Search results for: molecular and supramolecular structure

Authors: A. Chouaih, N. Benhalima, N. Boukabcha, R. Rahmani, F. Hamzaoui

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Zwitterionic compounds have received the interest of chemists and physicists due to their applications as nonlinear optical materials. Recently, zwitterionic compounds exhibiting high nonlinear optical activity have been investigated. In this context, the molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment have been determined in order to understand the nature of inter- and intramolecular charge transfer. The study reveals the nature of intermolecular interactions including charge transfer and hydrogen bonds in the title compound. In this crystal, the molecules form dimers via intermolecular hydrogen bonds. The dimers are further linked by C–H...O hydrogen bonds into chains along the c crystallographic axis. This study has also allowed us to determine various nonlinear optical properties such as molecular electrostatic potential, polarizability, and hyperpolarizability of the title compound.

Keywords: organic compounds, polarizability, hyperpolarizability, dipole moment

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Authors: Ehsan Khademi, Mahdi Jalili

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Despite the special features of bipartite networks, they are common in many systems. Real-world bipartite networks may show community structure, similar to what one can find in one-mode networks. However, the interpretation of the community structure in bipartite networks is different as compared to one-mode networks. In this manuscript, we compare a number of available methods that are frequently used to discover community structure of bipartite networks. These networks are categorized into two broad classes. One class is the methods that, first, transfer the network into a one-mode network, and then apply community detection algorithms. The other class is the algorithms that have been developed specifically for bipartite networks. These algorithms are applied on a model network with prescribed community structure.

Keywords: community detection, bipartite networks, co-clustering, modularity, network projection, complex networks

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Authors: Nicola G. G. Cecca

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In Italian IPSSEOAs, high schools that give a vocational education to students that will work in the field of Enogastronomy and Hotel Management, the course of Food Science allows the students to start and see food as a mixture of substances that they will transform during their profession. These substances are characterized not only by a chemical composition but also by a molecular structure that makes them nutritionally active. But the increasing number of new products proposed by Food Industry, the modern techniques of production and transformation, the innovative preparations required by customers have made many information reported in the most wide spread Food Science textbooks not up-to-date or too poor for the people who will work in catering sector. Often Authors offer information aged to Bohr’s Atomic Model and to the ‘Octet Rule’ proposed by G.N. Lewis to describe the Chemical Bond, without giving any reference to new as Orbital Atomic Model and Molecular Orbital Theory that, in the meantime, start to be old themselves. Furthermore, this antiquated information precludes an easy understanding of a wide range of properties of nutritive substances and many reactions in which the food constituents are involved. In this paper, our attention is pointed out to use GEOMAG™ to represent the dynamics with which the chemical bond is formed during the synthesis of the molecules. GEOMAG™ is a toy, produced by the Swiss Company Geomagword S.A., pointed to stimulate in children, aged between 6-10 years, their fantasy and their handling ability and constituted by metallic spheres and metallic magnetic bars coated by coloured plastic materials. The simulation carried out with GEOMAG™ is based on the similitude existing between the Coulomb’s force and the magnetic attraction’s force and in particular between the formulae with which they are calculated. The electrostatic force (F in Newton) that allows the formation of the chemical bond can be calculated by mean Fc = kc q1 q2/d2 where: q1 e q2 are the charge of particles [in Coulomb], d is the distance between the particles [in meters] and kc is the Coulomb’s constant. It is surprising to observe that the attraction’s force (Fm) acting between the magnetic extremities of GEOMAG™ used to simulate the chemical bond can be calculated in the same way by using the formula Fm = km m1 m2/d2 where: m1 e m2 represent the strength of the poles [A•m], d is the distance between the particles [m], km = μ/4π in which μ is the magnetic permeability of medium [N•A-2]. The magnetic attraction can be tested by students by trying to keep the magnetic elements of GEOMAG™ separate by hands or trying to measure by mean an appropriate dynamometric system. Furthermore, by using a dynamometric system to measure the magnetic attraction between the GEOMAG™ elements is possible draw a graphic F=f(d) to verify that the curve obtained during the simulation is very similar to that one hypnotized, around the 1920’s by Linus Pauling to describe the formation of H2+ in according with Molecular Orbital Theory.

