Search results for: molecular structure

Authors: Fadi Al Khatib, Raouf Mbarki, Malek Adouni

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In various sport and recreational activities, the patellofemoral joint undergoes large forces and moments while accommodating the significant knee joint movement. In doing so, this joint is commonly the source of anterior knee pain related to instability in normal patellar tracking and excessive pressure syndrome. One well-observed explanation of the instability of the normal patellar tracking is the patellofemoral ligaments and patellar tendon damage. Improved knowledge of the damage mechanism mediating ligaments and tendon injuries can be a great help not only in rehabilitation and prevention procedures but also in the design of better reconstruction systems in the management of knee joint disorders. This damage mechanism, specifically due to excessive mechanical loading, has been linked to the micro level of the fibred structure precisely to the tropocollagen molecules and their connection density. We argue defining a clear frame starting from the bottom (micro level) to up (macro level) in the hierarchies of the soft tissue may elucidate the essential underpinning on the state of the ligaments damage. To do so, in this study a multiscale fibril reinforced hyper elastoplastic Finite Element model that accounts for the synergy between molecular and continuum syntheses was developed to determine the short-term stresses/strains patellofemoral ligaments and tendon response. The plasticity of the proposed model is associated only with the uniaxial deformation of the collagen fibril. The yield strength of the fibril is a function of the cross-link density between tropocollagen molecules, defined here by a density function. This function obtained through a Coarse-graining procedure linking nanoscale collagen features and the tissue level materials properties using molecular dynamics simulations. The hierarchies of the soft tissues were implemented using the rule of mixtures. Thereafter, the model was calibrated using a statistical calibration procedure. The model then implemented into a real structure of patellofemoral ligaments and patellar tendon (OpenKnee) and simulated under realistic loading conditions. With the calibrated material parameters the calculated axial stress lies well with the experimental measurement with a coefficient of determination (R2) equal to 0.91 and 0.92 for the patellofemoral ligaments and the patellar tendon respectively. The ‘best’ prediction of the yielding strength and strain as compared with the reported experimental data yielded when the cross-link density between the tropocollagen molecule of the fibril equal to 5.5 ± 0.5 (patellofemoral ligaments) and 12 (patellar tendon). Damage initiation of the patellofemoral ligaments was located at the femoral insertions while the damage of the patellar tendon happened in the middle of the structure. These predicted finding showed a meaningful correlation between the cross-link density of the tropocollagen molecules and the stiffness of the connective tissues of the extensor mechanism. Also, damage initiation and propagation were documented with this model, which were in satisfactory agreement with earlier observation. To the best of our knowledge, this is the first attempt to model ligaments from the bottom up, predicted depending to the tropocollagen cross-link density. This approach appears more meaningful towards a realistic simulation of a damaging process or repair attempt compared with certain published studies.

Keywords: tropocollagen, multiscale model, fibrils, knee ligaments

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Authors: Tahani Hallek, Dhaou Akrout, Riadh Ahmadi, Mabrouk Montacer

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The present work is an organic geochemical study of the Fahdene Formation outcrops at the Mahjouba region belonging to the Eastern part of the Kalaat Senan structure in northwestern Tunisia (the Kef-Tedjerouine area). The analytical study of the organic content of the samples collected, allowed us to point out that the Formation in question is characterized by an average to good oil potential. This fossilized organic matter has a mixed origin (type II and III), as indicated by the relatively high values of hydrogen index. This origin is confirmed by the C29 Steranes abundance and also by tricyclic terpanes C19/(C19+C23) and tetracyclic terpanes C24/(C24+C23) ratios, that suggest a marine environment of deposit with high plants contribution. We have demonstrated that the heterogeneity of organic matter between the marine aspect, confirmed by the presence of foraminifera, and the continental contribution, is the result of an episodic anomaly in relation to the sequential stratigraphy. Given that the study area is defined as an outer platform forming a transition zone between a stable continental domain to the south and a deep basin to the north, we have explained the continental contribution by successive forced regressions, having blocked the albian transgression, allowing the installation of the lowstand system tracts. This aspect is represented by the incised valleys filling, in direct contact with the pelagic and deep sea facies. Consequently, the Fahdene Formation, in the Kef-Tedjerouine area, consists of transgressive system tracts (TST) brutally truncated by extras of continental progradation; resulting in a mixed influence deposition having retained a heterogeneous organic material.

Keywords: molecular geochemistry, biomarkers, forced regression, deposit environment, mixed origin, Northern Tunisia

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Authors: A. Akbarpour, M. R. Adib Ramezani, M. Zhian, N. Ghorbani Amirabad

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One way to improve the performance of structures against of earthquake is passive control which requires no external power source. In this research, tuned liquid column dampers which are among of systems with the capability to transfer energy between various modes of vibration, are used. For the first time, a liquid column damper for vibration control structure is presented. After modeling this structure in design building software and performing the static and dynamic analysis and obtaining the necessary parameters for the design of tuned liquid column damper, the whole structure will be analyzed in finite elements software. The tuned liquid column dampers are installed on the structure and nonlinear time-history analysis is done in two cases of structures; with and without dampers. Finally the seismic behavior of building in the two cases will be examined. In this study the nonlinear time-history analysis on a twelve-story steel structure equipped with damper subject to records of earthquake including Loma Prieta, Northridge, Imperiall Valley, Pertrolia and Landers was performed. The results of comparing between two cases show that these dampers have reduced lateral displacement and acceleration of levels on average of 10%. Roof displacement and acceleration also reduced respectively 5% and 12%. Due to structural asymmetric in the plan, the maximum displacements of surrounding structures as well as twisting were studied. The results show that the dampers lead to a 10% reduction in the maximum response of structure stories surrounding points. At the same time, placing the dampers, caused to reduce twisting on the floor plan of the structure, Base shear of structure in the different earthquakes also has been reduced on the average of 6%.

