Search results for: molecular dynamics

Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

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Authors: P. M. Fonseca Alfonso, E. A. Murillo Ruiz, M. Diaz Lagos

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Understanding the physicochemical properties and mineralogy of fly ash from a particular source is essential for to protect the environment and considering its possible applications, specifically, in the production of geopolymeric materials that solidify/stabilize heavy metals ions. The results of the characterization of three fly ash samples are shown in this paper. The samples were produced in the TERMOPAIPA IV thermal power plant in the State of Boyaca, Colombia. The particle size distribution, chemical composition, mineralogy, and molecular structure of three samples were analyzed using laser diffraction, X-ray fluorescence, inductively coupled plasma mass spectrometry, X-ray diffraction, and infrared spectroscopy respectively. The particle size distribution of the three samples probably ranges from 0.128 to 211 μm. Approximately 59 elements have been identified in the three samples. It is noticeable that the ashes are made up of aluminum and silicon compounds. Besides, the iron phase in low content was also found. According to the results found in this study, the fly ash samples type F has a great potential to be used as raw material for the manufacture of geopolymers with potential use in the stabilization/solidification of heavy metals; mainly due to the presence of amorphous aluminosilicates typical of this type of ash, which react effectively with alkali-activator.

Keywords: fly ash, geopolymers, molecular structure, physicochemical properties.

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Authors: Thiyam Tamphasana Devi, Bimlesh Kumar

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A Computational Fluid Dynamics (CFD) technique has been applied to simulate the gas-liquid phase in double stirred tank of Rushton impeller. Eulerian-Eulerian model was adopted to simulate the multiphase with standard correlation of Schiller and Naumann for drag co-efficient. The turbulence was modeled by using standard k-ε turbulence model. The present CFD model predicts flow pattern, local gas hold-up, and local specific area. It also predicts local kLa (mass transfer rate) for single impeller. The predicted results were compared with experimental and CFD results of published literature. The predicted results are slightly over predicted with the experimental results; however, it is in reasonable agreement with other simulated results of published literature.

Keywords: Eulerian-Eulerian, gas-hold up, gas-liquid phase, local mass transfer rate, local specific area, Rushton Impeller

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Authors: Jos Olijve

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Introduction and Purpose: Endotoxins are found in the outer membrane of gram-negative bacteria and have profound in vitro and in vivo responses. They can trigger strong immune responses and negatively affect various cellar activities particular cells expressing toll-like receptors. They are therefore unwanted contaminants of biomaterials sourced from natural raw materials, and their activity must be as low as possible. Collagen and gelatin are natural extracellular matrix components and have, due to their low allergenic potential, suitable biological properties, and tunable physical characteristics, high potential in biomedical applications. The purpose of this study was to determine the influence of autoclave sterilization of gelatin on physical properties and endotoxin level compared to surfactant purified gelatin. Methods: Type A gelatin from Sigma-Aldrich (G1890) with endotoxin level of 35000 endotoxin units (EU) per gram gelatin and type A gelatins from Rousselot Gent with endotoxin activity of 30000 EU per gram were used. A 10 w/w% G1890 gelatin solution was autoclave sterilized during 30 minutes at 121°C and 1 bar over pressure. The physical properties and the endotoxin level of the sterilized G1890 gelatin were compared to a type A gelatin from Rousselot purified with Triton X100 surfactant. The Triton X100 was added to a concentration of 0.5 w/w% which is above the critical micellar concentration. The gelatin surfactant mixtures were kept for 30-45 minutes under constant stirring at 55-60°C. The Triton X100 was removed by active carbon filtration. The endotoxin levels of the gelatins were measured using the Endozyme recombinant factor C method from Hyglos GmbH (Germany). Results and Discussion: Autoclave sterilization significantly affect the physical properties of gelatin. Molecular weight of G1890 decreased from 140 to 50kDa, and gel strength decreased from 300 to 40g. The endotoxin level of the gelatin reduced after sterilization from 35000 EU/g to levels of 400-500 EU/g. These endotoxin levels are however still far above the upper endotoxin level of 0.05 EU/ml, which resembles 5 EU/g gelatin based on a 1% gelatin solution, to avoid cell proliferation alteration. Molecular weight and gel strength of Rousselot gelatin was not altered after Triton X100 purification and remained 150kDa and 300g respectively. The endotoxin levels of Triton X100 purified Rousselot gelatin was < 5EU/g gelatin. Conclusion: Autoclave sterilization of gelatin is, in comparison to Triton X100 purification, not efficient to inactivate endotoxin levels in gelatin to levels below the upper limit to avoid cell proliferation alteration. Autoclave sterilization gave a significant decrease in molecular weight and gel strength which makes autoclave sterilized gelatin, in comparison to Triton X100 purified gelatin, not suitable for 3D printing.

Keywords: endotoxin, gelatin, molecular weight, sterilization, Triton X100

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Authors: Chukwuebuka Vincent Azuka, Chidimma Peace Odoh

