Search results for: Molecular Modeling

Authors: Chro Kawyan

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Endothelin-1 (ET-1), the principal individual from the newfound mammalian endothelin group of organically dynamic peptides, was initially distinguished as a 21 buildup powerful vasoconstrictor peptide in vascular endothelial cells. However, it has since been demonstrated to have a wide range of pharmacological activities in tissues both inside and outside the cardiovascular system. Additionally, peptides that have a striking resemblance to ET-1 have been identified as the primary toxic component of snake venom. In addition, late examinations have proposed that warm blooded creatures, including people, produce three unmistakable individuals from this peptide family, ET-1, ET-2 and ET-J, which might have various profiles of organic action and may follow up on particular subtypes of endothelin receptor. Masashi Yanagisawa and Tomoh Masaki survey the ongoing status of the organic chemistry and sub-atomic science of endothelin.

Keywords: thelin, microbiology, molecular biology, cell

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Authors: Jaroslav Krutil, František Pochylý, Simona Fialová, Vladimír Habán

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A mathematical model of the additional effects of the liquid in the hydrodynamic gap is presented in the paper. An in-compressible viscous fluid is considered. Based on computational modeling are determined the matrices of mass, stiffness and damping. The mathematical model is experimentally verified.

Keywords: computational modeling, mathematical model, hydrodynamic gap, matrices of mass, stiffness and damping

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behaviour.

Keywords: seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation

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Authors: Oke Oktavianty, Tadayuki Kyoutani, Shigeyuki Haruyama, Junji Kaneko, Ken Kaminishi

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Modelica has many advantages and it is very useful in modeling and simulation especially for the multi-domain with a complex technical system. However, the big obstacle for a beginner is to understand the basic concept and to build a new system model for a real system. In order to understand how to solve the simple circuit model by hand translation and to get a better understanding of how modelica works, we provide a detailed explanation about solver ordering system in horizontal and vertical sorting and make some proposals for improvement. In this study, some difficulties in using modelica software with the original concept and the comparison with Finite Element Method (FEM) approach is discussed. We also present our textual modeling approach using FEM concept for acausal and causal model construction. Furthermore, simulation results are provided that demonstrate the comparison between using textual modeling with original coding in modelica and FEM concept.

Keywords: FEM, a causal model, modelica, horizontal and vertical sorting

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Authors: Babak Safaei, A. M. Fattahi

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In the present study we have investigated axial buckling characteristics of nanocomposite beams reinforced by single-walled carbon nanotubes (SWCNTs). Various types of beam theories including Euler-Bernoulli beam theory, Timoshenko beam theory and Reddy beam theory were used to analyze the buckling behavior of carbon nanotube-reinforced composite beams. Generalized differential quadrature (GDQ) method was utilized to discretize the governing differential equations along with four commonly used boundary conditions. The material properties of the nanocomposite beams were obtained using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites which were embedded by amorphous polyethylene matrix. Then the results obtained directly from MD simulations were matched with those calculated by the mixture rule to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results were presented to indicate the influences of nanotube volume fractions and end supports on the critical axial buckling loads of nanocomposite beams relevant to long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, axial buckling, generalized differential quadrature (GDQ)

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Authors: Azher Jameel, Ghulam Ashraf Harmain

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In the recent years, the enriched techniques like the extended finite element method, the element free Galerkin method, and the Coupled finite element-element free Galerkin method have found wide application in modeling different types of discontinuities produced by cracks, contact surfaces, and bi-material interfaces. The extended finite element method faces severe mesh distortion issues while modeling large deformation problems. The element free Galerkin method does not have mesh distortion issues, but it is computationally more demanding than the finite element method. The coupled FE-EFGM proves to be an efficient numerical tool for modeling large deformation problems as it exploits the advantages of both FEM and EFGM. The present paper employs the coupled FE-EFGM to model large elastoplastic deformations in bi-material engineering components. The large deformation occurring in the domain has been modeled by using the total Lagrangian approach. The non-linear elastoplastic behavior of the material has been represented by the Ramberg-Osgood model. The elastic predictor-plastic corrector algorithms are used for the evaluation stresses during large deformation. Finally, several numerical problems are solved by the coupled FE-EFGM to illustrate its applicability, efficiency and accuracy in modeling large elastoplastic deformations in bi-material samples. The results obtained by the proposed technique are compared with the results obtained by XFEM and EFGM. A remarkable agreement was observed between the results obtained by the three techniques.