Keywords: retrofitting, passive control, tuned liquid column damper, finite element analysis

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Authors: Ouafae Baida, Najma Hamzaoui, Maha Akbib, Abdelfettah Sedqui, Abdelouahid Lyhyaoui

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Numerous scientific works present various methods to analyze the data for several domains, specially the comparison of classifications. In our recent work, we presented a new approach to help the user choose the best classification method from the results obtained by every method, by basing itself on the distances between the trees of classification. The result of our approach was in the form of a dendrogram contains methods as a succession of connections. This approach is much needed in phylogeny analysis. This discipline is intended to analyze the sequences of biological macro molecules for information on the evolutionary history of living beings, including their relationship. The product of phylogeny analysis is a phylogenetic tree. In this paper, we recommend the use of a new method of construction the phylogenetic tree based on comparison of different classifications obtained by different molecular genes.

Keywords: hierarchical classification, classification methods, structure of tree, genes, phylogenetic analysis

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

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Authors: Javed Iqbal

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The growing need for energy by the human society and depletion of conventional energy sources demands a renewable, safe, infinite, low-cost and omnipresent energy source. One of the most suitable ways to solve the foreseeable world’s energy crisis is to use the power of the sun. Photovoltaic devices are especially of wide interest as they can convert solar energy to electricity. Recently the best performing solar cells are silicon-based cells. However, silicon cells are expensive, rigid in structure and have a large timeline for the payback of cost and electricity. Organic photovoltaic cells are cheap, flexible and can be manufactured in a continuous process. Therefore, organic photovoltaic cells are an extremely favorable replacement. Organic photovoltaic cells utilize sunlight as energy and convert it into electricity through the use of conductive polymers/ small molecules to separate electrons and electron holes. A major challenge for these new organic photovoltaic cells is the efficiency, which is low compared with the traditional silicon solar cells. To overcome this challenge, usually two straightforward strategies have been considered: (1) reducing the band-gap of molecular donors to broaden the absorption range, which results in higher short circuit current density (JSC) of devices, and (2) lowering the highest occupied molecular orbital (HOMO) energy of molecular donors so as to increase the open-circuit voltage (VOC) of applications devices.8 Keeping in mind the cost of chemicals it is hard to try many materials on test basis. The best way is to find the suitable material in the bulk. For this purpose, we use computational approach to design molecules based on our organic chemistry knowledge and determine their physical and electronic properties. In this study, we did DFT calculations with different options to get high open circuit voltage and after getting suitable data from calculation we finally did synthesis of a novel D–π–A–π–D type low band-gap small molecular donor material (ZOPTAN-TPA). The Aarylene vinylene based bis(arylhalide) unit containing a cyanostilbene unit acts as a low-band- gap electron-accepting block, and is coupled with triphenylamine as electron-donating blocks groups. The motivation for choosing triphenylamine (TPA) as capped donor was attributed to its important role in stabilizing the separated hole from an exciton and thus improving the hole-transporting properties of the hole carrier.3 A π-bridge (thiophene) is inserted between the donor and acceptor unit to reduce the steric hindrance between the donor and acceptor units and to improve the planarity of the molecule. The ZOPTAN-TPA molecule features a low HOMO level of 5.2 eV and an optical energy gap of 2.1 eV. Champion OSCs based on a solution-processed and non-annealed active-material blend of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and ZOPTAN-TPA in a mass ratio of 2:1 exhibits a power conversion efficiency of 1.9 % and a high open-circuit voltage of over 1.0 V.

Keywords: high open circuit voltage, donor, triphenylamine, organic solar cells

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Authors: Yuanhao Chang, Senbo Xiao, Zhiliang Zhang, Jianying He

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The role of nanoparticles (NPs) in enhanced oil recovery (EOR) is being increasingly emphasized. In this study, the motion of NPs and local stress distribution of tapped oil droplet/nanofluid in nanochannels are studied with coarse-grained modeling and molecular dynamic simulations. The results illustrate three motion patterns for NPs: hydrophilic NPs are more likely to adsorb on the channel and stay near the three-phase contact areas, hydrophobic NPs move inside the oil droplet as clusters and more mixed NPs are trapped at the oil-water interface. NPs in each pattern affect the flow of fluid and the interfacial thickness to various degrees. Based on the calculation of atomistic stress, the characteristic that the higher value of stress occurs at the place where NPs aggregate can be obtained. Different occurrence patterns correspond to specific local stress distribution. Significantly, in the three-phase contact area for hydrophilic NPs, the local stress distribution close to the pattern of structural disjoining pressure is observed, which proves the existence of structural disjoining pressure in molecular dynamics simulation for the first time. Our results guide the design and screen of NPs for EOR and provide a basic understanding of nanofluid applications.