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Changes in agricultural practices and land use influence the storage and release of soil organic carbon and soil structural dynamics. To investigate this in Nsukka, southeastern Nigeria, soil samples were collected at 0-10 cm, 10-20 cm and 20-30 cm from three locations; Ovoko (OV), Obukpa (OB) and University of Nigeria, Nsukka (UNN) and three land use types; cultivated land (CL), forest land (FL) and grassland (GL)). Data were subjected to analysis of variance (ANOVA) using SPSS. Also, correlations between organic carbon stock, structural stability indices and other soil properties were established. The result showed that Ksat was significantly (p < 0.05) influenced by location with mean values of 68 cmhr⁻¹,121.63 cmhr⁻¹, 8.42 cmhr⁻¹ in OV, OB and UNN respectively. The MWD and aggregate stability (AS) were significantly (p < 0.05) influenced by land use and depth. The mean values of MWD are 0.85 (CL), 1.35 (FL) and 1.45 (GL), and 1.66 at 0-10 cm, 1.08 at 10-20 cm and 0.88 mm at 20-30 cm. The mean values of AS are; 27.66% (CL), 46.39% (FL) and 49.81% (GL), and 53.96% at 0-10cm, 40.22% at 10-20cm and 29.57% at 20-30cm. Clay flocculation (CFI) and dispersion indices (CDI) differed significantly (p < 0.05) among the land use. Soil pH differed significantly (p < 0.05) across the land use and locations with mean values ranging from 3.90-6.14. Soil organic carbon (SOC) significantly (p < 0.05) differed across locations and depths. SOC decreases as depth increases depth with mean values of 15.6 gkg⁻¹, 10.1 gkg⁻¹, and 8.6 gkg⁻¹ at 0-10 cm, 10-20 cm, and 20-30 cm respectively. SOC in the three land use was 8.8 g kg-1, 15.2 gkg⁻¹ and 10.4 gkg⁻¹ at CL, FL, and GL respectively. The highest aggregate-associated carbon was recorded in 0.5 mm across the land use and depth except in cultivated land and at 20-30 cm which recorded their highest SOC at 1mm. SOC stock, total nitrogen (TN) and CEC were significantly (p < 0.05) different across the locations with highest values of 23.43 t/ha, 0.07g/kg and 14.27 Cmol/kg respectively recorded in UNN. SOC stock was significantly (p < 0.05) influenced by depth as follows; 0-10>10-20>20-30 cm. TN was low with mean values ranging from 0.03-0.07 across the locations, land use and depths. The mean values of CEC ranged from 9.96-14.27 Cmol kg⁻¹ across the locations and land use. SOC stock showed correlation with silt, coarse sand, N and CEC (r = 0.40*, -0.39*, -0.65** and 0.64** respectively. AS showed correlation with BD, Ksat, pH in water and KCl, and SOC (r = -0.42*, 0.54**, -0.44*, -0.45* and 0.49** respectively. Thus, land use and location play a significant role in sustainable management of soil resources.

Keywords: agricultural practices, structural dynamics, sequestration, soil resources, management

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Authors: Leo Nnamdi Ozurumba-Dwight

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Messenger ribooxynucleic acid (mRNA) molecules are compositional, protein-based. These proteins, encoding mRNA molecules (which collectively connote the transcriptome), when analyzed by RNA sequencing (RNAseq), unveils the nature of gene expression in the RNA. The obtained gene expression provides clues of cellular traits and their dynamics in presentations. These can be studied in relation to function and responses. RNAseq is a practical concept in Genomics as it enables detection and quantitative analysis of mRNA molecules. Single cell and spatial transcriptomics both present varying avenues for expositions in genomic characteristics of single cells and pooled cells in disease conditions such as cancer, auto-immune diseases, hematopoietic based diseases, among others, from investigated biological tissue samples. Single cell transcriptomics helps conduct a direct assessment of each building unit of tissues (the cell) during diagnosis and molecular gene expressional studies. A typical technique to achieve this is through the use of a single-cell RNA sequencer (scRNAseq), which helps in conducting high throughput genomic expressional studies. However, this technique generates expressional gene data for several cells which lack presentations on the cells’ positional coordinates within the tissue. As science is developmental, the use of complimentary pre-established tissue reference maps using molecular and bioinformatics techniques has innovatively sprung-forth and is now used to resolve this set back to produce both levels of data in one shot of scRNAseq analysis. This is an emerging conceptual approach in methodology for integrative and progressively dependable transcriptomics analysis. This can support in-situ fashioned analysis for better understanding of tissue functional organization, unveil new biomarkers for early-stage detection of diseases, biomarkers for therapeutic targets in drug development, and exposit nature of cell-to-cell interactions. Also, these are vital genomic signatures and characterizations of clinical applications. Over the past decades, RNAseq has generated a wide array of information that is igniting bespoke breakthroughs and innovations in Biomedicine. On the other side, spatial transcriptomics is tissue level based and utilized to study biological specimens having heterogeneous features. It exposits the gross identity of investigated mammalian tissues, which can then be used to study cell differentiation, track cell line trajectory patterns and behavior, and regulatory homeostasis in disease states. Also, it requires referenced positional analysis to make up of genomic signatures that will be sassed from the single cells in the tissue sample. Given these two presented approaches to RNA transcriptomics study in varying quantities of cell lines, with avenues for appropriate resolutions, both approaches have made the study of gene expression from mRNA molecules interesting, progressive, developmental, and helping to tackle health challenges head-on.

Keywords: transcriptomics, RNA sequencing, single cell, spatial, gene expression.

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Authors: Valentina A. Mikhailova, Serguei V. Feskov, Anatoly I. Ivanov