Keywords: chemical bond, molecular orbital theory, magnetic attraction force, GEOMAG™

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Authors: Anita Jäger, Andrew Salazar, Jörg von Hagen, Harald Kolmar

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In the treatment of individuals with sensitive and psoriatic skin, several inflammation and itch-related molecular and cellular targets have been identified, but many of these have yet to be characterized. In this study, we present two potential targets in the skin that can be linked to the inflammation and itch cycle. 11ßHSD1 is the enzyme responsible for converting inactive cortisone to active cortisol used to transmit signals downstream. The activation of the receptor NK1R correlates with promoting inflammation and the perception of itch and pain in the skin. In this study, both targets have been investigated based on their involvement in inflammation. The role of both identified targets was characterized based on the secretion of inflammation cytokine- IL6, IL-8, and CCL2, as well as phosphorylation and signaling pathways. It was found that treating skin cells with molecules able to inhibit inflammatory pathways results in the reduction of inflammatory signaling molecules secreted by skin cells and increases their proliferative capacity. Therefore, these molecular targets and their associated pathways show therapeutic potential and can be mitigated via small molecules. This research can be used for further studies in inflammation and itch pathways and can help to treat pathological symptoms.

Keywords: inflammation, itch, signaling pathway, skin

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Authors: Youngseok Kim, Chul Park, Jonghwa Yi, Sangsik Choi

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The 2-MHz Side Scan SONAR (SSS) attached to the boat for inspection of underwater structures is affected by shaking. It is difficult to determine the exact scale of damage of structure. In this study, a motion sensor is attached to the inside of the 2-MHz SSS to get roll, pitch, and yaw direction data, and developed the image stabilization tool to correct the sonar image. We checked that reliable data can be obtained with an average error rate of 1.99% between the measured value and the actual distance through experiment. It is possible to get the accurate sonar data to inspect damage in underwater structure.

Keywords: image stabilization, motion sensor, safety inspection, sonar image, underwater structure

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Authors: Li Feng, Cheng Zhang, Chuanzhou Yuang

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Understanding the macromolecular structure of low-rank coal is very important for its gasification and liquefaction. The pyrolysis is one of the methods of analyzing the macromolecular structure of coal. The gaseous products decomposed directly by the raw lignite at 500 °C and indirectly by tar products from raw lignite pyrolysis at 500 °C were investigated and compared by thermogravimetry, gas chromatography and mass spectrum coupled instrument system (TG/GC/MS) in this paper. The results show that 52 kinds of products were found from the raw lignite and 70 kinds of products from the tar. The pyrolysis products directly from the lignite appear more monocyclic aromatic hydrocarbons and less substituent groups or branch chain, compared with the products from the tar. There is less linear chain and double bonds structure in the tar, which can be speculated that linear chain and double bonds structure took part in the generation of condensed rings and other reactions. There are more kinds of phenol and furan in the tar, which indicate that these products may be generated from the secondary reaction. The formation process of phenol, phenol naphthalene, naphthene and furan are discussed.

Keywords: composition and structure, lignite, pyrolysis of coal, tar, TG/GC/MS

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Authors: Jennifer Cuellar, Angie L. Parada, Kevin N. S. Chacon, Sol M. Mejia