Keywords: XFEM, EFGM, coupled FE-EFGM, level sets, large deformation

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Authors: Fadi Eleiwi, Taous Meriem Laleg-Kirati

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This paper presents a complete dynamic modeling of a membrane distillation process. The model contains two consistent dynamic models. A 2D advection-diffusion equation for modeling the whole process and a modified heat equation for modeling the membrane itself. The complete model describes the temperature diffusion phenomenon across the feed, membrane, permeate containers and boundary layers of the membrane. It gives an online and complete temperature profile for each point in the domain. It explains heat conduction and convection mechanisms that take place inside the process in terms of mathematical parameters, and justify process behavior during transient and steady state phases. The process is monitored for any sudden change in the performance at any instance of time. In addition, it assists maintaining production rates as desired, and gives recommendations during membrane fabrication stages. System performance and parameters can be optimized and controlled using this complete dynamic model. Evolution of membrane boundary temperature with time, vapor mass transfer along the process, and temperature difference between membrane boundary layers are depicted and included. Simulations were performed over the complete model with real membrane specifications. The plots show consistency between 2D advection-diffusion model and the expected behavior of the systems as well as literature. Evolution of heat inside the membrane starting from transient response till reaching steady state response for fixed and varying times is illustrated.

Keywords: membrane distillation, dynamical modeling, advection-diffusion equation, thermal equilibrium, heat equation

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Authors: Pouya Kaafi, Gholamreza Ghodrati Amiri

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Abnormal loads due to natural events, implementation errors and some other issues can lead to occurrence of progressive collapse in structures. Most of the past researches consist of 2- Dimensional (2D) models of steel frames without consideration of the floor system effects, which reduces the accuracy of the modeling. While employing a 3-Dimensional (3D) model and modeling the concrete slab system for the floors have a crucial role in the progressive collapse evaluation. In this research, a 3D finite element model of a 5-story steel building is modeled by the ABAQUS software once with modeling the slabs, and the next time without considering them. Then, the progressive collapse potential is evaluated. The results of the analyses indicate that the lack of the consideration of the slabs during the analyses, can lead to inaccuracy in assessing the progressive failure potential of the structure.

Keywords: abnormal loads, composite floor system, intermediate steel moment resisting frame system, progressive collapse

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Authors: Paromik Bhattacharyya, Vijay Kumar, Johannes Van Staden

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Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

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Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

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Authors: Sukriti Sabharwal, Sonali Bhattar, Shikhar Saxena

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Introduction: COVID-19 molecular diagnostic laboratory is the cornerstone of the COVID-19 disease diagnosis as the patient’s treatment and management protocol depend on the molecular results. For this purpose, it is extremely important that the laboratory conducting these results adheres to the quality management processes to increase the accuracy and validity of the reports generated. We started our own molecular diagnostic setup at the onset of the pandemic. Therefore, we conducted this study to generate our quality management data to help us in improving on our weak points. Materials and Methods: A total of 14561 samples were evaluated by the retrospective observational method. The quality variables analysed were classified into pre-analytical, analytical, and post-analytical variables, and the results were presented in percentages. Results: Among the pre-analytical variables, sample leaking was the most common cause of the rejection of samples (134/14561, 0.92%), followed by non-generation of SRF ID (76/14561, 0.52%) and non-compliance to triple packaging (44/14561, 0.3%). The other pre-analytical aspects assessed were incomplete patient identification (17/14561, 0.11%), insufficient quantity of samples (12/14561, 0.08%), missing forms/samples (7/14561, 0.04%), samples in the wrong vials/empty VTM tubes (5/14561, 0.03%) and LIMS entry not done (2/14561, 0.01%). We are unable to obtain internal quality control in 0.37% of samples (55/14561). We also experienced two incidences of cross-contamination among the samples resulting in false-positive results. Among the post-analytical factors, a total of 0.07% of samples (11/14561) could not be dispatched within the stipulated time frame. Conclusion: Adherence to quality control processes is foremost for the smooth running of any diagnostic laboratory, especially the ones involved in critical reporting. Not only do the indicators help in keeping in check the laboratory parameters but they also allow comparison with other laboratories.