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In the last decade the nonequilibrium charge transfer have attracted considerable interest from the scientific community. Examples of such processes are the charge recombination in excited donor-acceptor complexes and the intramolecular electron transfer from the second excited electronic state. In these reactions the charge transfer proceeds predominantly in the nonequilibrium mode. In the excited donor-acceptor complexes the nuclear nonequilibrium is created by the pump pulse. The intramolecular electron transfer from the second excited electronic state is an example where the nuclear nonequilibrium is created by the forward electron transfer. The kinetics of these nonequilibrium reactions demonstrate a number of peculiar properties. Most important from them are: (i) the absence of the Marcus normal region in the free energy gap law for the charge recombination in excited donor-acceptor complexes, (ii) extremely low quantum yield of thermalized charge separated state in the ultrafast charge transfer from the second excited state, (iii) the nonexponential charge recombination dynamics in excited donor-acceptor complexes, (iv) the dependence of the charge transfer rate constant on the excitation pulse frequency. This report shows that most of these kinetic features can be well reproduced in the framework of stochastic point-transition multichannel model. The model involves an explicit description of the nonequilibrium excited state formation by the pump pulse and accounts for the reorganization of intramolecular high-frequency vibrational modes, for their relaxation as well as for the solvent relaxation. The model is able to quantitatively reproduce complex nonequilibrium charge transfer kinetics observed in modern experiments. The interpretation of the nonequilibrium effects from a unified point of view in the terms of the multichannel point transition stochastic model allows to see similarities and differences of electron transfer mechanism in various molecular donor-acceptor systems and formulates general regularities inherent in these phenomena. The nonequilibrium effects in photoinduced ultrafast charge transfer which have been studied for the last 10 years are analyzed. The methods of suppression of the ultrafast charge recombination, similarities and dissimilarities of electron transfer mechanism in different molecular donor-acceptor systems are discussed. The extremely low quantum yield of the thermalized charge separated state observed in the ultrafast charge transfer from the second excited state in the complex consisting of 1,2,4-trimethoxybenzene and tetracyanoethylene in acetonitrile solution directly demonstrates that its effectiveness can be close to unity. This experimental finding supports the idea that the nonequilibrium charge recombination in the excited donor-acceptor complexes can be also very effective so that the part of thermalized complexes is negligible. It is discussed the regularities inherent to the equilibrium and nonequilibrium reactions. Their fundamental differences are analyzed. Namely the opposite dependencies of the charge transfer rates on the dynamical properties of the solvent. The increase of the solvent viscosity results in decreasing the thermal rate and vice versa increasing the nonequilibrium rate. The dependencies of the rates on the solvent reorganization energy and the free energy gap also can considerably differ. This work was supported by the Russian Science Foundation (Grant No. 16-13-10122).

Keywords: Charge recombination, higher excited states, free energy gap law, nonequilibrium

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Authors: Mohammad Ebrahim Arbabian

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This paper investigates the impact of 3D printing, also known as additive manufacturing, on a multi-item supply chain comprising a manufacturer and retailer. Operating under a wholesale-price contract and catering to stochastic customer demand, this study delves into the largely unexplored realm of how 3D printing technology reshapes supply chain dynamics. A distinguishing aspect of 3D printing is its versatility in producing various product types, yet its slower production pace compared to traditional methods poses a challenge. We analyze the trade-off between 3D printing's limited capacity and its enhancement of production flexibility. By delineating the economic circumstances favoring 3D printing adoption by the manufacturer, we establish the Stackelberg equilibrium in the retailer-manufacturer game. Additionally, we determine optimal order quantities for the retailer considering 3D printing as an option for the manufacturer, ascertain optimal wholesale prices in the presence of 3D printing, and compute optimal profits for both parties involved in the supply chain.

Keywords: additive manufacturing, supply chain management, contract theory, Stackelberg game, optimization

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Authors: Sedat Yayla, Azhin Abdullah

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In the process of constructing hydroelectric power plants, the Pelton turbine, which is characterized by its simple manufacturing and construction, is performed in high head and low water flow. Parameters of the turbine have to be comprised in the designing process for obtaining hydraulic turbine with the highest efficiency during different operating conditions. The present investigation applied three-dimensional computational fluid dynamics (CFD). In addition, the bucket of Pelton turbine models with different splitter angle and inlet velocity values were examined for determining the force and visualizing the flow pattern on the bucket. The study utilized two diverse bucket models at various inlet velocities (20, 25, 30,35and 40m/s) and four different splitter angles (55, 75,90and 115 degree) for finding out the impacts of every single parameter on the effective force on the bucket. The acquired outcomes revealed that there is a linear relationship between force and inlet velocity on the bucket. Furthermore, the results also uncovered that the relationship between splitter angle and force on the bucket is linear until 90 degree.

Keywords: bucket design, computational fluid dynamics (CFD), free surface flow, two-phase flow, volume of fluid (VOF)

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Authors: Atul K. Desai, Jigar K. Sevalia, Sandip A. Vasanwala

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When a building is located in an urban area, it is exposed to a wind of different characteristics then wind over an open terrain. This is development of turbulent wake region behind an upstream building. The interaction with upstream building can produce significant changes in the response of the tall building. Here, in this paper, an attempt has been made to study wind induced interference effects on tall building. In order to study wind induced interference effect (IF) on Tall Building, initially a tall building (which is termed as Principal Building now on wards) with square plan shape has been considered with different Height to Width Ratio and total drag force is obtained considering different terrain conditions as well as different incident wind direction. Then total drag force on Principal Building is obtained by considering adjacent building which is termed as Interfering Building now on wards with different terrain conditions and incident wind angle. To execute study, Computational Fluid Dynamics (CFD) Code namely Fluent and Gambit have been used.

Keywords: computational fluid dynamics, tall building, turbulent, wake region, wind

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Authors: Rosario Rivera Rubite, Ching-I Peng, Che-Wei Lin, Mark Hughes, Yoshiko Kono, Kuo-Fang Chung

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The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.

Keywords: conservation, endemic , herbarium , limestone, phylogenetics, taxonomy

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Authors: Revant Nayar

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In this work, we recast the equations describing large scale structure, and by extension all nonlinear fluids, in the path integral formalism. We first calculate the well known two and three point functions using Schwinger Keldysh formalism used commonly to perturbatively solve path integrals in non- equilibrium systems. Then we include EFT corrections due to pressure, viscosity, and noise as effects on the time-dependent propagator. We are able to express results for arbitrary two and three point correlation functions in LSS in terms of differential operators acting on a triple K master intergral. We also, for the first time, get analytical results for more general initial conditions deviating from the usual power law P∝kⁿ by introducing a mass scale in the initial conditions. This robust field theoretic formalism empowers us with tools from strongly coupled QFT to study the strongly non-linear regime of LSS and turbulent fluid dynamics such as OPE and holographic duals. These could be used to capture fully the strongly non-linear dynamics of fluids and move towards solving the open problem of classical turbulence.

