Search results for: molecular dynamics simulations

Authors: Abu Salim Mustafa

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Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing

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Authors: Ersin Bozkurt

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The aim of the study is to develop materials for understanding image formations through virtual objects in geometric optics. The images in physics course books are formed by using real objects. This results in mistakes in the features of images because of generalizations which leads to conceptual misunderstandings in learning. In this study it was intended to identify pre-service physics teachers misunderstandings arising from false generalizations. Focused group interview was used as a qualitative method. The findings of the study show that students have several misconceptions such as "the image in a plain mirror is always virtual". However a real image can be formed in a plain mirror. To explain a virtual object's image formation in a more understandable way an overhead projector and episcope and their design was illustrated. The illustrations are original and several computer simulations will be suggested.

Keywords: computer simulations, geometric optics, physics education, students' misconceptions in physics

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Authors: Nizar Tayem, AbuMuhammad Moinuddeen, Ahmed A. Hussain, Redha M. Radaydeh

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This research paper introduces an approach for estimating the direction of arrival (DOA) of multiple RF noncoherent sources in a uniform linear array (ULA). The proposed method utilizes a Capon-like estimation algorithm and incorporates LU decomposition to enhance the accuracy of DOA estimation while significantly reducing computational complexity compared to existing methods like the Capon method. Notably, the proposed method does not require prior knowledge of the number of sources. To validate its effectiveness, the proposed method undergoes validation through both software simulations and practical experimentation on a prototype testbed constructed using a software-defined radio (SDR) platform and GNU Radio software. The results obtained from MATLAB simulations and real-time experiments provide compelling evidence of the proposed method's efficacy.

Keywords: DOA estimation, real-time validation, software defined radio, computational complexity, Capon's method, GNU radio

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Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

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This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: Dena Alhaloul

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The Middle East and North Africa (MENA) region is characterized by diverse cultures, economies, and social structures. Fertility rates in MENA have seen significant changes over time, with variations among countries and subregions. Understanding fertility patterns in this region is essential due to its impact on demographic dynamics, healthcare, labor markets, and social policies. Rising or declining fertility rates have far-reaching consequences for the region's socioeconomic development. The main thrust of this study is to comprehensively examine fertility rates in the Middle East and North Africa (MENA) region. It aims to understand the distribution, determinants, and temporal trends of fertility rates in MENA countries. The study seeks to provide insights into the factors influencing fertility decisions, assess how fertility rates have evolved over time, and potentially develop statistical models to characterize these trends. As for the methodology of the study, the study uses descriptive statistics to summarize and visualize fertility rate data. It also uses regression analyses to identify determinants of fertility rates as well as statistical modeling to characterize temporal trends in fertility rates. The conclusion of this study The research will contribute to a deeper understanding of fertility dynamics in the MENA region, shedding light on the distribution of fertility rates, their determinants, and historical trends.

Keywords: fertility, distribution, modeling, regression

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Authors: Tobias Beyer, Christoph Friedrich

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Modern simulation methodology using finite element models is nowadays a recognized tool for product design/optimization. Likewise, manufacturing process design is increasingly becoming the focus of simulation methodology in order to enable sustainable results based on reduced real-life tests here as well. In this article, two process simulations -radial riveting and roller burnishing- used for mechanical joining of components are explained. In the first step, the required boundary conditions are developed and implemented in the respective simulation models. This is followed by process space validation. With the help of the validated models, the interdependencies of the input parameters are investigated and evaluated by means of sensitivity analyses. Limit case investigations are carried out and evaluated with the aid of the process simulations. Likewise, a comparison of the two joining methods to each other becomes possible.

Keywords: FEM, model-based process development, process simulation, radial riveting, roller burnishing, sensitivity analysis

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Authors: Sharat Chandra, Zilong Wang, Ru-Rong Ji, Andrey Bortsov