Keywords: local stress distribution, nanoparticles, enhanced oil recovery, molecular dynamics simulation, trapped oil droplet, structural disjoining pressure

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Authors: Steffen Illig, Alexander S. Eggeman, Alessandro Troisi, Stephen G. Yeates, John E. Anthony, Henning Sirringhaus

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Large-amplitude intermolecular vibrations in combination with complex shaped transfer integrals generate a thermally fluctuating energetic landscape. The resulting dynamic disorder and its intrinsic presence in organic semiconductors is one of the most fundamental differences to their inorganic counterparts. Dynamic disorder is believed to govern many of the unique electrical and optical properties of organic systems. However, the low energy nature of these vibrations makes it difficult to access them experimentally and because of this we still lack clear molecular design rules to control and reduce dynamic disorder. Applying a novel technique based on electron diffraction we encountered strong intermolecular, thermal vibrations in every single organic material we studied (14 up to date), indicating that a large degree of dynamic disorder is a universal phenomenon in organic crystals. In this paper a new molecular design strategy will be presented to avoid dynamic disorder. We found that small molecules that have their side chains attached to the long axis of their conjugated core have been found to be less likely to suffer from dynamic disorder effects. In particular, we demonstrate that 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene (C8-BTBT) and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene (C10DNTT) exhibit strongly reduced thermal vibrations in comparison to other molecules and relate their outstanding performance to their lower dynamic disorder. We rationalize the low degree of dynamic disorder in C8-BTBT and C10-DNTT with a better encapsulation of the conjugated cores in the crystal structure which helps reduce large amplitude thermal motions. The work presented in this paper provides a general strategy for the design of new classes of very high mobility organic semiconductors with low dynamic disorder.

Keywords: charge transport, C8-BTBT, C10-DNTT, dynamic disorder, organic semiconductors, thermal vibrations

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Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

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Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: crab, portunus pelagicus, morphology, RAPD, Carapace

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Authors: Yee Hooi Min, Mohdnasir Abdul Hadi

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Tensioned membrane structure in the form of Enneper minimal surface can be considered as a sustainable development for the green environment and technology, it also can be used to support the effectiveness used of energy and the structure. Soap film in the form of Enneper minimal surface model has been studied. The combination of shape and internal forces for the purpose of stiffness and strength is an important feature of membrane surface. For this purpose, form-finding using soap film model has been carried out for Enneper minimal surface models with variables u=v=0.6 and u=v=1.0. Enneper soap film models with variables u=v=0.6 and u=v=1.0 provides an alternative choice for structural engineers to consider the tensioned membrane structure in the form of Enneper minimal surface applied in the building industry. It is expected to become an alternative building material to be considered by the designer.

Keywords: Enneper, minimal surface, soap film, tensioned membrane structure

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Authors: Sara Zadunaisky Ehrlich, Batia Seroussi, Anat Stavans

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Text structure is a parameter of text quality. This study investigated the structure of written argumentative texts produced by elementary school age children. We set two objectives: to identify and trace the structural components of the argumentative texts and to investigate whether reading comprehension skills were correlated with text structure. 293 school children from 2nd to 5th grades were asked to write two argumentative texts about informal or everyday life controversial topics and completed two reading tasks that targeted different levels of text comprehension. The findings indicated, on the one hand, significant developmental differences between mature and more novice writers in terms of text length and mean proportion of clauses produced for a better elaboration of the different text components. On the other hand, with certain fluctuations, no meaningful differences were found in terms of presence of text structure: at all grade levels, elementary school children produced the basic and minimal structure that included the writer's argument and reasons or arguments' supports. Counter-arguments were scarce even in the upper grades. While the children captured that essentially an argument must be justified, the more the number of supports produced, the fewer the clauses the children produced. Last, weak to mild relations were found between reading comprehension and argumentative text structure. Nevertheless, children who scored higher on sophisticated questions that require inferential or world knowledge displayed more elaborated structures in terms of text length and size of supports to the writer's argument. These findings indicate how school-age children perceive the basic template of an argument with future implications regarding how to elaborate written arguments.

Keywords: argumentative text, text structure, elementary school children, written argumentations

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Authors: Andrew Youssef, David Matthews, Jie Pan

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Identifying the magnitude and direction of a force on an elastic solid is highly desirable, as this allows for investigation and continual monitoring of the dynamic loading. This was traditionally conducted by connecting the solid to the supporting structure by multi-axial force transducer, providing that the transducer will not change the mounting conditions. Polyvinylidene fluoride (PVDF) film is a versatile force transducer that can be easily embedded in structures. Here a PVDF sensor array is embedded inside a simple structure in an effort to determine the force vector applied to the structure is an inverse problem. In this paper, forces of different magnitudes and directions where applied to the structure with an impact hammer, and the output of the PVDF was captured and processed to gain an estimate of the forces applied by the hammer. The outcome extends the scope of application of PVDF sensors for measuring the external or contact force vectors.