Keywords: quantum field theory, cosmology, effective field theory, renormallisation

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Authors: Luther Ollier, Sylvie Thiria, Anastase Charantonis, Carlos E. Mejia, Michel Crépon

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Sea Surface Height Anomaly (SLA) is a signature of the sub-mesoscale dynamics of the upper ocean. Sea Surface Temperature (SST) is driven by these dynamics and can be used to improve the spatial interpolation of SLA fields. In this study, we focused on the temporal evolution of SLA fields. We explored the capacity of deep learning (DL) methods to predict short-term SLA fields using SST fields. We used simulated daily SLA and SST data from the Mercator Global Analysis and Forecasting System, with a resolution of (1/12)◦ in the North Atlantic Ocean (26.5-44.42◦N, -64.25–41.83◦E), covering the period from 1993 to 2019. Using a slightly modified image-to-image convolutional DL architecture, we demonstrated that SST is a relevant variable for controlling the SLA prediction. With a learning process inspired by the teaching-forcing method, we managed to improve the SLA forecast at five days by using the SST fields as additional information. We obtained predictions of a 12 cm (20 cm) error of SLA evolution for scales smaller than mesoscales and at time scales of 5 days (20 days), respectively. Moreover, the information provided by the SST allows us to limit the SLA error to 16 cm at 20 days when learning the trajectory.

Keywords: deep-learning, altimetry, sea surface temperature, forecast

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Authors: Imme Petersen, Wiebke Sick, Regine Kollek

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In systems medicine, high-throughput technologies produce large amounts of data on different biological and pathological processes, including (disturbed) gene expressions, metabolic pathways and signaling. The large volume of data of different types, stored in separate databases and often located at different geographical sites have posed new challenges regarding data handling and processing. Tools based on bioinformatics have been developed to resolve the upcoming problems of systematizing, standardizing and integrating the various data. However, the heterogeneity of data gathered at different levels of biological complexity is still a major challenge in data analysis. To build multilayer disease modules, large and heterogeneous data of disease-related information (e.g., genotype, phenotype, environmental factors) are correlated. Therefore, a great deal of attention in systems medicine has been put on data standardization, primarily to retrieve and combine large, heterogeneous datasets into standardized and incorporated forms and structures. However, this data-centred concept of standardization in systems medicine is contrary to the debate in science and technology studies (STS) on standardization that rather emphasizes the dynamics, contexts and negotiations of standard operating procedures. Based on empirical work on research consortia that explore the molecular profile of diseases to establish systems medical approaches in the clinic in Germany, we trace how standardized data are processed and shaped by bioinformatics tools, how scientists using such data in research perceive such standard operating procedures and which consequences for knowledge production (e.g. modeling) arise from it. Hence, different concepts and meanings of standardization are explored to get a deeper insight into standard operating procedures not only in systems medicine, but also beyond.

Keywords: data, science and technology studies (STS), standardization, systems medicine

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Authors: Nigel Q. Kelly, Zaid Siddiqi, Jin W. Lee

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It is known that using Coanda aerosurfaces can drastically augment the lift forces when applied to an Unmanned Aerial Vehicle (UAV) platform. However, Coanda saucer UAVs, which commonly use a dish-like, radially-extending structure, have shown no significant increases in thrust/lift force and therefore have never been commercially successful: the additional thrust/lift generated by the Coanda surface diminishes since the airstreams emerging from the rotor compartment expand radially causing serious loss of momentums and therefore a net loss of total thrust/lift. To overcome this technical weakness, we propose to examine a Coanda surface of straight, cylindrical design and optimize its geometry for highest thrust/lift utilizing computational fluid dynamics software ANSYS Fluent®. The results of this study reveal that a Coanda UAV configured with 4 sides of straight, cylindrical Coanda surface achieve an overall 45% increase in lift compared to conventional Coanda Saucer UAV configurations. This venture integrates with an ongoing research project where a Coanda prototype is being assembled. Additionally, a custom thrust-stand has been constructed for thrust/lift measurement.

Keywords: CFD, Coanda, lift, UAV

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Authors: Hyeon Su Kim, Sungjin Park, Hae Ryung Chang, Hae Rim Jung, Young Zoo Ahn, Yon Hui Kim, Seungyoon Nam

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Ependymoma, one of the most common parenchymal spinal cord tumor, represents 3-6% of all CNS tumor. Especially intracranial ependymomas, which are more frequent in childhood, have a more poor prognosis and more malignant than spinal ependymomas. Although there are growing needs to understand pathogenesis, detailed molecular understanding of pathogenesis remains to be explored. A cancer cell is composed of complex signaling pathway networks, and identifying interaction between genes and/or proteins are crucial for understanding these pathways. Therefore, we explored each ependymoma in terms of differential expressed genes and signaling networks. We used Microsoft Excel™ to manipulate microarray data gathered from NCBI’s GEO Database. To analyze and visualize signaling network, we used web-based PATHOME algorithm and Cytoscape. We show HOX family and NEFL are down-regulated but SCL family is up-regulated in cerebrum and posterior fossa cancers over a spinal cancer, and JAK/STAT signaling pathway and Chemokine signaling pathway are significantly different in the both intracranial ependymoma comparing to spinal ependymoma. We are considering there may be an age-dependent mechanism under different histological pathogenesis. We annotated mutation data of each gene subsequently in order to find potential target genes.