Keywords: laboratory quality management, COVID-19, molecular diagnostics, healthcare

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Authors: Mojtaba Valinejadshoubi, Azin Shakibabarough, Ashutosh Bagchi

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Facilities such as residential buildings, office buildings, and hospitals house large density of occupants. Therefore, a low-cost facility management program (FMP) should be used to provide a satisfactory built environment for these occupants. Facility management (FM) has been recently used in building projects as a critical task. It has been effective in reducing operation and maintenance cost of these facilities. Issues of information integration and visualization capabilities are critical for reducing the complexity and cost of FM. Building information modeling (BIM) can be used as a strong visual modeling tool and database in FM. The main objective of this study is to examine the applicability of BIM in the FM process during a building’s operational phase. For this purpose, a seven-storey office building is modeled Autodesk Revit software. Authors integrated the cloud-based environment using a visual programming tool, Dynamo, for the purpose of having a real-time cloud-based communication between the facility managers and the participants involved in the project. An appropriate and effective integrated data source and visual model such as BIM can reduce a building’s operational and maintenance costs by managing the building life cycle properly.

Keywords: building information modeling, facility management, operational phase, building life cycle

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Authors: Hemin Yuan, Yun Wang, Xiangchun Wang

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Gas hydrate is drawing attention due to the fact that it has an enormous amount all over the world, which is almost twice the conventional hydrocarbon reserves, making it a potential alternative source of energy. It is widely distributed in permafrost and continental ocean shelves, and many countries have launched national programs for investigating the gas hydrate. Gas hydrate is mainly explored through seismic methods, which include bottom simulating reflectors (BSR), amplitude blanking, and polarity reverse. These seismic methods are effective at finding the gas hydrate formations but usually contain large uncertainties when applying to invert the micro-scale petrophysical properties of the formations due to lack of constraints. Rock physics modeling links the micro-scale structures of the rocks to the macro-scale elastic properties and can work as effective constraints for the seismic methods. A number of rock physics models have been proposed for gas hydrate modeling, which addresses different mechanisms and applications. However, these models are generally not well classified, and it is confusing to determine the appropriate model for a specific study. Moreover, since the modeling usually involves multiple models and steps, it is difficult to determine the source of uncertainties. To solve these problems, we summarize the developed models/methods and make four classifications of the models according to the hydrate micro-scale morphology in sediments, the purpose of reservoir characterization, the stage of gas hydrate generation, and the lithology type of hosting sediments. Some sub-categories may overlap each other, but they have different priorities. Besides, we also analyze the priorities of different models, bring up the shortcomings, and explain the appropriate application scenarios. Moreover, by comparing the models, we summarize a general workflow of the modeling procedure, which includes rock matrix forming, dry rock frame generating, pore fluids mixing, and final fluid substitution in the rock frame. These procedures have been widely used in various gas hydrate modeling and have been confirmed to be effective. We also analyze the potential sources of uncertainties in each modeling step, which enables us to clearly recognize the potential uncertainties in the modeling. In the end, we explicate the general problems of the current models, including the influences of pressure and temperature, pore geometry, hydrate morphology, and rock structure change during gas hydrate dissociation and re-generation. We also point out that attenuation is also severely affected by gas hydrate in sediments and may work as an indicator to map gas hydrate concentration. Our work classifies rock physics models of gas hydrate into different categories, generalizes the modeling workflow, analyzes the modeling uncertainties and potential problems, which can facilitate the rock physics characterization of gas hydrate bearding sediments and provide hints for future studies.

Keywords: gas hydrate, rock physics model, modeling classification, hydrate morphology

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Authors: Ali S. Gargoum

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Graphical modeling plays an important role in providing efficient probability calculations in high dimensional problems (computational efficiency). In this paper, we address one of such problems where we discuss fragmenting puff models and some distributional assumptions concerning models for the instantaneous, emission readings and for the fragmenting process. A graphical representation in terms of a junction tree of the conditional probability breakdown of puffs and puff fragments is proposed.