Keywords: embedded sensor, monitoring, PVDF, vibration

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Authors: Y. Z. Gad

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Disorders of Sex Development (DSD) are defined as congenital conditions in which development of chromosomal, gonadal or anatomical sex is atypical. The DSD are relatively prevalent in Egypt. In spite of that, the relative rarity of the individual disease types or their molecular pathologies frequently resulted in reporting on single or few cases. This augmented the challenging nature of phenotype-genotype correlation in this disease group and its utilization in the management of such medical emergency. Through critical assessment of the published DSD reports, the current review aims at analyzing the clinical characteristics of the various DSD forms in relation to the underlying molecular pathologies. A systematic literature search was done in Pubmed, using relevant keywords (Egypt versus DSD, genital ambiguity or ambiguous genitalia, the old terms of 'intersex, hermaphroditism and pseudohermaphroditism', and a list of the DSD entities and their related genes). The search yielded 24 reports of molecular data in Egyptian patients presenting with ambiguous genitalia. However, only 21 publications fulfilled the criteria of inclusion of detailed clinical descriptions and definitive molecular diagnoses of individual patients. Curation of the data yielded a total of 53 cases that were ascertained from 40 families. Fifty-one patients present with ambiguous genitalia only while 2 had multiple congenital anomalies. Parental consanguinity was noted in 60% of cases. Sex of rearing at initial presentation was female in 75% and 60% in 46,XY and 46,XX DSD cases, respectively. The external genital phenotype in 2/3 of the 46,XY DSD cases showed moderate undermasculinization [Quigley scores 3 & 4] and 1/3 had severe presentations [scores 5 & 6]. For 46,XX subjects, 1 had severe virilization of the external genitalia while 8 had moderate phenotype. Hormonal data were inconclusive or contradictory to final diagnosis in a forth of cases. Collectively, 31 families [31/40, 77.5%] with 46,XY DSD had molecular defects in the genes, 5 alpha reductase 2 (SRD5A2) [12/31], 17 beta-hydroxysteroid dehydrogenase 3 [8/31], androgen receptor [7/31], Steroidogenic factor 1 [2/31], luteinizing hormone receptor [1/31], and fibroblast growth factor receptor 1 [1/31]. In a multiethnic study, 9 families afflicted with 46,XX DSD due to 11 beta hydroxylase (CYP11B1) deficiency were documented. Two recurrent mutations, G34R and N160D, in SRD5A2 were present, respectively, in 42 and 17% of cases. Similarly, 4 recurrent mutations resulted in 89% of the CYP11B1 presentations. In conclusion, this analysis highlights the importance of autosomal recessive inheritance and inbreeding among DSD presentations, the importance of founder effect in at least 2 disorders, the difficulties in relating the genotype with the indeterminate genital phenotype, the under-reporting of some DSD subtypes, and the notion that the reported mutational profiles among Egyptian DSD cases are relatively different from those reported in other ethnic groups.

Keywords: disorders of sex development, genital ambiguity, mutation, molecular diagnosis, Egypt

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Authors: Christian Rathgeber, Franz Winkler, Dirk Odenthal, Steffen Müller

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In this contribution a structure for high level lateral vehicle tracking control based on the disturbance observer is presented. The structure is characterized by stationary compensating side forces disturbances and guaranteeing a cooperative behavior at the same time. Driver inputs are not compensated by the disturbance observer. Moreover the structure is especially useful as it robustly stabilizes the vehicle. Therefore the parameters are selected using the Parameter Space Approach. The implemented algorithms are tested in real world scenarios.

Keywords: disturbance observer, trajectory tracking, robust control, autonomous driving, cooperative driving

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Authors: C. Venkataraman B. E., J. Nagarajan B. E., V. Srinivasan M. Tech

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For a better understanding on sulfide stress corrosion cracking, a theoretical approach based on crystal structure, molecule behavior, flow of electrons and electrochemical reaction is developed. Its impact on different materials such as carbon steel, low alloy, alloy for sour (H2S) environments is studied. This paper describes the theories on various disaster and failures occurred in the industry by Stress Corrosion Cracking (SCC). Parameters such as pH of process fluid, partial pressure of CO2, O2, Chlorine, effect of internal pressure (crystal structure deformation by stress), and external environment condition are considered. An analytical line graph is then created for process fluid parameter verses time, temperature, induced/residual stress due to local pressure build-up. By comparison with the load test result of NACE and ASTM, it is possible to predict and simplify the control of SCC by use of materials like ferritic, Austenitic material in the oil and gas & petroleum industries.

Keywords: crystal structure deformation, failure assessment, alloy-environment combination, H2S

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Authors: Malay Bhattacharyya, Saparya Suresh

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The Correlation Structure associated with a portfolio is subjected to vary across time. Studying the structural breaks in the time-dependent Correlation matrix associated with a collection had been a subject of interest for a better understanding of the market movements, portfolio selection, etc. The current paper proposes a methodology for testing the change in the time-dependent correlation structure of a portfolio in the high dimensional data using the techniques of generalized inverse, singular valued decomposition and multivariate distribution theory which has not been addressed so far. The asymptotic properties of the proposed test are derived. Also, the performance and the validity of the method is tested on a real data set. The proposed test performs well for detecting the change in the dependence of global markets in the context of high dimensional data.