Keywords: systems biology, ependymoma, deg, network analysis

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Authors: T. Y. Liu, C. H. Lin, Y. M. Ferng

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Wind energy is one of the clean renewable energy. However, the low frequency (20-200HZ) noise generated from the wind turbine blades, which bothers the residents, becomes the major problem to be developed. It is useful for predicting the aerodynamic noise by flow field and pressure distribution analysis on the wind turbine blades. Therefore, the main objective of this study is to use different turbulence models to analyse the flow field and pressure distributions of the wing blades. Three-dimensional Computation Fluid Dynamics (CFD) simulation of the flow field was used to calculate the flow phenomena for the National Renewable Energy Laboratory (NREL) Phase VI horizontal axis wind turbine rotor. Two different flow cases with different wind speeds were investigated: 7m/s with 72rpm and 15m/s with 72rpm. Four kinds of RANS-based turbulence models, Standard k-ε, Realizable k-ε, SST k-ω, and v2f, were used to predict and analyse the results in the present work. The results show that the predictions on pressure distributions with SST k-ω and v2f turbulence models have good agreements with experimental data.

Keywords: horizontal axis wind turbine, turbulence model, noise, fluid dynamics

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Authors: Zhong-Dan Tu, Wang-Xi Fan, Yi-Chen Huang, Jen-Taut Yeh

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Novel ultrahigh molecular weight polyethylene (UHMWPE)/cellulose nanofiber (CNF) (F100CNFy) and UHMWPE/modified cellulose nanofiber (MCNF) (F100MCNFxy) as-prepared nanocomposite fibers were prepared by spinning F100CNFy and F100MCNFxy gel solutions, respectively. Cellulose nanofibers were successfully prepared by proper acid treatment of cotton fibers using sulfuric acid solutions. The best prepared CNF is with specific surface areas around 120 m2/g and a nanofiber diameter of 20 nm. Modified cellulose nanofiber was prepared by grafting maleic anhydride grafted polyethylene (PE-g-MAH) onto cellulose nanofibers. The achievable draw ratio (Dra) values of each F100MCNFxy as-prepared fiber series specimens approached a maximal value as their MCNF contents reached the optimal value at 0.05 phr. In which, the maximum Dra value obtained for F100MCNFx0.05 as-prepared fiber specimen prepared at the optimal MCNF content reached another maximum value as the weight ratio of PE-g-MAH to CNF approach an optimal value at 6. Similar to those found for the achievable drawing properties of the as-prepared fibers, the orientation factor, tensile strength (σ f) and initial modulus (E) values of drawn F100MCNF6y fiber series specimens with a fixed draw ratio reach a maximal value as their MCNF contents approach the optimal value, wherein the σ f and E values of the drawn F100MCNFxy fiber specimens are significantly higher than those of the drawn F100 fiber specimens and corresponding drawn F100CNFy fiber specimens prepared at the same draw ratios and CNF contents but without modification. To understand the interesting ultradrawing, thermal, orientation and tensile properties of F100CNFy and F100MCNFxy fiber specimens, Fourier transform infra-red, specific surface areas, and transmission electron microcopic analyses of the original and modified CNF nanofillers were performed in this study.

Keywords: ultradrawing, cellulose nanofibers, ultrahigh molecular weight polyethylene, nanocomposite fibers

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Authors: Hung-Jiun Chi, Cheng-En Tsai, Jia-Ying Tu

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Semi-active control of Magnetorheological (MR) dampers for vibration reduction of structural systems has received considerable attention in civil and earthquake engineering, because the effective stiffness and damping properties of MR fluid can change in a very short time in reaction to external loading, requiring only a low level of power. However, the inherent nonlinear dynamics of hysteresis raise challenges in the modeling and control processes. In order to control the MR damper, an innovative Duffing-like equation is proposed to approximate the hysteresis dynamics in a deterministic and systematic manner than previously has been possible. Then, the model-reference adaptive control technique based on the Duffing-like model and the Lyapunov method is discussed. Parameter identification work with experimental data is presented to show the effectiveness of the Duffing-like model. In addition, simulation results show that the resulting adaptive gains enable the MR damper force to track the desired response of the reference model satisfactorily, verifying the effectiveness of the proposed modeling and control techniques.

Keywords: magnetorheological damper, duffing equation, model-reference adaptive control, Lyapunov function, hysteresis

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Authors: Tannaz Alizadeh Ashrafi

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Seasonal variability in biological and ecological factors together with relevant socio-economic determinants affect the choice of fishing gear, frequency of its usage and decision about gear conversion under multi-species situation. In order to deal with the complex dynamics of fisheries, fishers, constantly, have to make decisions about how long to fish, when to go fishing, what species to target, and which gear to deploy. In this regard, the purpose of this study is to examine the dynamics of gear/ species combination in Norwegian fishery. A comprehensive vessel-level set of data for the main economically important species including: cod, haddock, saithe, shrimp and mixed catch have been obtained from the Norwegian Directorate of Fisheries covering the daily data in 2010. The present study further analyzes the level of flexibility and rationality of the fishers operating in the trawl fishery. The results show the disproportion between intention of the trawl fishers to maximize profitability of each fishing trip and their harvesting behavior in reality. Discussion is based on so-called maximizing behavior.

