 'urban floods.' It directly relates to fierce raise of paving in the cities. Resolving this problem requires a change in philosophy of draining the rainfall by wider use of retention, infiltration and usage of rainwater. In systemic approach to managing the safety of urban drainage systems the risk, which is directly connected to safety failures, has been accepted as a measure. The risk level defines the probability of occurrence of losses greater than the ones forecast for a given time frame. The procedure of risk modelling, enabling its numeric analysis by using appropriate weights, is a significant issue in this paper.

Keywords: risk management, drainage system, urban areas, urban floods

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Authors: Olga V. Korotkaya

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This article is devoted to an important problem of calculation of deflected mode of the combustion chamber and the nozzle end of a new liquid-propellant rocket cruise engine. A special attention is given to the methodology of calculation. Three operating modes are considered. The analysis has been conducted in ANSYS software. The methods of conducted research are mathematical modelling, substructure method, cyclic symmetry, and finite element method. The calculation has been carried out to order of S. P. Korolev Rocket and Space Corporation «Energia». The main results are practical. Proposed methodology and created models would be able to use for a wide range of strength problems.

Keywords: combustion chamber, cyclic symmetry, finite element method, liquid-propellant rocket engine, nozzle end, substructure

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Authors: Jichan Jang

Abstract:

Mycobacterium abscessus is a rapidly growing life-threatening mycobacterium with multiple drug-resistance mechanisms. In this study, we screened the library to identify active molecules targeting Mycobacterium abscessus using resazurin live/dead assays. In this screening assay, the Z-factor was 0.7, as an indication of the statistical confidence of the assay. A cut-off of 80% growth inhibition in the screening resulted in the identification of four different compounds at a single concentration (20 μM). Dose-response curves identified three different hit candidates, which generated good inhibitory curves. All hit candidates were expected to have different molecular targets. Thus, we found that compound X, identified, may be a promising candidate in the M. abscessus drug discovery pipeline.

Keywords: Mycobacterium abscessus, antibiotics, drug discovery, emerging Pathogen

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Authors: Divij Gupta

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Pendular systems have a range of both mathematical and engineering applications, ranging from modelling the behaviour of a continuous mass-density rope to utilisation as Tuned Mass Dampers (TMD). Thus, it is of interest to study the differential equations governing the motion of such systems. Here we attempt to generalise these equations of motion for the plane compound pendulum with a finite number of N point masses. A Lagrangian approach is taken, and we attempt to find the generalised form for the Euler-Lagrange equations of motion for the i-th bob of the N -bob pendulum. The co-ordinates are parameterized as angular quantities to reduce the number of degrees of freedom from 2N to N to simplify the form of the equations. We analyse the form of these equations up to N = 4 to determine the general form of the equation. We also develop a MATLAB program to compute a solution to the system for a given input value of N and a given set of initial conditions.

Keywords: classical mechanics, differential equation, lagrangian analysis, pendulum

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Authors: Recep Kesli, Cengiz Demir, Riza Durmaz, Zekiye Bakkaloglu, Aysegul Bukulmez

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Objective: Acute diarrhea disease in children is a major cause of morbidity worldwide and is a leading cause of mortality, and it is the most common agent responsible for acute gastroenteritis in developing countries. With hospitalized children suffering from acute enteric disease up to 50% of the analyzed specimen were positive for rotavirus. Further molecular surveillance could provide a sound basis for improving the response to epidemic gastroenteritis and could provide data needed for the introduction of vaccination programmes in the country. The aim of this study was to investigate the prevalence of viral etiology of the gastroenteritis in children aged 0-6 years with acute gastroenteritis and to determine predominant genotypes of rotaviruses in the province of Afyonkarahisar, Turkey. Methods: An epidemiological study on rotavirus was carried out during 2016. Fecal samples obtained from the 144 rotavirus positive children with 0-6 years of ages and applied to the Pediatric Diseases Outpatient of ANS Research and Practice Hospital, Afyon Kocatepe University with the complaint of diarrhea. Bacterial agents causing gastroenteritis were excluded by using bacteriological culture methods and finally, no growth observed. Rotavirus antigen was examined by both the immunochromatographic (One Step Rotavirus and Adenovirus Combo Test, China) and ELISA (Premier Rotaclone, USA) methods in stool samples. Rotavirus RNA was detected by using one step real-time reverse transcription-polymerase chain reaction (RT-PCR). G and P genotypes were determined using RT-PCR with consensus primers of VP7 and VP4 genes, followed by semi nested type-specific multiplex PCR. Results: Of the total 144 rotavirus antigen-positive samples with RT-PCR, 4 (2,8%) were rejected, 95 (66%) were examined, and 45 (31,2%) have not been examined for PCR yet. Ninety-one (95,8%) of the 95 examined samples were found to be rotavirus positive with RT-PCR. Rotavirus subgenotyping distributions in G, P and G/P genotype groups were determined as; G1:45%, G2:27%, G3:13%, G9:13%, G4:1% and G12:1% for G genotype, and P[4]:33%, P[8]:66%, P[10]:1% for P genotype, and G1P[8]:%37, G2P[4]:%21, G3P[8]:%10, G4P[8]:%1, G9P[8]:%8, G2P[8]:%3 for G/P genotype . Not common genotype combination were %20 in G/P genotype. Conclusions: This study subscribes to the global agreement of the molecular epidemiology of rotavirus which will be useful in guiding the alternative and application of rotavirus vaccines or effective control and interception. Determining the diversity and rates of rotavirus genotypes will definitely provide guidelines for developing the most suitable vaccine.