Keywords: graphical models, influence diagrams, junction trees, Bayesian nets

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Authors: Mohammad Sheikhalishahi, Vahid Ebrahimipour, Amir Hossein Radman-Kian

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This paper proposes an Ontology framework for knowledge modeling and representation of the equipment integrity process in a typical oil and gas production plant. Our aim is to construct a knowledge modeling that facilitates translation, interpretation, and conversion of human-readable integrity interpretation into computer-readable representation. The framework provides a function structure related to fault propagation using ISO 14224 and ISO 15926 OWL-Lite/ Resource Description Framework (RDF) to obtain a generic system-level model of asset integrity that can be utilized in the integrity engineering process during the equipment life cycle. It employs standard terminology developed by ISO 15926 and ISO 14224 to map textual descriptions of equipment failure and then convert it to a causality-driven logic by semantic interpretation and computer-based representation using Lite/RDF. The framework applied for an offshore gas riser. The result shows that the approach can cross-link the failure-related integrity words and domain-specific logic to obtain a representation structure of equipment integrity with causality inference based on semantic extraction of inspection report context.

Keywords: asset integrity modeling, interoperability, OWL, RDF/XML

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Authors: Mustapha Kamel Mihoubi, Hocine Dahmani

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Over recent years much progress has been achieved in the fields of numerical modeling shoreline processes: waves, currents, waves and current. However, there are still some problems in the existing models to link the on the first, the hydrodynamics of waves and currents and secondly, the sediment transport processes and due to the variability in time, space and interaction and the simultaneous action of wave-current near the shore. This paper is the establishment of a numerical modeling to forecast the sediment transport from development scenarios of harbor structure. It is established on the basis of a numerical simulation of a water-sediment model via a 2D model using a set of codes calculation MIKE 21-DHI software. This is to examine the effect of the sediment transport drivers following the dominant incident wave in the direction to pass input harbor work under different variants planning studies to find the technical and economic limitations to the sediment transport and protection of the harbor structure optimum solution.

Keywords: swell, current, radiation, stress, mesh, mike21, sediment

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Authors: Ghazanfar Ali, Fahad N Almajhdi

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This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

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Authors: Muhammad Fanseem E. M., Rama Satya Satish Kumar, Indrajeet Bhausaheb Bhavar, Deepak M.

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Keeping the right balance of electricity between the supply and demand sides of the grid is one of the most important objectives of electrical grid operation. Power generation and demand forecasting are the core of power management and generation scheduling. Large, centralized producing units were used in the construction of conventional power systems in the past. A certain level of balance was possible since the generation kept up with the power demand. However, integrating renewable energy sources into power networks has proven to be a difficult challenge due to its intermittent nature. The power imbalance caused by rising demands and peak loads is negatively affecting power quality and dependability. Demand side management and demand response were one of the solutions, keeping generation the same but altering or rescheduling or shedding completely the load or demand. However, shedding the load or rescheduling is not an efficient way. There comes the significance of virtual power plants. The virtual power plant integrates distributed generation, dispatchable load, and distributed energy storage organically by using complementing control approaches and communication technologies. This would eventually increase the utilization rate and financial advantages of distributed energy resources. Most of the writing on virtual power plant models ignored technical limitations, and modeling was done in favor of a financial or commercial viewpoint. Therefore, this paper aims to address the modeling intricacies of VPPs and their technical limitations, shedding light on a holistic understanding of this innovative power management approach.

Keywords: cost optimization, distributed energy resources, dynamic modeling, model quality tests, power system modeling

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Authors: Leila Momenzadeh, Alexander V. Evteev, Elena V. Levchenko, Tanvir Ahmed, Irina Belova, Graeme Murch

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In this work, the phonon thermal conductivity of f.c.c. Al is investigated in detail in the temperature range 100 – 900 K within the framework of equilibrium molecular dynamics simulations making use of the Green-Kubo formalism and one of the most reliable embedded-atom method potentials. It is found that the heat current auto-correlation function of the f.c.c. Al model demonstrates a two-stage temporal decay similar to the previously observed for f.c.c Cu model. After the first stage of decay, the heat current auto-correlation function of the f.c.c. Al model demonstrates a peak in the temperature range 100-800 K. The intensity of the peak decreases as the temperature increases. At 900 K, it transforms to a shoulder. To describe the observed two-stage decay of the heat current auto-correlation function of the f.c.c. Al model, we employ decomposition model recently developed for phonon-mediated thermal transport in a monoatomic lattice. We found that the electronic contribution to the total thermal conductivity of f.c.c. Al dominates over the whole studied temperature range. However, the phonon contribution to the total thermal conductivity of f.c.c. Al increases as temperature decreases. It is about 1.05% at 900 K and about 12.5% at 100 K.