Keywords: trawl fishery, gear substitution, rationality, profit maximizing behavior

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Authors: Fatimah A. Alhomaid

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The present study was planned to investigate the role of molecular changes and immunohistochemical in early detection of liver cancer in Saudi patients. our results were carried out on 54 patients liver cancer. We obtained our data from laboratory in King Khalid University Hospital. The specimens were taken (54) patients with liver cancer 34 male and 14 female and 2 control. The average age of varied from 37-85 years. The tumor was diagnosed as grade I in tow patients (male and female) and grade 2 in 45 patients (28 male and 17 female) while the grade 3 in 4 patients (all males). The specimens were processed for haematoxylin and eosin staining, immunohistochemical technique and flow cytometry analysis. Our study noted that most patients had adenocarcinoma which characterized by presence of signet-ring cells were very clear in advanced patients with adenocarcinoma. Our sections in adenocarcinoma in grade 2 and stage 3 had an increase in signet ring cells,an increase in the acini of glands and an increase in number of lymphocytes which spread to the muscular layer. With advancing the disease, there were haemorrhage in blood and increase in lymphocytes and increase in the number of nuclei in the tubular glands. Our study was carried on 48 patients, immunohistochemical diagnosis (CK20, PCNA, P53) and the analysis of DNA content by flow cytometry technique. Our study indicated that the presence of correlation between the immunohistochemical analysis for P53 and the grades. The reaction of P53 appeared as strong in nucleus in grades &stage 3 and appeared in other sections as dark brown pigment. Our study indicated that the absence of correlation between the immunohistochemical analysis for PCAN and the grades. In our sections there were strong reaction in the more 80% of nuclei in grade 1& stage 2. Our study indicated that the presence of correlation between the immunohistochemical analysis for CK20 and the grades. Our results indicated the presence of positive reaction in cytoplasm varied from weak to moderate in grade 3 & stage 4. Concerning the Flow cytometry technique our results indicated that the presence of correlation between the DNA and different stages of liver cancer.

Keywords: cancer, CK20, DNA, cytometry analysis, liver, immunohistochemical, molecular changes, PCNA, p53

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Authors: Arpita Roy, Navneeta Bharadvaja

Abstract:

Cancer is an uncontrolled growth of abnormal cells in the body. It is one of the most serious diseases on which extensive research work has been going on all over the world. Structure-based drug designing is a computational approach which helps in the identification of potential leads that can be used for the development of a drug. Plumbagin is a naphthoquinone derivative from Plumbago zeylanica roots and belongs to one of the largest and diverse groups of plant metabolites. Anticancer and antiproliferative activities of plumbagin have been observed in animal models as well as in cell cultures. Plumbagin shows inhibitory effects on multiple cancer-signaling proteins; however, the binding mode and the molecular interactions have not yet been elucidated for most of these protein targets. In this investigation, an attempt to provide structural insights into the binding mode of plumbagin against four cancer receptors using molecular docking was performed. Plumbagin showed minimal energy against targeted cancer receptors, therefore suggested its stability and potential towards different cancers. The least binding energies of plumbagin with COX-2, TACE, and CDK6 are -5.39, -4.93, -and 4.81 kcal/mol, respectively. Comparison studies of plumbagin with different receptors showed that it is a promising compound for cancer treatment. It was also found that plumbagin obeys the Lipinski’s Rule of 5 and computed ADMET properties which showed drug likeliness and improved bioavailability. Since plumbagin is from a natural source, it has reduced side effects, and these results would be useful for cancer treatment.

Keywords: cancer, receptor, plumbagin, docking

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Authors: Md. Baki Billah, Suraiya Parveen, Shuvra Kanti Dey

Abstract:

Bangladesh is earning a lot of foreign currency by exporting shrimp, but this industry is facing a tremendous problem due to the infection of white spot syndrome virus (WSSV). This study was undermined to develop rapid detection method of WSSV. A total of shrimp samples 240 collected from the 12 shrimp farms of different coastal regions (Satkhira, Khulna, and Bagerhat) were analyzed by conventional PCR using VP28 and VP664 gene-specific primers. In satkhira, Bagerhat and Khulna 39, 41 and 29 samples were found WSSV positive respectively. Real-time PCR using 71-bp amplicon for VP664 gene correlated well with conventional PCR data. The prevalence rates of WSSV among the collected 240 samples were Satkhira 38%, Khulna 47% and Bagerhat 50%. Molecular analysis of the VP28 gene sequences of WSSV revealed that Bangladeshi strains phylogenetically affiliated to the strains belong to India. This work concluded that WSSV infections are widely distributed in the coastal regions cultured shrimp in Bangladesh. Physico-chemical parameters were within the range of fish culture.

Keywords: coastal regions of Bangladesh, PCR, shrimp, white spot syndrome virus

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Authors: Eleni Stefanidou, Nikolaos Katsenios, Ioanna Karamichali, Aspasia Efthimiadou, Panagiotis Madesis

Abstract:

The excessive use of pesticides and fertilizers has significant environmental and human health-related negative effects. In the frame of the development of sustainable agriculture practices, especially in the context of extreme environmental changes (climate change), it is important to develop alternative practices to increase productivity and biotic and abiotic stress tolerance. Beneficial bacteria, such as symbiotic bacteria in legumes (rhizobia) and symbiotic or free-living Plant Growth Promoting Rhizobacteria (PGPR), which could act as "plant probiotics", can promote plant growth and significantly increase the resistance of crops under adverse environmental conditions. In this study, we explored the symbiotic relationships between Faba bean (Vicia faba L.) cultivars with different PGPR bacteria, aiming to identify the possible influence on yield and biotic-abiotic phytoprotection benefits. Transcriptomic analysis of root and whole plant samples was executed for two Vicia faba L. cultivars (Polikarpi and Solon) treated with selected PGPR bacteria (6 treatments: B. subtilis + Rhizobium-mixture, A. chroococcum + Rhizobium-mixture, B. subtilis, A. chroococcum and Rhizobium-mixture). Preliminary results indicate a significant yield (Seed weight and Total number of pods) increase in both varieties, ranging around 25%, in comparison to the control, especially for the Solon cultivar. The increase was observed for all treatments, with the B. subtilis + Rhizobium-mixture treatment being the highest performing. The correlation of the physiological and morphological data with the transcriptome analysis revealed molecular mechanisms and molecular targets underlying the observed yield increase, opening perspectives for the use of nitrogen-fixing bacteria as a natural, more ecological enhancer of legume crop productivity.