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The purification of bio-ethanol through distillation methods is an unresolved issue at the biofuel industry because of the ethanol-water azeotrope formation, which increases the steps of the purification process and subsequently increases the production costs. Therefore, understanding the mixture nature at the molecular level could provide new insights for improving the current methods and/or designing new and more efficient purification methods. For that reason, the present study focuses on the evaluation and analysis of (ethanol)₉-water heterodecamers, as the systems with the minimum molecular proportion that represents the azeotropic concentration (96 %m/m in ethanol). The computational modelling was carried out with B3LYP-D3/6-311++G(d,p) in Gaussian 09. Initial explorations of the potential energy surface were done through two methods: annealing simulated runs and molecular dynamics trajectories besides intuitive structures obtained from smaller (ethanol)n-water heteroclusters, n = 7, 8 and 9. The energetic order of the seven stable heterodecamers determines the most stable heterodecamer (Hdec-1) as a structure forming a bicyclic geometry with the O-H---O hydrogen bonds (HBs) where the water is a double proton donor molecule. Hdec-1 combines 1 water molecule and the same quantity of every ethanol conformer; this is, 3 trans, 3 gauche 1 and 3 gauche 2; its abundance is 89%, its decamerization energy is -80.4 kcal/mol, i.e. 13 kcal/mol most stable than the less stable heterodecamer. Besides, a way to understand why methanol does not form an azeotropic mixture with water, analogous systems ((ethanol)10, (methanol)10, and (methanol)9-water)) were optimized. Topologic analysis of the electron density reveals that Hec-1 forms 33 weak interactions in total: 11 O-H---O, 8 C-H---O, 2 C-H---C hydrogen bonds and 12 H---H interactions. The strength and abundance of the most unconventional interactions (H---H, C-H---O and C-H---O) seem to explain the preference of the ethanol for forming heteroclusters instead of clusters. Besides, O-H---O HBs present a significant covalent character according to topologic parameters as the Laplacian of electron density and the relationship between potential and kinetic energy densities evaluated at the bond critical points; obtaining negatives values and values between 1 and 2, for those two topological parameters, respectively.

Keywords: ADMP, DFT, ethanol-water azeotrope, Grimme dispersion correction, simulated annealing, weak interactions

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Authors: Oktira Roka Aji, Maelita R. Moeis, Ihsanawati, Ernawati A. Giri-Rachman

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Globally, tuberculosis (TB) remains a leading cause of death. The emergence of multidrug-resistant strains and extensively drug-resistant strains have become a major public concern. One of the potential candidates for drug target is the cytoplasmic domain of PhoR Histidine Kinase, a part of the Two Component System (TCS) PhoR-PhoP in Mycobacterium tuberculosis (Mtb). TCS PhoR-PhoP relay extracellular signal to control the expression of 114 virulent associated genes in Mtb. The 3D structure of PhoR cytoplasmic domain is needed to screen novel drugs using structure based drug discovery. The PhoR cytoplasmic domain from Mtb H37Rv was overexpressed in E. coli BL21(DE3), then purified using IMAC Ni-NTA Agarose his-tag affinity column and DEAE-ion exchange column chromatography. The molecular weight of the purified protein was estimated to be 37 kDa after SDS-PAGE analysis. This sample was used for pre-crystallization screening by applying sitting drop vapor diffusion method using Natrix (HR2-116) 48 solutions crystal screen kit at 25ºC. Needle-like crystals were observed after the seventh day of incubation in test solution No.47 (0.1 M KCl, 0.01 M MgCl2.6H2O, 0.05 M Tris-Cl pH 8.5, 30% v/v PEG 4000). Further testing is required for confirming the crystal.

Keywords: tuberculosis, two component system, histidine kinase, needle-like crystals

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Authors: A. G. Barua, Uttam Rajkhowa, Pranjal Moni Nath, Nur Abdul Kadir