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Chronic pain (CP) therapeutic approaches have limited efficacy. As a result, doctors are prescribing opioids for chronic pain, leading to opioid overuse, abuse, and addiction epidemic. Therefore, the development of effective and safe CP drugs remains an unmet medical need. Voltage-gated sodium (Nav) channels act as cardiovascular and neurological disorder’s molecular targets. Nav channels selective inhibitors are hard to design because there are nine closely-related isoforms (Nav1.1-1.9) that share the protein sequence segments. We are targeting the Nav1.7 found in the peripheral nervous system and engaged in the perception of pain. The objective of this project was to screen a 1.5 million compound library for identification of inhibitors for Nav1.7 with analgesic effect. In this study, we designed a protocol for identification of isoform-selective inhibitors of Nav1.7, by utilizing the prior information on isoform-selective antagonists. First, a similarity search was performed; then the identified hits were docked into a binding site on the fourth voltage-sensor domain (VSD4) of Nav1.7. We used the FTrees tool for similarity searching and library generation; the generated library was docked in the VSD4 domain binding site using FlexX and compounds were shortlisted using a FlexX score and SeeSAR hyde scoring. Finally, the top 25 compounds were tested with molecular dynamics simulation (MDS). We reduced our list to 9 compounds based on the MDS root mean square deviation plot and obtained them from a vendor for in vitro and in vivo validation. Whole-cell patch-clamp recordings in HEK-293 cells and dorsal root ganglion neurons were conducted. We used patch pipettes to record transient Na⁺ currents. One of the compounds reduced the peak sodium currents in Nav1.7-HEK-293 stable cell line in a dose-dependent manner, with IC50 values at 0.74 µM. In summary, our computer-aided analgesic discovery approach allowed us to develop pre-clinical analgesic candidate with significant reduction of time and cost.

Keywords: chronic pain, voltage-gated sodium channel, isoform-selective antagonist, similarity search, virtual screening, analgesics development

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Authors: Jyothi Nagraj, Sudeshna Mukherjee, Rajdeep Chowdhury

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Autophagy has recently been linked with cancer cell survival post drug insult contributing to acquisition of resistance. However, the molecular signaling governing autophagic survival response is poorly explored. In our study, in osteosarcoma (OS) cells cisplatin shock was found to activate both MAPK and autophagy signaling. An activation of JNK and autophagy acted as pro-survival strategy, while ERK1/2 triggered apoptotic signals upon cisplatin stress. An increased sensitivity of the cells to cisplatin was obtained with simultaneous inhibition of both autophagy and JNK pathway. Furthermore, we observed that the autophagic stimulation upon drug stress regulates other developmentally active signaling pathways like the Hippo pathway in OS cells. Cisplatin resistant cells were thereafter developed by repetitive drug exposure followed by clonal selection. Basal levels of autophagy were found to be high in resistant cells to. However, the signaling mechanism leading to autophagic up-regulation and its regulatory effect differed in OS cells upon attaining drug resistance. Our results provide valuable clues to regulatory dynamics of autophagy that can be considered for development of improved therapeutic strategy against resistant type cancers.

Keywords: JNK, autophagy, drug resistance, cancer

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Authors: Christopher Deekia Nwimae, Nigel Simms, Liyun Lao

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Erosion in pipe bends caused by particles is a major obstacle in the oil and gas fields and might cause the breakdown of production equipment. This work studied the effects imposed by flow velocity and impact of solid particles diameter in an elbow; erosion rate was verified with experimental data using the computational fluid dynamics (CFD) approach. Two-way coupled Euler-Lagrange and discrete phase model was employed to calculate the air/solid particle flow in an elbow. One erosion model and three-particle rebound models were used to predict the erosion rate on the 90° elbows. The generic erosion model was used in the CFD-based erosion model, and after comparing it with experimental data, results showed agreement with the CFD-based predictions as observed.

Keywords: erosion, prediction, elbow, computational fluid dynamics

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: K. Jagannath, Akhilesh Kotian, S. S. Sharma, Achutha Kini U., P. R. Prabhu

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Boiling process is characterized by the rapid formation of vapour bubbles at the solid–liquid interface (nucleate boiling) with pre-existing vapour or gas pockets. Computational fluid dynamics (CFD) is an important tool to study bubble dynamics. In the present study, CFD simulation has been carried out to determine the bubble detachment diameter and its terminal velocity. Volume of fluid method is used to model the bubble and the surrounding by solving single set of momentum equations and tracking the volume fraction of each of the fluids throughout the domain. In the simulation, bubble is generated by allowing water-vapour to enter a cylinder filled with liquid water through an inlet at the bottom. After the bubble is fully formed, the bubble detaches from the surface and rises up during which the bubble accelerates due to the net balance between buoyancy force and viscous drag. Finally when these forces exactly balance each other, it attains a constant terminal velocity. The bubble detachment diameter and the terminal velocity of the bubble are captured by the monitor function provided in FLUENT. The detachment diameter and the terminal velocity obtained is compared with the established results based on the shape of the bubble. A good agreement is obtained between the results obtained from simulation and the equations in comparison with the established results.