Keywords: correlation structure, high dimensional data, multivariate distribution theory, singular valued decomposition

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Authors: Elisa Y. M. Ang, Teng Yong Ng, Jingjie Yeo, Rongming Lin, Zishun Liu, K. R. Geethalakshmi

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By stacking carbon nanotubes (CNT) one on top of another, single layer CNT arrays can perform water-salt separation with ultra-high permeability and selectivity. Such outer-wall CNT slit membrane is named as the transverse flow CNT membrane. By adjusting the slit size between neighboring CNTs, the membrane can be configured to sieve out different solutes, right down to the separation of monovalent salt ions from water. Molecular dynamics (MD) simulation results show that the permeability of transverse flow CNT membrane is more than two times that of conventional axial-flow CNT membranes, and orders of magnitude higher than current reverse osmosis membrane. In addition, by carrying out MD simulations with different CNT size, it was observed that the variance in desalination performance with CNT size is small. This insensitivity of the transverse flow CNT membrane’s performance to CNT size is a distinct advantage over axial flow CNT membrane designs. Not only does the membrane operate well under constant pressure desalination operation, but MD simulations further indicate that oscillatory operation can further enhance the membrane’s desalination performance, making it suitable for operation such as electrodialysis reversal. While there are still challenges that need to be overcome, particularly on the physical fabrication of such membrane, it is hope that this versatile membrane design can bring the idea of using low dimensional structures for desalination closer to reality.

Keywords: carbon nanotubes, membrane desalination, transverse flow carbon nanotube membrane, molecular dynamics

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Authors: Huda Qari, I. A. Hassan

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The brown alga Padina boryanawas was used for bioassay of polycyclic aromatic hydrocarbons (PAHs) accumulation at the seashore of Jeddah city. PAHs were determined in the coastal water and algal tissues by GC-MS. Acenaphthene (Ace) and dibenzo (a,h) anthracene (dB(a,h)An) were the main PAHs in seawater (50.02 and 46.18) and algal tissues (64.67 and 72.45), respectively. The ratios of low molecular weight/high molecular weight hydrocarbons (1.76 – 1.44), fluoranthene/pyrene (1.57 – 1.52) and phenanthrene/anthracene (0.86 – 0.67) in seawater and algal tissues, respectively, indicated the origin of the PAHs to be mainly petrogenic. This study has demonstrated the utility of using Padina boryanawas as a biomonitor of PAH contamination and bioavailability in the coastal waters.

Keywords: polycyclic aromatic hydrocarbons, Padina boryanawas, bioaccumulation, waste water

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Authors: A. I. Khalafalla, K. A. Al-Busada, I. M. El-Sabagh

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Pox and pox-like diseases of camels are a group of exanthematous skin conditions that have become increasingly important economically. They may be caused by three distinct viruses: camelpox virus (CMPV), camel contagious ecthyma virus (CCEV) and camel papillomavirus (CAPV). These diseases are difficult to differentiate based on clinical presentation in disease outbreaks. Molecular methods such as PCR targeting species-specific genes have been developed and used to identify CMPV and CCEV, but not simultaneously in a single tube. Recently, multiplex PCR has gained reputation as a convenient diagnostic method with cost- and time–saving benefits. In the present communication, we describe the development, optimization and validation a multiplex PCR assays able to detect simultaneously the genome of the three viruses in one single test allowing for rapid and efficient molecular diagnosis. The assay was developed based on the evaluation and combination of published and new primer sets, and was applied to the detection of 110 tissue samples. The method showed high sensitivity, and the specificity was confirmed by PCR-product sequencing. In conclusion, this rapid, sensitive and specific assay is considered a useful method for identifying three important viruses in specimens from camels and as part of a molecular diagnostic regime.

Keywords: multiplex PCR, diagnosis, pox and pox-like diseases, camels

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Authors: Gizaw Mamo Gebeyehu, Marianna Pap, Geza Makkai, Tibor Z. Janosi, Shima Rashidian, Tibor A. Rauch

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Sepsis poses a significant global health threat, necessitating extensive exploration of indicators tied to its pathological mechanisms and multi-organ dysfunction. While murine studies have shed light on sepsis, the intricate cellular and molecular landscape in human sepsis remains enigmatic. Exploring the influence of activated monocyte-derived exosomes in sepsis sheds light on a promising pathway for understanding the intricate cellular and molecular mechanisms involved in this condition in humans. In sepsis, exosome-borne mRNA and miRNA orchestrate immune response gene expression in recipient cells. Yet, the specifics of exosome-mediated cell-to-cell communication, especially how mRNA cargoes modulate gene expression in recipient cells, remain poorly understood. This study aims to elucidate the precise molecular pathways through which exosomal mRNA cargo, particularly MAFB, contributes to the developing sepsis-induced molecular aberrations in liver tissues, employing rigorously defined cell culture conditions. THP-1 cells were treated with LPS to induce changes in exosomal RNA profiles. Exosomes were isolated and characterized using microscopy and mass spectrometry. RNA was extracted from exosomes and sequenced. The most abundant exosomal mRNAs were subjected to GO analysis for functional annotation analysis and KEGG database analysis to identify the involved enriched pathways. PCR (Polymerase Chain Reaction), RNA sequencing, and Western blotting were involved to analyze changes in gene expression, protein levels, and signaling pathways within the liver cells( HepG2) after exposure to exosomal MAFB. This study pinpoints exosomal MAFB as a potential key regulator linked to liver cell damage during sepsis, along with associated genes (miR155HG, H3F3A, and possibly JARD2) forming a crucial molecular pathway contributing to liver cell injury, Together, these elements indicate a vital molecular pathway that plays a significant role in the emergence of liver cell injury during sepsis.. These findings suggest the importance of further research on these components for potential therapeutic interventions in managing acute liver damage in sepsis.