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Mycobacterium tuberculosis (MTB) is one of the most closely-related intracellular bacterial pathogens, grouped as the M. tuberculosis complex (MTC). MTB, the primary agent of human tuberculosis (TB), can develop clinical TB in animals as 75 percent of canine mycobacterial infection is caused by close contact with an infected human being. In the present study, molecular detection of TB in dogs in three North-eastern states of India, Assam Mizoram, and Nagaland was carried out. So far, there has been a lack of systematic study in these regions, hampered by slow diagnostic methods and poor infrastructure. In an attempt to rectify this situation, molecular epidemiology was carried out for nine months to detect canine TB in a sample of 340 dogs. Isolation of DNA was done with swabs (throat/nasal), nodules of lungs and fluids from 100 suspected dogs and the molecular study were carried out with the help of conventional and real-time PCR. Post-mortem study was also carried out. Our results showed that the prevalence of clinical TB in dogs from a high-risk setting was 1 percent. However, the prevalence of immunological sensitization to M. tuberculosis antigen in dogs living in contact with sputum smeared positive TB cases was almost 50 percent. The latter setting had the maximum impact in terms of TB transmission. During the study period, a survey with a standard questionnaire was carried out in the TB hospitals to study reverse zoonosis. It was observed that an infected human being was one of the major risk factors for dogs to contract the infection. This observation was drawn by examining the probable airborne transmission from humans to their pets or strays. The present study helped to discover the nuances of TB transmission more clearly and systematically as compared to other sporadic tests to detect MTB in canine.

Keywords: Assam and Nagaland, canine TB, India, molecular detection, tuberculosis

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Authors: Emily Rabe, Stephanie Candelaria, Rachel Malone, Olivia Lenz, Greg Newbloom

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Electrodialysis (ED) is a well-developed technology for ion removal in a variety of applications. However, many industries generate harsh wastewater streams that are incompatible with traditional ion exchange membranes. Membrion® has developed novel ceramic-based ion exchange membranes (IEMs) offering several advantages over traditional polymer membranes: high performance in low pH, chemical resistance to oxidizers, and a rigid structure that minimizes swelling. These membranes are synthesized with our patented silane-based sol-gel techniques. The pore size, shape, and network structure are engineered through a molecular self-assembly process where thermodynamic driving forces are used to direct where and how pores form. Either cationic or anionic groups can be added within the membrane nanopore structure to create cation- and anion-exchange membranes. The ceramic IEMs are produced on a roll-to-roll manufacturing line with low-temperature processing. Membrane performance testing is conducted using in-house permselectivity, area-specific resistance, and ED stack testing setups. Ceramic-based IEMs show comparable performance to traditional IEMs and offer some unique advantages. Long exposure to highly acidic solutions has a negligible impact on ED performance. Additionally, we have observed stable performance in the presence of strong oxidizing agents such as hydrogen peroxide. This stability is expected, as the ceramic backbone of these materials is already in a fully oxidized state. This data suggests ceramic membranes, made using sol-gel chemistry, could be an ideal solution for acidic and/or oxidizing wastewater streams from processes such as semiconductor manufacturing and mining.

Keywords: ion exchange, membrane, silane chemistry, nanostructure, wastewater

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Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

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The objective of this study is to analyze the prophylactic usage of low molecular weight heparine (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January–31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25-35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients, were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparine was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: hypercoagulable state, low moleculare weight heparine, month of pregnancy, pregnant women

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Abbasali Raz, Javad Dadgar Pakdel, Kourosh Azizi, Aboozar Soltani, Mohammad Djaefar Moemenbellah-Fard

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Background: Maggot debridement therapy is an appropriate, effective, and controlled method using sterilized larvae of Luciliasericata (L.sericata) to treat wounds. Netrin-A is an enzyme in the Laminins family which secreted from salivary gland of L.sericata with a central role in neural regeneration and angiogenesis. This study aimed to production of new recombinant Netrin-A protein of Luciliasericata larvae by baculovirus expression vector system (BEVS) in SF9. Material and methods: In the first step, gene structure was subjected to the in silico studies, which were include determination of Antibacterial activity, Prion formation risk, homology modeling, Molecular docking analysis, and Optimization of recombinant protein. In the second step, the Netrin-A gene was cloned and amplified in pTG19 vector. After digestion with BamH1 and EcoR1 restriction enzymes, it was cloned in pFastBac HTA vector. It was then transformed into DH10Bac competent cells, and the recombinant Bacmid was subsequently transfected into insect Sf9 cells. The expressed recombinant Netrin-A was thus purified in the Ni-NTA agarose. This protein evaluation was done using SDS-PAGE and western blot, respectively. Finally, its concentration was calculated with the Bradford assay method. Results: The Bacmid vector structure with Netrin-A was successfully constructed and then expressed as Netrin-A protein in the Sf9 cell lane. The molecular weight of this protein was 52 kDa with 404 amino acids. In the in silico studies, fortunately, we predicted that recombinant LSNetrin-A have Antibacterial activity and without any prion formation risk.This molecule hasa high binding affinity to the Neogenin and a lower affinity to the DCC-specific receptors. Signal peptide located between amino acids 24 and 25. The concentration of Netrin-A recombinant protein was calculated to be 48.8 μg/ml. it was confirmed that the characterized gene in our previous study codes L. sericata Netrin-A enzyme. Conclusions: Successful generation of the recombinant Netrin-A, a secreted protein in L.sericata salivary glands, and because Luciliasericata larvae are used in larval therapy. Therefore, the findings of the present study could be useful to researchers in future studies on wound healing.