Keywords: aluminum, gGreen-Kubo formalism, molecular dynamics, phonon thermal conductivity

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Authors: Reema K. AlEssa, Sahar Alshomer, Abdullah Alfaleh, Sultan ALkhenaizan, Mohammed Albalwi

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Ichthyosis is a disorder of abnormal keratinization, characterized by excessive scaling, and consists of more than twenty subtypes varied in severity, mode of inheritance, and the genes involved. There is insufficient data in the literature about the epidemiology and characteristics of ichthyosis locally. Our aim is to identify the histopathological features and genetic profile of ichthyosis. Method: It is an observational retrospective case series study conducted in March 2020, included all patients who were diagnosed with Ichthyosis and confirmed by histological and molecular findings over the last 20 years in King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. Molecular analysis was performed by testing genomic DNA and checking genetic variations using the AmpliSeq panel. All disease-causing variants were checked against HGMD, ClinVar, Genome Aggregation Database (gnomAD), and Exome Aggregation Consortium (ExAC) databases. Result: A total of 60 cases of Ichthyosis were identified with a mean age of 13 ± 9.2. There is an almost equal distribution between female patients 29 (48%) and males 31 (52%). The majority of them were Saudis, 94%. More than half of patients presented with general scaling 33 (55%), followed by dryness and coarse skin 19 (31.6%) and hyperlinearity 5 (8.33%). Family history and history of consanguinity were seen in 26 (43.3% ), 13 (22%), respectively. History of colloidal babies was found in 6 (10%) cases of ichthyosis. The most frequent genes were ALOX12B, ALOXE3, CERS3, CYP4F22, DOLK, FLG2, GJB2, PNPLA1, SLC27A4, SPINK5, STS, SUMF1, TGM1, TGM5, VPS33B. Most frequent variations were detected in CYP4F22 in 16 cases (26.6%) followed by ALOXE3 6 (10%) and STS 6 (10%) then TGM1 5 (8.3) and ALOX12B 5 (8.3). The analysis of molecular genetic identified 23 different genetic variations in the genes of ichthyosis, of which 13 were novel mutations. Homozygous mutations were detected in the majority of ichthyosis cases, 54 (90%), and only 1 case was heterozygous. Few cases, 4 (6.6%) had an unknown type of ichthyosis with a negative genetic result. Conclusion: 13 novel mutations were discovered. Also, about half of ichthyosis patients had a positive history of consanguinity.

Keywords: ichthyosis, genetic profile, molecular characterization, congenital ichthyosis

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Authors: Jing Yuan, Hongwei Yang

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This paper aims to understand U.S. middle school students’ mathematics achievements by examining relevant student and school-level predictors. Through a variance component analysis, the study first identifies evidence supporting the use of multilevel modeling. Then, a multilevel analysis is performed under Bayesian statistical inference where prior information is incorporated into the modeling process. During the analysis, independent variables are entered sequentially in the order of theoretical importance to create a hierarchy of models. By evaluating each model using Bayesian fit indices, a best-fit and most parsimonious model is selected where Bayesian statistical inference is performed for the purpose of result interpretation and discussion. The primary dataset for Bayesian modeling is derived from the Program for International Student Assessment (PISA) in 2012 with a secondary PISA dataset from 2003 analyzed under the traditional ordinary least squares method to provide the information needed to specify informative priors for a subset of the model parameters. The dependent variable is a composite measure of mathematics literacy, calculated from an exploratory factor analysis of all five PISA 2012 mathematics achievement plausible values for which multiple evidences are found supporting data unidimensionality. The independent variables include demographics variables and content-specific variables: mathematics efficacy, teacher-student ratio, proportion of girls in the school, etc. Finally, the entire analysis is performed using the MCMCpack and MCMCglmm packages in R.

Keywords: Bayesian multilevel modeling, mathematics education, PISA, multilevel

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Authors: Mustafa Tosun, Kevser Dincer

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In this study, analysis on whether the lightweight concrete walled structures used in four climatic regions of Turkey are also capable of insulating sound was conducted. As a new approach, first the wall’s thermal insulation sufficiency’s were calculated and then, artificial neural network (ANN) modeling was used on their cross sections to check if they are sound transmitters too. The ANN was trained and tested by using MATLAB toolbox on a personal computer. ANN input parameters that used were thickness of lightweight concrete wall, frequency and density of lightweight concrete wall, while the transmitted sound was the output parameter. When the results of the TS analysis and those of ANN modeling are evaluated together, it is found from this study, that sound transmit loss increases at higher frequencies, higher wall densities and with larger wall cross sections.