Keywords: plant probiotics, PGPR, legumes, sustainable agriculture

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Authors: Lola T. Alimkhodjaeva, Lola T. Zakirova, Soniya S. Ziyavidenova

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Background: Breast cancer occupies the first place among the cancer in women in the world. It is urgent today to study the role of molecular markers which are capable of predicting the dynamics and outcome of the disease. The aim of this study is to define the prognostic value of the content of estrogen receptor (ER), progesterone receptor (PgR), and amplification of HER-2 / neu oncoprotein by studying 3 and 5-year overall and relapse-free survival in 470 patients with primary operable and 280 patients with locally–advanced breast cancer. Materials and methods: Study results of 3 and 5-year overall and relapse-free survival, depending on the content of RE, PgR in primary operable patients showed that ER positive (+) and PgR (+) survival was 100 (96.2%) and 97.3 (94.6%), for ER negative (-) and PgR (-) - 69.2 (60.3%) and 65.4 (57.7%), for ER positive (+) and negative PgR (-) 87.4 (80.1%) and 81.5 (79.3%), for ER negative (-) and positive PgR (+) - 97.4 (93.4%) and 90.4 (88.5%), respectively. Survival results depended also on the level of HER-2 / neu expression. In patients with HER-2 / neu negative the survival rates were as follows: 98.6 (94.7%) and 96.2 (92.3%). In group of patients with the level of HER-2 / neu (2+) expression these figures were: 45.3 (44.3%) and 45.1 (40.2%), and in group of patients with the level of HER-2 / neu (3+) expression - 41.2 (33.1%) and 34.3 (29.4%). The combination of ER negative (-), PgR (-), HER-2 / neu (-) they were 27.2 (25.4%) and 19.5 (15.3%), respectively. In patients with locally-advanced breast cancer the results of 3 and 5-year OS and RFS for ER (+) and PgR (+) were 76.3 (69.3%) and 62.2 (61.4%), for ER (-) and RP (-) 29.1 (23.7%) and 18.3 (12.6%), for ER (+) and PgR (-) 61.2 (47.2%) and 39.4 (25.6%), for ER (-) and PgR (+) 54.3 (43.1%) and 41.3 (18.3%), respectively. The level of HER-2 / neu expression also affected the survival results. Therefore, in HER-2/ neu negative patients the survival rate was 74.1 (67.6%) and 65.1 (57.3%), with the level of expression (2+) 20.4 (14.2%) and 8.6 (6.4%), with the level of expression (3+) 6.2 (3.1%) and 1.2 (1.5%), respectively. The combination for ER, PgR, HER-2 / neu negative was 22.1 (14.3%) and 8.4 (1.2%). Conclusion: Thus, the presence of steroid hormone receptors in breast tumor tissues at primary operable and locally- advanced process as the lack of HER-2/neu oncoprotein correlates with the highest rates of 3- and 5-year overall and relapse-free survival. The absence of steroid hormone receptors as well as of HER-2/neu overexpression in malignant breast tissues significantly degrades the 3- and 5-year overall and relapse-free survival. Tumors with ER, PgR and HER-2/neu negative have the most unfavorable prognostics.

Keywords: breast cancer, estrogen receptor, oncoprotein, progesterone receptor

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Authors: Ramin Mehdiabadi, Neda Menbari, Mohammad Nazir Menbari

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As a pressing public health concern, breast cancer stands as the predominant oncological diagnosis and principal cause of cancer-related mortality among women globally, accounting for 11.7% of new cancer incidences and 6.9% of cancer-related deaths. The annual figures indicate that approximately 230,480 women are diagnosed with breast cancer in the United States alone, with 39,520 succumbing to the disease. While developed economies have reported a deceleration in both incidence and mortality rates across various forms of cancer, including breast cancer, emerging and low-income economies manifest a contrary escalation, largely attributable to lifestyle-mediated risk factors such as tobacco usage, physical inactivity, and high caloric intake. Breast cancer is distinctly characterized by molecular heterogeneity, manifesting in specific subtypes delineated by biomarkers—Estrogen Receptors (ER), Progesterone Receptors (PR), and Human Epidermal Growth Factor Receptor 2 (HER2). These subtypes, comprising Luminal A, Luminal B, HER2-enriched, triple-negative/basal-like, and normal-like, necessitate nuanced, subtype-specific therapeutic regimens, thereby challenging the applicability of generalized treatment protocols. Within this molecular complexity, the transcription factor Forkhead Box M1 (FoxM1) has garnered attention as a significant driver of cellular proliferation, tumorigenesis, metastatic progression, and treatment resistance in a spectrum of human malignancies, including breast cancer. Concurrently, microRNAs (miRs), specifically miR-216b-5p, have been identified as post-transcriptional gene expression regulators and potential tumor suppressors. The overarching objective of this academic investigation is to explicate the multifaceted interrelationship between FoxM1 and miR-216b-5p across the disparate molecular subtypes of breast cancer. Employing a methodologically rigorous, interdisciplinary research design that incorporates cutting-edge molecular biology techniques, sophisticated bioinformatics analytics, and exhaustive meta-analyses of extant clinical data, this scholarly endeavor aims to unveil novel biomarker-specific therapeutic pathways. By doing so, this research is positioned to make a seminal contribution to the advancement of personalized, efficacious, and minimally toxic treatment paradigms, thus profoundly impacting the global efforts to ameliorate the burden of breast cancer.