Keywords: blowfly, BEVS, gene, immature insect, recombinant protein, Sf9

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Authors: Walid Mousa, Mohamed Nayel, Ahmed Zaghawa, Akram Salama, Ahmed El-Sify, Hesham Rashad, Dina El-Shafey

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Mycoplasmosis in small ruminants constitutes a serious contagious problem in smallholders causing severe economic losses worldwide. This study was conducted to determine the clinical, Minimum Inhibitory Concentration (MIC) and molecular characterization of Mycoplasma species associated in sheep breeding herds in Menoufiya governorate, Egypt. Out of the examination of 400 sheep, 104 (26%) showed respiratory manifestations, nasal discharges, cough and conjunctivitis with systemic body reaction. Meanwhile, out of these examined sheep, only 56 (14%) were positive for mycoplasma isolation onto PPLO(Pleuropneumonia-like organisms) specific medium. The MIC for evaluating the efficacy of sensitivity of Mycoplasma isolates against different antibiotics groups revealed that both the Linospectin and Tylosin with 2ug, 0.25ug/ml concentration were the most effective antibiotics for Mycoplasma isolates. The application of PCR was the rapid, specific and sensitive molecular approach for detection of M. ovipneumoniae, and M. arginine at 390 and 326 bp, respectively, in all tested isolates. In conclusion, the diagnosis of Mycoplsamosis in sheep is important to achieve effective control measures and minimizing the disease dissemination among sheep herds.

Keywords: MIC, mycoplasmosis, PCR, sheep

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Authors: Mizam Doğan

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In service life; structures can be damaged if they are subjected to dead and live loads which are greater than design values. For preventing this case; possible loads must be correctly calculated, structure must be designed according to determined loads, and structure must not be used out of its function. If loading case of the structure changes when its function changes; it must be reinforced for continuing it is new function. Reinforcement is a process that is made by increasing the existing strengths of structural system elements of the structure as reinforced concrete walls, beams, and slabs. Reinforcement can be done by casting reinforced concrete, placing steel and fiber structural elements. In this paper, reinforcing of columns and slabs of a structure of which function is changed is studied step by step. This reinforcement is made for increasing vertical and lateral load carrying capacity of the building. Not for repairing damaged structural system.

Keywords: strengthening, RC slabs, seismic load, steel beam, structural irregularity

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Authors: Hosam Abdelhady

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Filming the behaviors of individual DNA molecules in their environment when they interact with individual medicinal nano-polymers in a molecular scale has opened the door to understand the effect of the molecular shape, size, and incubation time with nanocarriers on optimizing the design of robust genetic Nano molecules able to resist the enzymatic degradation, enter the cell, reach to the nucleus and kill individual cancer cells in their environment. To this end, we will show how we applied the 4D AFM as a guide to finetune the design of genetic nanoparticles and to film the effects of these nanoparticles on the nanomechanical and morphological profiles of individual cancer cells.