Keywords: bubble growth, computational fluid dynamics, detachment diameter, terminal velocity

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Fuyuan Ma, Ying Wang, Xin Wang

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Social networks have become breeding grounds for the rapid spread of rumors and malicious information, posing threats to societal stability and causing significant public harm. Existing research focuses on simulating the spread of information and its impact on users through propagation dynamics and applies methods such as greedy approximation strategies to approximate the optimal control solution at the global scale. However, the greedy strategy at the global scale may fall into locally optimal solutions, and the approximate simulation of information spread may accumulate more errors. Therefore, we propose a multi-scale control model for network group behavior, introducing individual and group scales on top of the greedy strategy’s global scale. At the individual scale, we calculate the propagation influence of nodes based on their structural attributes to alleviate the issue of local optimality. At the group scale, we conduct precise propagation simulations to avoid introducing cumulative errors from approximate calculations without increasing computational costs. Experimental results on three real-world datasets demonstrate the effectiveness of our proposed multi-scale model in controlling network group behavior.

Keywords: influence blocking maximization, competitive linear threshold model, social networks, network group behavior

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Authors: M. Ezkurra, J. A. Esnaola, M. Martinez-Agirre, U. Etxeberria, U. Lertxundi, L. Colomo, M. Begiristain, I. Zurutuza

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Butterfly valves are widely used industrial piping components as on-off and flow controlling devices. The main challenge in the design process of this type of valves is the correct dimensioning to ensure proper mechanical performance as well as to minimise flow losses that affect the efficiency of the system. Butterfly valves are typically dimensioned in a closed position based on mechanical approaches considering uniform hydrostatic pressure, whereas the flow losses are analysed by means of CFD simulations. The main limitation of these approaches is that they do not consider either the influence of the dynamics of the manoeuvring stage or coupled phenomena. Recent works have included the influence of the flow on the mechanical behaviour for different opening angles by means of one-way FSI approach. However, these works consider steady-state flow for the selected angles, not capturing the effect of the transient flow evolution during the manoeuvring stage. Two-way FSI modelling approach could allow overcoming such limitations providing more accurate results. Nevertheless, the use of this technique is limited due to the increase in the computational cost. In the present work, the applicability of FSI one-way and two-way approaches is evaluated for the analysis of butterfly valves, showing that not considering fluid-structure coupling involves not capturing the most critical situation for the valve disc.

Keywords: butterfly valves, fluid-structure interaction, one-way approach, two-way approach

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Barbora Chmelova, Radek Sachl

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Gangliosides are amphipathic membrane lipids. Due to the composition of bulky oligosaccharide chains containing one or more sialic acids linked to the hydrophobic ceramide base, gangliosides are classified among glycosphingolipids. This unique structure induces a high self-aggregating tendency of gangliosides and, therefore, the formation of nanoscopic clusters called nanodomains. Gangliosides are preferentially present in an extracellular membrane leaflet of all human tissues and thus have an impact on a huge number of biological processes, such as intercellular communication, cell signalling, membrane trafficking, and regulation of receptor activity. Defects in their metabolism, impairment of proper ganglioside function, or changes in their organization lead to serious health conditions such as Alzheimer´s and Parkinson´s diseases, autoimmune diseases, tumour growth, etc. This work mainly focuses on ganglioside organization into nanodomains and their dynamics within the plasma membrane. Current research investigates static ganglioside nanodomains characterization; nevertheless, the information about their diffusion is missing. In our study, fluorescence correlation spectroscopy is implemented together with stimulated emission depletion (STED-FCS), which combines the diffraction-unlimited spatial resolution with high temporal resolution. By comparison of the experiments performed on model vesicles containing 4 % of either GM1, GM2, or GM3 and Monte Carlo simulations of diffusion on the plasma membrane, the description of ganglioside clustering, diffusion of nanodomains, and even diffusion of ganglioside molecules inside investigated nanodomains are described.