Keywords: breast cancer, fox m1, microRNAs, mir-216b-5p, gene expression

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Authors: Masoud Sheidai, Fahimeh Koohdar, Hashem Sharifi

Abstract:

Juglans regia (L.) commonly known as Persian walnut of the genus Juglans L. (Juglandaceae) is one of the most important cultivated plant species due to its high-quality wood and edible nuts. The genetic diversity analysis is essential for conservation and management of tree species. Persian walnut is native from South-Eastern Europe to North-Western China through Tibet, Nepal, Northern India, Pakistan, and Iran. The species like Persian walnut, which has a wide range of geographical distribution, should harbor extensive genetic variability to adapt to environmental fluctuations they face. We aimed to study the population genetic structure of seven Persian walnut populations including three wild and four cultivated populations by using ISSR (Inter simple sequence repeats) and SRAP (Sequence related amplified polymorphism) molecular markers. We also aimed to compare the genetic variability revealed by ISSR neutral multilocus marker and rDNA ITS sequences. The studied populations differed in morphological features as the samples in each population were clustered together and were separate from the other populations. Three wild populations studied were placed close to each other. The mantel test after 5000 times permutation performed between geographical distance and morphological distance in Persian walnut populations produced significant correlation (r = 0.48, P = 0.002). Therefore, as the populations become farther apart, they become more divergent in morphological features. ISSR analysis produced 47 bands/ loci, while we obtained 15 SRAP bands. Gst and other differentiation statistics determined for these loci revealed that most of the ISSR and SRAP loci have very good discrimination power and can differentiate the studied populations. AMOVA performed for these loci produced a significant difference (< 0.05) supporting the above-said result. AMOVA produced significant genetic difference based on ISSR data among the studied populations (PhiPT = 0.52, P = 0.001). AMOVA revealed that 53% of the total variability is due to among population genetic difference, while 47% is due to within population genetic variability. The results showed that both multilocus molecular markers and ITS sequences can differentiate Persian walnut populations. The studied populations differed genetically and showed isolation by distance (IBD). ITS sequence based MP and Bayesian phylogenetic trees revealed that Iranian walnut cultivars form a distinct clade separated from the cultivars studied from elsewhere. Almost all clades obtained have high bootstrap value. The results indicated that a combination of multilpcus and sequencing molecular markers can be used in genetic differentiation of Persian walnut.

Keywords: genetic diversity, population, molecular markers, genetic difference

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Authors: Paolo Russu

Abstract:

This paper investigates the economic and ecological dynamics that emerge in Protected Areas (PAs) due to interactions between visitors and the animals that live there. The PAs contain two species whose interactions are determined by the Lotka-Volterra equations system. Visitors' decisions to visit PAs are influenced by the entrance cost required to enter the park and the chance of witnessing the species living there. Visitors have contradictory effects on the species and thus on the sustainability of the protected areas: on the one hand, an increase in the number of tourists damages the natural habitat of the regions and thus the species living there; on the other hand, it increases the total amount of entrance fees that the managing body of the PAs can use to perform defensive expenditures that protect the species from extinction. For a given set of parameter values, saddle-node bifurcation, Hopf bifurcation, homoclinic orbits, and a Bogdanov–Takens bifurcation of codimension two has been investigated. The system displays periodic doubling and chaotic solutions, as numerical examples demonstrate. Pontryagin's Maximum Principle was utilised to develop an optimal admission charge policy that maximised social gain and ecosystem conservation.

Keywords: chaos, bifurcation points, dynamical model, optimal control

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Authors: Xie Kai, Laith K. Abbas, Chen Dongyang, Yang Fufeng, Rui Xiaoting

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Effect of plunging motion on the pitch oscillating NACA0012 airfoil is investigated using computational fluid dynamics (CFD). A simulation model based on overset grid technology and k - ω shear stress transport (SST) turbulence model is established, and the numerical simulation results are compared with available experimental data and other simulations. Two cases of phase angle φ = 0, μ which represents the phase difference between the pitching and plunging motions of an airfoil are performed. Airfoil vortex generation, moving, and shedding are discussed in detail. Good agreements have been achieved with the available literature. The upward plunging motion made the equivalent angle of attack less than the actual one during pitching analysis. It is observed that the formation of the stall vortex is suppressed, resulting in a decrease in the lift coefficient and a delay of the stall angle. However, the downward plunging motion made the equivalent angle of attack higher the actual one.

Keywords: dynamic stall, pitching-plunging, computational fluid dynamics, helicopter blade rotor, airfoil

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Authors: Bharti Saini, Sukanta K. Dash

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In this work polymeric Nanofiltration (NF) membranes of polysulfone (PSF) (average molecular weight of 22400 Da) were prepared using polyethylene glycol (PEG) (average molecular weight of 200 Da) as an organic additive and ZnCl2 as an inorganic additive. Dimethyl acetamide (DMAc) was used as the solvent, and Deionised water as nonsolvent. The membranes were prepared by phase inversion (immersion precipitation) method. PEG 200 and ZnCl2 in varying concentration are directly added into the casting solution of PSF and DMAc. PEG 200 was used in concentration varying from 0 to 10 % (w/w) in the solution of PSF and DMAc, while ZnCl2 is varied from 0 to 2% (w/w). Membranes were characterized for surface morphology, water uptake, porosity and contact angle, with respect to concentration of PEG and ZnCl2. It was observed that with the increase in additive PEG 200, the porosity and hence, hydrophilicity increase. As a result, the number of pores increases as justified by the SEM analysis as well. The study revealed that the synergistic effect of PEG with ZnCl2 is more effective, and the best results were produced by the solution containing 2% PEG 200 and 1% ZnCl2. It was inferred that with the increase in concentration of additives, the pore size goes on decreasing. The membranes obtained gradually move from microfiltration range to nanofiltration range, and this change is primarily brought about by the addition of ZnCl2.

Keywords: membrane, phase inversion method, polysulfone, porous structure

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