Keywords: artificial neuron network, lightweight concrete, sound insulation, sound transmit loss

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Authors: Anahita Aris

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Geometry always plays a key role in natural structures, which can be a source of inspiration for architects and urban designers to create spaces. By understanding formative principles in nature, a variety of options can be provided that lead to freedom of formation. The main purpose of this paper is to analyze the geometrical order found in pomegranate to find formative principles explaining its complex structure. The point is how spherical arils of pomegranate pressed together inside the fruit and filled the space as they expand in the growing process, which made a self-organized system leads to the formation of each of the arils are unique in size, topology and shape. The main challenge of this paper would be using advanced architectural modeling techniques to discover these principles.

Keywords: advanced modeling techniques, architectural modeling, computational design, the geometry of natural formation, geometrical analysis, the natural order of pomegranate, voronoi diagrams

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Authors: Amanda M. Tadini, Houssam Hajjoul, Gustavo Nicolodelli, Stéphane Mounier, Célia R. Montes, Débora M. B. P. Milori

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Soil organic matter (SOM) plays an important role in maintaining soil productivity and accounting for the promotion of biological diversity. The main components of the SOM are the humic substances which can be fractionated according to its solubility in humic acid (HA), fulvic acids (FA) and humin (HU). The determination of the chemical properties of organic matter as well as its interaction with metallic species is an important tool for understanding the structure of the humic fractions. Fluorescence spectroscopy has been studied as a source of information about what is happening at the molecular level in these compounds. Specially, soils of Amazon region are an important ecosystem of the planet. The aim of this study is to understand the molecular and structural composition of HA samples from Spodosol of Amazonia using the fluorescence Emission-Excitation Matrix (EEM) and Time Resolved Fluorescence Spectroscopy (TRFS). The results showed that the samples of HA showed two fluorescent components; one has a more complex structure and the other one has a simpler structure, which was also seen in TRFS through the evaluation of each sample lifetime. Thus, studies of this nature become important because it aims to evaluate the molecular and structural characteristics of the humic fractions in the region that is considered as one of the most important regions in the world, the Amazon.

Keywords: Amazonian soil, characterization, fluorescence, humic acid, lifetime

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Authors: Vincent Iacobellis, Kamran Behdinan

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A finite element cohesive zone model is used to predict the temperature dependent material properties of a polyimide matrix composite with unidirectional carbon fiber arrangement. The cohesive zone parameters have been obtained from previous research involving an atomistic-to-continuum multiscale simulation of the fiber-matrix interface using the bridging cell multiscale method. The goal of the research was to both investigate the effect of temperature change on the composite behavior with respect to transverse loading as well as the validate the use of cohesive parameters obtained from atomistic-to-continuum multiscale modeling to predict fiber-matrix interfacial cracking. From the multiscale model cohesive zone parameters (i.e. maximum traction and energy of separation) were obtained by modeling the interface between the coarse-grained polyimide matrix and graphite based carbon fiber. The cohesive parameters from this simulation were used in a cohesive zone model of the composite microstructure in order to predict the properties of the macroscale composite with respect to changes in temperature ranging from 21 ˚C to 316 ˚C. Good agreement was found between the microscale RUC model and experimental results for stress-strain response, stiffness, and material strength at low and high temperatures. Examination of the deformation of the composite through localized crack initiation at the fiber-matrix interface also agreed with experimental observations of similar phenomena. Overall, the cohesive zone model was shown to be both effective at modeling the composite properties with respect to transverse loading as well as validated the use of cohesive zone parameters obtained from the multiscale simulation.