Keywords: gangliosides, nanodomains, STED-FCS, flourescence microscopy, membrane diffusion

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Authors: Tolga Arda Eraslan

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The quality of the indoor environment is significant to occupants’ health, comfort, and productivity, as Covid-19 spread throughout the world, people started spending most of their time indoors. Since buildings are getting bigger, mechanical ventilation systems are widely used where natural ventilation is insufficient. Four primary tasks of a ventilation system have been identified indoor air quality, comfort, contamination control, and energy performance. To fulfill such requirements, air diffusers, which are a part of the ventilation system, have begun to enter our lives in different airflow distribution systems. Detailed observations are needed to assure that such devices provide high levels of comfort effectiveness and energy efficiency. This study addresses these needs. The objective of this article is to observe air characterizations of different air diffusers at different angles and their effect on people by the thermal comfort model in CFD simulation and to validate the outputs with the help of data results based on a simulated office room. Office room created to provide validation; Equipped with many thermal sensors, including head height, tabletop, and foot level. In addition, CFD simulations were carried out by measuring the temperature and velocity of the air coming out of the supply diffuser. The results considering the flow interaction between diffusers and surroundings showed good visual illustration.

Keywords: computational fluid dynamics, fanger’s model, predicted mean vote, thermal comfort

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Authors: Richa Mardianingrum, Srie R. N. Endah

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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Philip Symonds, Jon Taylor, Zaid Chalabi, Michael Davies

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With the world climate projected to warm and major cities in developing countries becoming increasingly populated and polluted, governments are tasked with the problem of overheating and air quality in residential buildings. This paper presents the development of an adaptable model of these risks. Simulations are performed using the EnergyPlus building physics software. An accurate metamodel is formed by randomly sampling building input parameters and training on the outputs of EnergyPlus simulations. Metamodels are used to vastly reduce the amount of computation time required when performing optimisation and sensitivity analyses. Neural Networks (NNs) are compared to a Radial Basis Function (RBF) algorithm when forming a metamodel. These techniques were implemented using the PyBrain and scikit-learn python libraries, respectively. NNs are shown to perform around 15% better than RBFs when estimating overheating and air pollution metrics modelled by EnergyPlus.

Keywords: neural networks, radial basis functions, metamodelling, python machine learning libraries

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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Authors: Bhavesh Dadhich, Fenil Bamnoliya, Akshita Swaminathan

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This project aims to design a system to generate energy from flowing wind due to the motion of a vehicle on the road or from the flow of wind in compact areas to utilize the wasteful energy into a useful one. It is envisaged through a design and aerodynamic performance improvement of a Savonius vertical axis wind turbine rotor and used in an integrated system with a Triboelectric Nanogenerator (TENG) that can generate a good amount of electrical energy. Aerodynamic calculations are performed numerically using Computational Fluid Dynamics software, and TENG's performance is evaluated analytically. The Turbine's coefficient of power is validated with published results for an inlet velocity of 7 m/s with a Tip Speed Ratio of 0.75 and found to reasonably agree with that of experiment results. The baseline design is modified with a new blade arc angle and rotor position angle based on the recommended parameter ranges suggested by previous researchers. Simulations have been performed for different T.S.R. values ranging from 0.25 to 1.5 with an interval of 0.25 with two applicable free stream velocities of 5 m/s and 7m/s. Finally, the newly designed VAWT CFD performance results are used as input for the analytical performance prediction of the triboelectric nanogenerator. The results show that this approach could be feasible and useful for small power source applications.

Keywords: savonius turbine, power, overlap ratio, tip speed ratio, TENG

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Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin

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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².

Keywords: chromophore, organic solar cells, photoactive materials, small molecule