Keywords: sepsis, exososome, exosomal MAFB, LPS-induced THP-1 cells, RNA profiles, sepsis-triggered liver injury

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Authors: Seyedeh Samaneh Hosseini Yousefi

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Space does not play role just in mentioning the place or locations. It also takes part in people attendance and social structures. Urban space is of substantial aspects of city which is a public sphere for free and unlimited appearance of citizens. Along with such appearances and regarding physical, environmental and functional conditions, different personal and social behaviors can be seen and analyzed toward people. The main principle of an urban space is including social relations and communications. In this survey, urban space has been referred to one in which physical, environmental and functional attractions cause pause and staying of people. Surveys have shown that urban designers have discussed about place more than architects or planners. With attention to mutual relations between urban space, society and civilization, proper policy making and planning are essential due to achieving an ideal urban space. The survey has been decided to analyze the effect of functional and physical structure of urban spaces on citizens' social behaviors. Hence, Valiasr crossroads, Tehran identified public space, has been selected in which analytic-descriptive method utilized. To test the accuracy of assumptions, statistical test has been accomplished by SPSS. Findings have shown that functional structure affects social behaviors, relations, integration and participation more than physical structure does.

Keywords: citizens' social behavior, functional structure, physical structure, urban space

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Authors: Aibek Kukpayev, Dhawal Shah

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Combustion of sour fuels containing high amount of sulfur leads to the formation of sulfur oxides, which adversely harm the environment and has a negative impact on human health. Considering this, several legislations have been imposed to bring down the sulfur content in fuel to less than 10 ppm. In recent years, novel deep eutectic solvents (DESs) have been developed to achieve deep desulfurization, particularly to extract thiophenic compounds from liquid fuels. These novel DESs, considered as analogous to ionic liquids are green, eco-friendly, inexpensive, and sustainable. We herein, using molecular dynamic simulation, analyze the interactions of metal-based DESs with model oil consisting of thiophenic compounds. The DES used consists of polyethylene glycol (PEG-200) as a hydrogen bond donor, choline chloride (ChCl) or tetrabutyl ammonium chloride (TBAC) as a hydrogen bond acceptor, and cobalt chloride (CoCl₂) as metal salt. In particular, the combination of ChCl: PEG-200:CoCl₂ at a ratio 1:2:1 and the combination of TBAC:PEG-200:CoCl₂ at a ratio 1:2:0.25 were simulated, separately, with model oil consisting of octane and thiophenes at 25ᵒC and 1 bar. The results of molecular dynamics simulations were analyzed in terms of interaction energies between different components. The simulations revealed a stronger interaction between DESs/thiophenes as compared with octane/thiophenes, suggestive of an efficient desulfurization process. In addition, our analysis suggests that the choice of hydrogen bond acceptor strongly influences the efficiency of the desulfurization process. Taken together, the results also show the importance of the metal ion, although present in small amount, in the process, and the role of the polymer in desulfurization of the model fuel.

Keywords: deep eutectic solvents, desulfurization, molecular dynamics simulations, thiophenes

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Authors: Abhishikta Ghosh Roy

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Breast cancer is the most common malignancy among women globally, including India. Human breast cancer results from the genetic and environmental interaction. The present study attempts to understand the molecular heterogeneity of BRCA1 and BRCA2 genes, as well as to understand the association of various lifestyle and reproductive variables for the Breast Cancer risk. The study was conducted amongst 110 patients and 128 controls with total DNA sequencing of flanking and coding regions of BRCA1 BRCA2 genes that revealed ten Single Nucleotide Polymorphisms (SNPs) (6 novels). The controls selected for the study were age, sex and ethnic group matched. After written and informed consent biological samples were collected from the subjects. After detailed molecular analysis, significant (p < 0.005) molecular heterogeneity is revealed in terms of SNPs in BRCA1 (4 Exonic & 1 Intronic) and BRCA2 (2exonic and 3 Intronic) genes. The augmentation study investigated significant (p < 0.05) association with positive family history, early age at menarche, irregular menstrual periods, menopause, prolong contraceptive use, nulliparity, history of abortions, consumption of alcohol and smoking for breast cancer risk. To the best of authors knowledge, this study is the first of its kind, envisaged that the identification of the SNPs and modification of the lifestyle factors might aid to minimize the risk among the Bengalee Hindu females.

Keywords: breast cancer, BRCA, lifestyle, India

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Authors: Khaled M. Nabil

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This paper introduces the Nested Vortexes conception of the universe structure and interprets all the physical phenomena according this conception. The paper first reviews recent physics theories, either in microscopic scale or macroscopic scale, to collect evidence that the space is not empty. But, these theories describe the property of the space medium without determining its structure. Determining the structure of space medium is essential to understand the mechanism that leads to its properties. Without determining the space medium structure, many phenomena; such as electric and magnetic fields, gravity, or wave-particle duality remain uninterpreted. Thus, this paper introduces a conception about the structure of the universe. It assumes that the universe is a medium of ultra-tiny homogeneous particles which are still undiscovered. Like any medium with certain movements, possibly because of a great asymmetric explosion, vortexes have occurred. A vortex condenses the ultra-tiny particles in its center forming a bigger particle, the bigger particles, in turn, could be trapped in a bigger vortex and condense in its center forming a much bigger particle and so on. This conception describes galaxies, stars, protons as particles at different levels. Existing of the particle’s vortexes make the consistency of the speed of light postulate is not true. This conception shows that the vortex motion dynamic agrees with the motion of all the universe particles at any level. An experiment has been carried out to detect the orbiting effect of aggregated vortexes of aligned atoms of a permanent magnet. Based on the described particle’s structure, the gravity force of a particle and attraction between particles as well as charge, electric and magnetic fields and quantum mechanics characteristics are interpreted. All augmented physics phenomena are solved.