Keywords: cohesive zone model, fiber-matrix interface, microscale damage, multiscale modeling

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Authors: Nishaben Desai Dholakiya, Anirban Roy, Ranjan Dey

Abstract:

Understanding ocean thermodynamics has become increasingly critical as Earth's oceans serve as the primary planetary heat regulator, absorbing approximately 93% of excess heat energy from anthropogenic greenhouse gas emissions. This investigation presents a comprehensive analysis of Arabian Sea surface seawater thermodynamics, focusing specifically on heat capacity (Cp) and thermal expansion coefficient (α) - parameters fundamental to global heat distribution patterns. Through high-precision experimental measurements of ultrasonic velocity and density across varying temperature (293.15-318.15K) and salinity (0.5-35 ppt) conditions, it characterize critical thermophysical parameters including specific heat capacity, thermal expansion, and isobaric and isothermal compressibility coefficients in natural seawater systems. The study employs advanced machine learning frameworks - Random Forest, Gradient Booster, Stacked Ensemble Machine Learning (SEML), and AdaBoost - with SEML achieving exceptional accuracy (R² > 0.99) in heat capacity predictions. the findings reveal significant temperature-dependent molecular restructuring: enhanced thermal energy disrupts hydrogen-bonded networks and ion-water interactions, manifesting as decreased heat capacity with increasing temperature (negative ∂Cp/∂T). This mechanism creates a positive feedback loop where reduced heat absorption capacity potentially accelerates oceanic warming cycles. These quantitative insights into seawater thermodynamics provide crucial parametric inputs for climate models and evidence-based environmental policy formulation, particularly addressing the critical knowledge gap in thermal expansion behavior of seawater under varying temperature-salinity conditions.

Keywords: climate change, arabian sea, thermodynamics, machine learning

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Authors: Onyebuchi Mogbo, Abdulsalam Mohammed, Salsabila Wali

Abstract:

This research discusses the design and modeling of an amphibious building. The amphibious building is a house with the function of floating during a flood event. Over the years, houses have been built to resist flood events some of which have failed. The floating house is designed to work with nature and not against it. In the event of a flood, the house will rise with the increasing water level and protect the house from sinking. For the design and modeling of this house an estimated cost of N250, 000, approximately $700, will be needed. It is expected that the house will rise when lightweight materials are incorporated in the design, and the concrete dock (in form of a hollow box) carrying the entire house in its hollow space is well designed. When there is flooding the water will fill up the concrete dock, and the house will rise upwards with vertical guides preventing it from moving side to side or out of its boundary. Architectural and Structural designs will be used in this project.

Keywords: amphibious building, flood, housing, design and modelling

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Authors: Neslihan Şahin Çelik, Ali Eraslan

Abstract:

In recent years, mathematics educators have frequently stressed the necessity of instructing students about models and modeling approaches that encompass cognitive and metacognitive thought processes, starting from the first years of school and continuing on through the years of higher education. The purpose of this study is to examine the thought processes of 4th-grade primary school students in their modeling activities and to explore the difficulties encountered in these processes, if any. The study, of qualitative design, was conducted in the 2015-2016 academic year at a public state-school located in a central city in the Black Sea Region of Turkey. A preliminary study was first implemented with designated 4th grade students, after which the criterion sampling method was used to select three students that would be recruited into the focus group. The focus group that was thus formed was asked to work on the model eliciting activity of the Paper Airplane Problem and the entire process was recorded on video. The Paper Airplane Problem required the students to determine the winner with respect to: (a) the plane that stays in the air for the longest time; (b) the plane that travels the greatest distance in a straight-line path; and (c) the overall winner for the contest. A written transcript was made of the video recording, after which the recording and the students' worksheets were analyzed using the Blum and Ferri modeling cycle. The results of the study revealed that the students tested the hypotheses related to daily life that they had set up, generated ideas of their own, verified their models by making connections with real life, and tried to make their models generalizable. On the other hand, the students had some difficulties in terms of their interpretation of the table of data and their ways of operating on the data during the modeling processes.

Keywords: primary school students, model eliciting activity, mathematical modeling, modeling process, paper airplane problem

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Authors: Desouky Abd El Haleem, Sahar Zaki

Abstract:

This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.

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Authors: Mohammad Yousefikia, Sara Moridpour, Ehsan Mazloumi

Abstract:

Perceiving track geometry deterioration decisively influences the optimization of track maintenance operations. The effective management of this deterioration and increasingly utilized system with limited financial resources is a significant challenge. This paper provides a review of degradation models relevant for railroad tracks. Furthermore, due to the lack of long term information on the condition development of tram infrastructures, presents the methodology which will be used to derive degradation models from the data of Melbourne tram network.

Keywords: deterioration modeling, asset management, railway, tram

Procedia PDF Downloads 379