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Authors: Ákos Tótin

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In crop production the most modern hybrids are available for us, therefore the yield and yield stability is determined by the agro-technology. The purpose of the experiment is to adapt the modern agrotechnology to the new type of hybrids. The long-term experiment was set up in 2015-2016 on chernozem soil in the Hajdúság (eastern Hungary). The plots were set up in 75 thousand ha-1 plant density. We examined some mainly use hybrids of Hungary. The conducted studies are: germination dynamic, growing dynamic and the effect of annual weather for the yield. We use three different sowing date as early, average and late, and measure how many plant germinated during the germination process. In the experiment, we observed the germination dynamics in 6 hybrid in 4 replication. In each replication, we counted the germinated plants in 2m long 2 row wide area. Data will be shown in the average of the 6 hybrid and 4 replication. Growing dynamics were measured from the 10cm (4-6 leaf) plant highness. We measured 10 plants’ height in two weeks replication. The yield was measured buy a special plot harvester - the Sampo Rosenlew 2010 – what measured the weight of the harvested plot and also took a sample from it. We determined the water content of the samples for the water release dynamics. After it, we calculated the yield (t/ha) of each plot at 14% of moisture content to compare them. We evaluated the data using Microsoft Excel 2015. The annual weather in each crop year define the maize germination dynamics because the amount of heat is determinative for the plants. In cooler crop year the weather is prolonged the germination. At the 2015 crop year the weather was cold in the beginning what prolonged the first sowing germination. But the second and third sowing germinated faster. In the 2016 crop year the weather was much favorable for plants so the first sowing germinated faster than in the previous year. After it the weather cooled down, therefore the second and third sowing germinated slower than the last year. The statistical data analysis program determined that there is a significant difference between the early and late sowing date growing dynamics. In 2015 the first sowing date had the highest amount of yield. The second biggest yield was in the average sowing time. The late sowing date has lowest amount of yield.

Keywords: germination, maize, sowing date, yield

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Authors: Christina Eleftheria Tzeliou, Demeter Tzeli

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Introduction: Molecular Logic Gates (MLGs) are molecular machines that can perform complex work, such as solving logic operations. Molecular switches, which are molecules that can experience chemical changes are examples of successful types of MLGs. Recently, Quintana-Romero and Ariza-Castolo studied experimentally six stable pseudo-hemi-indigo-derived MLGs capable of solving complex logic operations. The MLG design relies on a molecular switch that experiences Z and E isomerism, thus the molecular switch's axis has to be a double bond. The hemi-indigo structure was preferred for the assembly of molecular switches due to its interaction with visible light. Z and E pseudo-hemi-indigo isomers can also be utilized for selective isomerization as they have distinct absorption spectra. Methodology: Here, the photophysical properties of pseudo-hemi-indigo derivatives are examined, i.e., derivatives of molecule 1 with anthracene, naphthalene, phenanthrene, pyrene, and pyrrole. In conjunction with some trials that were conducted, the level of theory mentioned subsequently was determined. The structures under study were optimized in both cis and trans conformations at the PBE0/6-31G(d,p) level of theory. The absorption spectra of the structures were calculated at PBE0/DEF2TZVP. In all cases, the absorption spectra of the studied systems were calculated including up to 50 singlet- and triplet-spin excited electronic states. Transition states (cis → cis, cis → trans, and trans → trans) were obtained in cases where it was possible, with PBE0/6-31G(d,p) for the optimization of the transition states and PBE0/DEF2TZVP for the respective absorption spectra. Emission spectra were obtained for the first singlet state of each molecule in cis both and trans conformations in PBE0/DEF2TZVP as well. All studies were performed in chloroform solvent that was added as a dielectric constant and the polarizable continuum model was also employed. Findings: Shifts of up to 25 nm are observed in the absorption spectra due to cis-trans isomerization, while the transition state is shifted up to about 150 nm. The electron density distribution is also examined, where charge transfer and electron transfer phenomena are observed regarding the three excitations of interest, i.e., H-1 → L, H → L and H → L+1. Emission spectra calculations were also carried out at PBE0/DEF2TZVP for the complete investigation of these molecules. Using protonation as input, selected molecules act as MLGs. Conclusion: Theoretical data so far indicate that both cis-trans isomerization, and cis-cis and trans-trans conformer isomerization affect the UV-visible absorption and emission spectra. Specifically, shifts of up to 30 nm are observed, while the transition state is shifted up to about 150 nm in cis-cis isomerization. The computational data obtained are in agreement with available experimental data, which have predicted that the pyrrole derivative is a MLG at 445 nm and 400 nm using protonation as input, while the anthracene derivative is a MLG that operates at 445 nm using protonation as input. Finally, it was found that selected molecules are candidates as MLG using protonation and light as inputs. These MLGs could be used as chemical sensors or as particular intracellular indicators, among several other applications. Acknowledgements: The author acknowledges the Hellenic Foundation for Research and Innovation for the financial support of this project (Fellowship Number: 21006).