Keywords: astrophysics, cosmology, particles’ structure model, particles’ forces

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Authors: Alena Semeradtova, Marcel Stofik, Lucie Mareckova, Petr Maly, Ondrej Stanek, Jan Maly

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Recently, novel strategies based on so-called molecular evolution were shown to be effective for the production of various peptide ligand libraries with high affinities to molecular targets of interest comparable or even better than monoclonal antibodies. The major advantage of these peptide scaffolds is mainly their prevailing low molecular weight and simple structure. This study describes a new high-affinity binding molecules based immunesensor using a simple optical system for human serum albumin (HSA) detection as a model molecule. We present a comparison of two variants of recombinant binders based on albumin binding domain of the protein G (ABD) performed on micropatterned glass chip. Binding domains may be tailored to any specific target of interest by molecular evolution. Micropatterened glass chips were prepared using UV-photolithography on chromium sputtered glasses. Glass surface was modified by (3-aminopropyl)trietoxysilane and biotin-PEG-acid using EDC/NHS chemistry. Two variants of high-affinity binding molecules were used to detect target molecule. Firstly, a variant is based on ABD domain fused with TolA chain. This molecule is in vivo biotinylated and each molecule contains one molecule of biotin and one ABD domain. Secondly, the variant is ABD domain based on streptavidin molecule and contains four gaps for biotin and four ABD domains. These high-affinity molecules were immobilized to the chip surface via biotin-streptavidin chemistry. To eliminate nonspecific binding 1% bovine serum albumin (BSA) or 6% fetal bovine serum (FBS) were used in every step. For both variants range of measured concentrations of fluorescently labelled HSA was 0 – 30 µg/ml. As a control, we performed a simultaneous assay without high-affinity binding molecules. Fluorescent signal was measured using inverse fluorescent microscope Olympus IX 70 with COOL LED pE 4000 as a light source, related filters, and camera Retiga 2000R as a detector. The fluorescent signal from non-modified areas was substracted from the signal of the fluorescent areas. Results were presented in graphs showing the dependence of measured grayscale value on the log-scale of HSA concentration. For the TolA variant the limit of detection (LOD) of the optical immunosensor proposed in this study is calculated to be 0,20 µg/ml for HSA detection in 1% BSA and 0,24 µg/ml in 6% FBS. In the case of streptavidin-based molecule, it was 0,04 µg/ml and 0,07 µg/ml respectively. The dynamical range of the immunosensor was possible to estimate just in the case of TolA variant and it was calculated to be 0,49 – 3,75 µg/ml and 0,73-1,88 µg/ml respectively. In the case of the streptavidin-based the variant we didn´t reach the surface saturation even with the 480 ug/ml concentration and the upper value of dynamical range was not estimated. Lower value was calculated to be 0,14 µg/ml and 0,17 µg/ml respectively. Based on the obtained results, it´s clear that both variants are useful for creating the bio-recognizing layer on immunosensors. For this particular system, it is obvious that the variant based on streptavidin molecule is more useful for biosensing on glass planar surfaces. Immunosensors based on this variant would exhibit better limit of detection and wide dynamical range.

Keywords: high affinity binding molecules, human serum albumin, optical immunosensor, protein G, UV-photolitography

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Authors: B. Razmi, F. Rafiee, M. Baziar, A. Saeedi Azizkandi

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In the present research, a series of 3-D finite element numerical modeling was performed to study the effect of system frequency and excitation specifications on the internal forces of the piled raft (PR) system in a dry sand layer. The results of numerical simulations were first compared with those associated with centrifuge tests. The natural frequency of superstructure, modeled on the piled raft foundation, was smaller than the natural frequency of the fixed-base super-structure. This difference was greater for super-structures with higher frequencies. In PR systems, the excitation with a frequency close to the system frequency produced the largest responses. Furthermore, based on the results of presented numerical analyses, ignoring the interactions and characteristics of all components of a pile-raft-structure, may lead to highly uneconomical design.

Keywords: centrifuge test, excitation frequency, natural frequency of super-structure, piled raft foundation, 3-D finite element model

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Authors: Jian-Li Shao

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Using Molecular Dynamic (MD) simulations, we simulated the microjet from the metal surface under decaying shock loading. The microjetting processes under release melting conditions are presented in detail, and some properties on the microjet mass and velocity are revealed. The phased increase of microjet mass with shock pressure is found. For all cases, the ratio of the maximal jetting velocity to the surface velocity approximately keeps a constant for liquid state. In addition, the temperature of the microjet can be always above the melting point. When introducing slow decaying profiles, the microjet mass begins to increase with the decay rate, which is dominated by the deformation of the bubble during pull-back. When the decay rate becomes fast enough, the microspall occurs as expected, meanwhile, the microjet appears to reduce because of the shock energy reduction.