Keywords: AFM, dendrimers, nanoparticles, DNA, gene therapy, imaging

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Authors: Oscar Corredor, Alexander Guzman, Adan Leon

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Density is a bulk physical property that indicates the quality of a petroleum fraction. It is also a useful property to estimate various physicochemical properties of fraction and petroleum fluids; however, the determination of density of extra heavy residual (EHR) fractions by standard methodologies, (ASTM D70) shows limitations for samples with higher densities than 1.0879 g/cm3. For this reason, a dilution methodology was developed in order to determinate density for those particular fractions, 87 (EHR) fractions were obtained as products of the fractionation of Colombian typical Vacuum Distillation Residual Fractions using molecular distillation (MD) and extraction with Solvent N-hexane in Supercritical Conditions (SFEF) pilot plants. The proposed methodology showed reliable results that can be demonstrated with the standard deviation of repeatability and reproducibility values of 0.0031 and 0.0061 g/ml respectively. In the same way, it was possible to determine densities in fractions EHR up to 1.1647g/cm3 and °API values obtained were ten times less than the water reference value.

Keywords: API, density, vacuum residual, molecular distillation, supercritical fluid extraction

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Authors: Ho Young Son, Bu Seog Ju, Woo Young Jung

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This study presents the seismic safety evaluation of weir structure subjected to strong earthquake ground motions, as a flood defense structure in civil engineering structures. The seismic safety analysis procedure was illustrated through development of Finite Element (FE) and InFinite Element (IFE) method in ABAQUS platform. The IFE model was generated by CINPS4, 4-node linear one-way infinite model as a sold continuum infinite element in foundation areas of the weir structure and then nonlinear FE model using friction model for soil-structure interactions was applied in this study. In order to understand the complex behavior of weir structures, nonlinear time history analysis was carried out. Consequently, it was interesting to note that the compressive stress gave more vulnerability to the weir structure, in comparison to the tensile stress, during an earthquake. The stress concentration of the weir structure was shown at the connection area between the weir body and stilling basin area. The stress both tension and compression was reduced in IFE model rather than FE model of weir structures.

Keywords: seismic, numerical analysis, FEM, weir, boundary condition

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Authors: Sarah Gaßmeyer, Nadine Hülsemann, Raphael Stoll, Kenji Miyamoto, Robert Kourist

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Enzymatic racemization allows the smooth interconversion of stereocenters under very mild reaction conditions. Racemases find frequent applications in deracemization and dynamic kinetic resolutions. Arylmalonate decarboxylase (AMDase) from Bordetella Bronchiseptica has high structural similarity to amino acid racemases. These cofactor-free racemases are able to break chemically strong CH-bonds under mild conditions. The racemase-like catalytic machinery of mutant G74C conveys it a unique activity in the racemisation of pharmacologically relevant derivates of 2-phenylpropionic acid (profenes), which makes AMDase G74C an interesting object for the mechanistic investigation of cofactor-independent racemases. Structure-guided protein engineering achieved a variant of this unique racemase with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. By saturation–transfer–difference NMR spectroscopy (STD-NMR), substrate binding during catalysis was investigated. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose variation increased the activity of G74C. While single-amino acid exchanges increased the activity moderately, structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering.

Keywords: racemase, rational protein design, STD-NMR, structure guided saturation mutagenesis

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Authors: Murat Avci, Fatih Kosar, Ismail Yilmaz

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In this study, structure-flow interaction for water brake mechanism is studied with Abaqus CEL approach. The water brake mechanism is used for dynamic systems such as sled system on rail. For the achievement of these system tests, structure-flow interaction should be investigated in detail. This study is about a sled test of an aircraft subsystem which rises to supersonic speeds thanks to rocket engines. To decrease or to stop the thrusting rocket sleds, water brake mechanisms are used. Water brake mechanism provides the deceleration of the structures that have supersonic speeds. Therefore, structure-flow interaction may cause damage to the water brake mechanism. To verify all design revisions with system tests are so costly so that some decisions are taken in accordance with numerical methods. In this study, structure-flow interaction that belongs to water brake mechanism is solved with Abaqus CEL approach. Fluid and deformation on the structure behaviors are modeled at the same time thanks to CEL approach. Provided analysis results are corrected with the dynamic tests. Deformation zones seen in numerical analysis are also observed in dynamic tests. Finally, Johnson-Cook material model parameters used for this analysis are proven, and it is understood that these parameters can be used for dynamic analysis like water brake mechanism.