Keywords: absorption spectra, DFT calculations, isomerization, molecular logic gates

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Authors: J. Joy, T. H. New, I. H. Ibrahim

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A computational study on bio-inspired NACA634-021 hydrofoils with leading-edge protuberances has been carried out to investigate their hydrodynamic flow control characteristics at a Reynolds number of 14,000 and different angles-of-attack. The numerical simulations were performed using ANSYS FLUENT and based on Reynolds-Averaged Navier-Stokes (RANS) solver mode incorporated with k-ω Shear Stress Transport (SST) turbulence model. The results obtained indicate varying flow phenomenon along the peaks and troughs over the span of the hydrofoils. Compared to the baseline hydrofoil with no leading-edge protuberances, the leading-edge modified hydrofoils tend to reduce flow separation extents along the peak regions. In contrast, there are increased flow separations in the trough regions of the hydrofoil with leading-edge protuberances. Interestingly, it was observed that dissimilar flow separation behaviour is produced along different peak- or trough-planes along the hydrofoil span, even though the troughs or peaks are physically similar at each interval for a particular hydrofoil. Significant interactions between adjacent flow structures produced by the leading-edge protuberances have also been observed. These flow interactions are believed to be responsible for the dissimilar flow separation behaviour along physically similar peak- or trough-planes.

Keywords: computational fluid dynamics, flow separation control, hydrofoils, leading-edge protuberances

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Authors: Y. Trantafyllou, C. Alexandraki

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Music interpretation accounts to the way musicians shape their performance by deliberately deviating from composers’ intentions, which are commonly communicated via some form of music transcription, such as a music score. For transcribed and non-improvised music, music expression is manifested by introducing subtle deviations in tempo, dynamics and articulation during the evolution of performance. This paper presents an application, named FlameCens, which, given two recordings of the same piece of music, presumably performed by different musicians, allow visualising deviations in tempo and dynamics during playback. The application may also compare a certain performance to the music score of that piece (i.e. MIDI file), which may be thought of as an expression-neutral representation of that piece, hence depicting the expressive queues employed by certain performers. FlameCens uses the Dynamic Time Warping algorithm to compare two audio sequences, based on CENS (Chroma Energy distribution Normalized Statistics) audio features. Expressive deviations are illustrated in a moving flame, which is generated by an animation of particles. The length of the flame is mapped to deviations in dynamics, while the slope of the flame is mapped to tempo deviations so that faster tempo changes the slope to the right and slower tempo changes the slope to the left. Constant slope signifies no tempo deviation. The detected deviations in tempo and dynamics can be additionally recorded in a text file, which allows for offline investigation. Moreover, in the case of monophonic music, the color of particles is used to convey the pitch of the notes during performance. FlameCens has been implemented in Python and it is openly available via GitHub. The application has been experimentally validated for different music genres including classical, contemporary, jazz and popular music. These experiments revealed that FlameCens can be a valuable tool for music specialists (i.e. musicians or musicologists) to investigate the expressive performance strategies employed by different musicians, as well as for music audience to enhance their listening experience.

Keywords: audio synchronization, computational music analysis, expressive music performance, information visualization

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Authors: Hassan Athari, Abdurrahim Bolukbasi, Dogan Ciloglu

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This study represented the respiratory alveoli system, and determined the trajectory of inhaled particles more accurately using the modified three-dimensional model with deformable walls of alveoli. The study also considered the tissue tension in the model to demonstrate the effect of lung. Tissue tensions are transferred by the lung parenchyma and produce the pressure gradient. This load expands the alveoli and establishes a sub-ambient (vacuum) pressure within the lungs. Thus, at the alveolar level, the flow field and movement of alveoli wall lead to an integrated effect. In this research, we assume that the three-dimensional alveolus has a visco-elastic tissue (walls). For accurate investigation of pulmonary tissue mechanical properties on particle transport and alveolar flow field, the actual relevance between tissue movement and airflow is solved by two-way FSI (Fluid Structure Interaction) simulation technique in the alveolus. Therefore, the essence of real simulation of pulmonary breathing mechanics can be achieved by developing a coupled FSI computational model. We, therefore conduct a series of FSI simulations over a range of tissue models and breathing rates. As a result, the fluid flows and streamlines have changed during present flexible model against the rigid models and also the two-way coupling particle trajectories have changed against the one-way particle coupling.

Keywords: FSI, two-way particle coupling, alveoli, CDF

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