Keywords: gastroenteritis, genotyping, rotavirus, RT-PCR

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Authors: Sanjeev Kumar Appicharla

Abstract:

This paper presents the results of the modelling and analysis of the European Railway Traffic Management (ERTMS) safety-critical incident to raise awareness of biases in the systems engineering process on the Cambrian Railway in the UK using the RAIB 17/2019 as a primary input. The RAIB, the UK independent accident investigator, published the Report- RAIB 17/2019 giving the details of their investigation of the focal event in the form of immediate cause, causal factors, and underlying factors and recommendations to prevent a repeat of the safety-critical incident on the Cambrian Line. The Systems for Investigation of Railway Interfaces (SIRI) is the methodology used to model and analyze the safety-critical incident. The SIRI methodology uses the Swiss Cheese Model to model the incident and identify latent failure conditions (potentially less than adequate conditions) by means of the management oversight and risk tree technique. The benefits of the systems for investigation of railway interfaces methodology (SIRI) are threefold: first is that it incorporates the “Heuristics and Biases” approach advanced by 2002 Nobel laureate in Economic Sciences, Prof Daniel Kahneman, in the management oversight and risk tree technique to identify systematic errors. Civil engineering and programme management railway professionals are aware of the role “optimism bias” plays in programme cost overruns and are aware of bow tie (fault and event tree) model-based safety risk modelling techniques. However, the role of systematic errors due to “Heuristics and Biases” is not appreciated as yet. This overcomes the problems of omission of human and organizational factors from accident analysis. Second, the scope of the investigation includes all levels of the socio-technical system, including government, regulatory, railway safety bodies, duty holders, signaling firms and transport planners, and front-line staff such that lessons are learned at the decision making and implementation level as well. Third, the author’s past accident case studies are supplemented with research pieces of evidence drawn from the practitioner's and academic researchers’ publications as well. This is to discuss the role of system thinking to improve the decision-making and risk management processes and practices in the IEC 15288 systems engineering standard and in the industrial context such as the GB railways and artificial intelligence (AI) contexts as well.

Keywords: accident analysis, AI algorithm internal audit, bounded rationality, Byzantine failures, heuristics and biases approach

Procedia PDF Downloads 185

Authors: Jadwiga Królikowska, Andrzej Królikowski, Jarosław Bajer

Abstract:

The work delineates the threats of maladjustment of the capacity of rain canals, designed and built in the early 20th century, in connection to heavy rainfall, especially in summer. This is the cause of the so called 'urban floods.' It directly relates to fierce raise of paving in the cities. Resolving this problem requires a change in philosophy of draining the rainfall by wider use of retention, infiltration and usage of rainwater. In systemic approach to managing the safety of urban drainage systems the risk, which is directly connected to safety failures, has been accepted as a measure. The risk level defines the probability of occurrence of losses grater than the ones forecast for a given time frame. The procedure of risk modelling, enabling its numeric analysis by using appropriate weights, is a significant issue in this paper.

Keywords: drainage system, urban areas, risk measurement, systemic approach

Procedia PDF Downloads 285

Authors: Stefania Fortino, Petr Hradil, Timo Avikainen

Abstract:

Timber bridges have an excellent environmental performance, are economical, relatively easy to build and can have a long service life. However, the durability of these bridges is the main problem because of their exposure to outdoor climate conditions. The moisture content accumulated in wood for long periods, in combination with certain temperatures, may cause conditions suitable for timber decay. In addition, moisture content variations affect the structural integrity, serviceability and loading capacity of timber bridges. Therefore, the monitoring of the moisture content in wood is important for the durability of the material but also for the whole superstructure. The measurements obtained by the usual sensor-based techniques provide hygro-thermal data only in specific locations of the wood components. In this context, the monitoring can be assisted by numerical modelling to get more information on the hygro-thermal response of the bridges. This work presents a hygro-thermal model based on a multi-phase moisture transport theory to predict the distribution of moisture content, relative humidity and temperature in wood. Below the fibre saturation point, the multi-phase theory simulates three phenomena in cellular wood during moisture transfer, i.e., the diffusion of water vapour in the pores, the sorption of bound water and the diffusion of bound water in the cell walls. In the multi-phase model, the two water phases are separated, and the coupling between them is defined through a sorption rate. Furthermore, an average between the temperature-dependent adsorption and desorption isotherms is used. In previous works by some of the authors, this approach was found very suitable to study the moisture transport in uncoated and coated stress-laminated timber decks. Compared to previous works, the hygro-thermal fluxes on the external surfaces include the influence of the absorbed solar radiation during the time and consequently, the temperatures on the surfaces exposed to the sun are higher. This affects the whole hygro-thermal response of the timber component. The multi-phase model, implemented in a user subroutine of Abaqus FEM code, provides the distribution of the moisture content, the temperature and the relative humidity in a volume of the timber deck. As a case study, the hygro-thermal data in wood are collected from the ongoing monitoring of the stress-laminated timber deck of Tapiola Bridge in Finland, based on integrated humidity-temperature sensors and the numerical results are found in good agreement with the measurements. The proposed model, used to assist the monitoring, can contribute to reducing the maintenance costs of bridges, as well as the cost of instrumentation, and increase safety.

Keywords: moisture content, multi-phase models, solar radiation, timber decks, FEM

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Authors: Hamza Javar Magnier, Robin Curtis

Abstract:

There have been rapid advances in the upstream processing of protein therapeutics, which has shifted the bottleneck to downstream purification and formulation. Finding liquid formulations with shelf lives of up to two years is increasingly difficult for some of the newer therapeutics, which have been engineered for activity, but their formulations are often viscous, can phase separate, and have a high propensity for irreversible aggregation1. We explore means to develop improved predictive ability from a better understanding of how protein-protein interactions on formulation conditions (pH, ionic strength, buffer type, presence of excipients) and how these impact upon the initial steps in protein self-association and aggregation. In this work, we study the initial steps in the aggregation pathways using a minimal protein model based on square-well potentials and discontinuous molecular dynamics. The effect of model parameters, including range of interaction, stiffness, chain length, and chain sequence, implies that protein models fold according to various pathways. By reducing the range of interactions, the folding- and collapse- transition come together, and follow a single-step folding pathway from the denatured to the native state2. After parameterizing the model interaction-parameters, we developed an understanding of low-temperature conformational properties and fluctuations, and the correlation to the folding transition of proteins in isolation. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This implies that fluctuations at low-temperature can be correlated to the folding transition at the melting temperature. Because proteins “breath” at low temperatures, defining a native-state as a single structure with conserved contacts and a fixed three-dimensional structure is misleading. Rather, we introduce a new definition of a native-state ensemble based on our understanding of the core conservation, which takes into account the native fluctuations at low temperatures. This approach permits the study of a large range of length and time scales needed to link the molecular interactions to the macroscopically observed behaviour. In addition, these models studied are parameterized by fitting to experimentally observed protein-protein interactions characterized in terms of osmotic second virial coefficients.

Keywords: protein folding, native-ensemble, conformational fluctuation, aggregation

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Authors: James Li, Darko Joksimovic

Abstract:

Urban development changes the natural hydrologic cycle, resulting in storm water impacts such as flooding, water quality degradation, receiving water erosion, and ecosystem deterioration. An integrated storm water managementapproach utilizing source and conveyance (termed green infrastructure) and end-of-pipe control measures is an effective way to manage urban storm water impacts. This paper focuses onplanning green infrastructure (GI) at the source and along the drainage system on a city level. It consists of (1)geospatial analysis of feasible GI using physical suitability; (2) modelling of cumulative GI's stormwater performance; and (3) cost-effectiveness analysis to prioritize the implementation of GI. A case study of the City of Barrie in Ontario, Canada, was used to demonstrate the GI's planning.

Keywords: cost-effectiveness of storm water controls, green infrastructure, urban storm water, city-level master planning

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Authors: M. Ghali, M. Elnimr, G. F. Ali, A. M. Eissa, H. Talaat

Abstract:

CuIn₃Se₅ material is indexed as ordered vacancy compounds having excellent matching properties with CuInGaSe (CIGS) solar absorber layer. For example, the valence band offset of CuIn₃Se₅ with CIGS is nearly 0.3 eV, and the lattice mismatch is less than 1%, besides the absence of discontinuity in their conduction bands. Thus, CuIn₃Se₅ can work as a passivation layer for repelling holes from CIGS/CdS interface and hence to reduce the interface carriers recombination and consequently enhancing the efficiency of CIGS/CdS solar cells. Theoretically, it was reported earlier that an improvement in the efficiency of p-CIGS-based solar cell with a thin ~100 nm of n-CuIn₃Se₅ layer is expected. Recently, a reported experiment demonstrated significant improvement in the efficiency of Molecular Beam Epitaxy (MBE) grown CIGS solar cells from 13.4 to 14.5% via inserting a thin layer of MBE-grown Cu(In,Ga)₃Se₅ layer at the CdS/CIGS interface. It should be mentioned that CuIn₃Se₅ material in either bulk or thin film form, are usually fabricated by high vacuum physical vapor deposition techniques (e.g., three-source co-evaporation, RF sputtering, flash evaporation, and molecular beam epitaxy). In addition, achieving photosensitive films of n-CuIn₃Se₅ material is important for new hybrid organic/inorganic structures, where inorganic photo-absorber layer, with n-type conductivity, can form n–p junction with organic p-type material (e.g., conductive polymers). A detailed study of the physical properties of CuIn₃Se₅ is still necessary for better understanding of device operation and further improvement of solar cells performance. Here, we report on the low-cost synthesis of CuIn₃Se₅ material in nano-scale size, with an average diameter ~10nm, using simple solution-based colloidal chemistry. In contrast to traditionally grown bulk tetragonal CuIn₃Se₅ crystals using high Vacuum-based technology, our colloidal CuIn₃Se₅ nanocrystals show cubic crystal structure with a shape of nanoparticles and band gap ~1.33 eV. Ink-coated thin films prepared from these nanocrystals colloids; display n-type character, 1.26 eV band gap and strong photo-responsive behavior with incident white light. This suggests the potential use of colloidal CuIn₃Se₅ as an active layer in all-solution-processed thin film solar cells.

Keywords: nanocrystals, CuInSe, thin film, optical properties

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Authors: Rizwan Ahmed Bhutto, Noor ul ain Hira Bhutto, Mingwei Wang, Shahid Iqbal, Jiang Yi

Abstract:

Curcumin, a natural polyphenolic compound, boasts numerous health benefits; however, its industrial applications are hindered by instabilities and poor solubility. Encapsulating curcumin in Pickering emulsion presents a promising strategy to enhance its bioavailability. Yet, the development of an efficient and straightforward method to fabricate a natural emulsifier for Pickering emulsion poses a significant challenge. Chitosan has garnered attention due to its non-toxicity and excellent emulsifying properties. This study aimed to prepare four distinct types of self-aggregated chitosan particles using a pH-responsive self-assembling approach. The properties of the aggregated particles were adjusted by pH, degree of deacetylation (DDA), and molecular weight (MW), thereby controlling surface charge, size (ranging from nano to micro and floc), and contact angle. Pickering emulsions were then formulated using these various aggregated particles. As MW and pH increased and DDA decreased, the networked structures of the aggregated particles formed, resulting in highly elastic gels that were more resistant to the breakdown of Pickering emulsion at ambient temperature. With elevated temperatures, the kinetic energy of the aggregated particles increased, disrupting hydrogen bonds and potentially transforming the systems from fluids to gels. The Pickering emulsion based on aggregated particles served as a carrier for curcumin encapsulation. It was observed that DDA and MW played crucial roles in regulating drug loading, encapsulation efficiency, and release profile. This research sheds light on selecting suitable chitosan for controlling the release of bioactive compounds in Pickering emulsions, considering factors such as adjustable rheological properties, microstructure, and macrostructure. Furthermore, this study introduces an environmentally friendly and cost-effective synthesis of pH-responsive aggregate particles without the need for high-pressure homogenizers. It underscores the potential of aggregate particles with various MWs and DDAs for encapsulating other bioactive compounds, offering valuable applications in industries including food, flavor/fragrance, cosmetics, and medicine.

Keywords: chitosan, molecular weight, rheological properties, curcumin encapsulation

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Authors: Muhammad Asghar Saqib, Saad Saleem Khan, Syed Abdul Rahman Kashif

Abstract:

In order to have higher efficiency, performance and reliability the regular monitoring of an electrical motor is required. This article presents a novel view of the air-gap magnetic field analysis of a switched reluctance motor under rotor cracks and rotor tilt along its shaft axis. The fault diagnosis is illustrated on the basis of a 3-D model of the motor using finite element analysis (FEA). The analytical equations of flux linkages have been used to determine the inductance. The results of the 3-D finite element analysis on a 6/4 switched reluctance motor (SRM) shows the variation of mutual inductance with the tilting of the rotor shaft and cracked rotor conditions. These results present useful information regarding the detection of shaft tilting and cracked rotors.

Keywords: switched reluctance motor, finite element analysis, cracked rotor, 3-D modelling of a srm

Procedia PDF Downloads 653