Keywords: microjetting, shock, metal, molecular dynamics

Procedia PDF Downloads 174

Authors: Ankit Kargeti, Ravikant Shrivastav, Tabish Rasheed

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The electronic structure calculation for the nanoclusters of AsSiTeB/SiAsBTe quaternary semiconductor alloy belonging to the III-V Group elements was performed. Motivation for this research work was to look for accurate electronic and geometric data of small nanoclusters of AsSiTeB/SiAsBTe in the gaseous form. The two clusters, one in the linear form and the other in the bent form, were studied under the framework of Density Functional Theory (DFT) using the B3LYP functional and LANL2DZ basis set with the software packaged Gaussian 16. We have discussed the Optimized Energy, Frontier Orbital Energy Gap in terms of HOMO-LUMO, Dipole Moment, Ionization Potential, Electron Affinity, Binding Energy, Embedding Energy, Density of States (DoS) spectrum for both structures. The important findings of the predicted nanostructures are that these structures have wide band gap energy, where linear structure has band gap energy (Eg) value is 2.375 eV and bent structure (Eg) value is 2.778 eV. Therefore, these structures can be utilized as wide band gap semiconductors. These structures have high electron affinity value of 4.259 eV for the linear structure and electron affinity value of 3.387 eV for the bent structure form. It shows that electron acceptor capability is high for both forms. The widely known application of these compounds is in the light emitting diodes due to their wide band gap nature.

Keywords: density functional theory, DFT, density functional theory, nanostructures, HOMO-LUMO, density of states

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Authors: Subhojyoti Chatterjee, Peter J. Mahon, Feng Wang

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Resveratrol (RvL), a phenolic compound, is a key ingredient in wine and tomatoes that has been studied over the years because of its important bioactivities such as anti-oxidant, anti-aging and antimicrobial properties. Out of the two isomeric forms of resveratrol i.e. trans and cis, the health benefit is primarily associated with the trans form. Thus, studying the structural properties of the isomers will not only provide an insight into understanding the RvL isomers, but will also help in designing parameters for differentiation in order to achieve 99.9% purity of trans-RvL. In the present study, density function theory (DFT) study is conducted, using the B3LYP/6-311++G** model to explore the through bond and through space intramolecular interactions. Properties such as vibrational spectroscopy (IR and Raman), nuclear magnetic resonance (NMR) spectra, excess orbital energy spectrum (EOES), energy based decomposition analyses (EDA) and Fukui function are calculated. It is discovered that the structure of trans-RvL, although it is C1 non-planar, the backbone non-H atoms are nearly in the same plane; whereas the cis-RvL consists of two major planes of R1 and R2 that are not in the same plane. The absence of planarity gives rise to a H-bond of 2.67Å in cis-RvL. Rotation of the C(5)-C(8) single bond in trans-RvL produces higher energy barriers since it may break the (planar) entire conjugated structure; while such rotation in cis-RvL produces multiple minima and maxima depending on the positions of the rings. The calculated FT-IR spectrum shows very different spectral features for trans and cis-RvL in the region 900 – 1500 cm-1, where the spectral peaks at 1138-1158 cm-1 are split in cis-RvL compared to a single peak at 1165 cm-1 in trans-RvL. In the Raman spectra, there is significant enhancement of cis-RvL in the region above 3000cm-1. Further, the carbon chemical environment (13C NMR) of the RvL molecule exhibit a larger chemical shift for cis-RvL compared to trans-RvL (Δδ = 8.18 ppm) for the carbon atom C(11), indicating that the chemical environment of the C group in cis-RvL is more diverse than its other isomer. The energy gap between highest occupied molecular orbital (HOMO) and the lowest occupied molecular orbital (LUMO) is 3.95 eV for trans and 4.35 eV for cis-RvL. A more detailed inspection using the recently developed EOES revealed that most of the large energy differences i.e. Δεcis-trans > ±0.30 eV, in their orbitals are contributed from the outer valence shell. They are MO60 (HOMO), MO52-55 and MO46. The active sites that has been captured by Fukui function (f + > 0.08) are associated with the stilbene C=C bond of RvL and cis-RvL is more active at these sites than in trans-RvL, as cis orientation breaks the large conjugation of trans-RvL so that the hydroxyl oxygen’s are more active in cis-RvL. Finally, EDA highlights the interaction energy (ΔEInt) of the phenolic compound, where trans is preferred over the cis-RvL (ΔΔEi = -4.35 kcal.mol-1) isomer. Thus, these quantum mechanics results could help in unwinding the diversified beneficial activities associated with resveratrol.

Keywords: resveratrol, FT-IR, Raman, NMR, excess orbital energy spectrum, energy decomposition analysis, Fukui function

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Authors: Ming Lu, Xiaojun Li, Bodi Lu, Juehui Xing

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Earthquake damage phenomenon of each large earthquake gives comprehensive and profound real test to the dynamic performance and failure mechanism of different engineering structures. Cognitive engineering structure characteristics through seismic damage phenomenon are often far superior to expensive shaking table experiments. After the earthquake, people will record a variety of different types of engineering damage photos. However, a large number of earthquake damage photographs lack sufficient information and reduce their using value. To improve the research value and the use efficiency of engineering seismic damage photographs, this paper objects to explore and show seismic damage background information, which includes the earthquake magnitude, earthquake intensity, and the damaged structure characteristics. From the research requirement in earthquake engineering field, the authors use the 2008 China Wenchuan M8.0 earthquake photographs, and provide four kinds of attribute indexes and classification, which are seismic information, structure types, earthquake damage parts and disaster causation factors. The final object is to set up an engineering structural seismic damage database based on these four attribute indicators and classification, and eventually build a website providing seismic damage photographs.

Keywords: attribute index, classification method, earthquake damage picture, engineering structure

Procedia PDF Downloads 745