Keywords: aircraft, rocket, structure-flow, supersonic

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Authors: Mark-Adam Kellerman

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Proteins are capable of exploring vast mutational spaces. This makes it difficult for protein engineers to devise rational methods to improve stability and function via mutagenesis. Deciding which residues to mutate requires knowledge of the characteristics they elicit. We probed the characteristics of residues in granulocyte-colony stimulating factor (G-CSF) using a thermal melt (from 295K to 323K) to denature it in a 700 MHz Bruker spectrometer. These characteristics included dynamics, micro-environmental changes experienced/ induced during denaturing and structure-function relationships. 15N-1H HSQC experiments were performed at 2K increments along with this thermal melt. We observed that dynamic residues that also undergo a lot of change in their microenvironment were predominantly in unstructured regions. Moreover, we were able to identify four residues (G4, A6, T133 and Q134) that we class as high priority targets for mutagenesis, given that they all appear in both the top 10% of measures for environmental changes and dynamics (∑Δ and ∆PI). We were also able to probe these NMR observables and combine them with molecular dynamics (MD) to elucidate what appears to be an opening motion of G-CSFs binding site III. V48 appears to be pivotal to this opening motion, which also seemingly distorts the loop region between helices A and B. This observation is in agreement with previous findings that the conformation of this loop region becomes altered in an aggregation-prone state of G-CSF. Hence, we present here an approach to profile the characteristics of residues in order to highlight their potential as rational mutagenesis targets and their roles in important conformational changes. These findings present not only an opportunity to effectively make biobetters, but also open up the possibility to further understand epistasis and machine learn residue behaviours.

Keywords: protein engineering, rational mutagenesis, NMR, molecular dynamics

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Authors: Nisha Prakash, Kritika Anand, Arun Barvat, Prabir Pal, Sonachand Adhikari, Suraj P. Khanna

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Group-III nitride semiconductors (GaN, AlN, InN and their ternary and quaternary compounds) have attracted a great deal of attention for the development of high-performance Ultraviolet (UV) photodetectors. Any midgap defect states in the epitaxial grown film have a direct influence on the photodetectors responsivity. The proportion of the midgap defect states can be controlled by the growth parameters. To study this we have grown high quality epitaxial GaN films on MOCVD- grown GaN template using plasma-assisted molecular beam epitaxy (PAMBE) with different growth parameters. Optical and electrical properties of the films were characterized by room temperature photoluminescence and photoconductivity measurements, respectively. The observed persistent photoconductivity behaviour is proportional to the yellow luminescence (YL) and the absolute responsivity has been found to decrease with decreasing YL. The results will be discussed in more detail later.

Keywords: gallium nitride, plasma-assisted molecular beam epitaxy, photoluminescence, photoconductivity, persistent photoconductivity, yellow luminescence

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Authors: Nader H. Ghareeb, Mohamed S. Gaith, Sayed M. Soleimani

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In modern engineering, weight optimization has a priority during the design of structures. However, optimizing the weight can result in lower stiffness and less internal damping, causing the structure to become excessively prone to vibration. To overcome this problem, active or smart materials are implemented. The coupled electromechanical properties of smart materials, used in the form of piezoelectric ceramics in this work, make these materials well-suited for being implemented as distributed sensors and actuators to control the structural response. The smart structure proposed in this paper is composed of a cantilevered steel beam, an adhesive or bonding layer, and a piezoelectric actuator. The static deflection of the structure is derived as function of the piezoelectric voltage, and the outcome is compared to theoretical and experimental results from literature. The relation between the voltage and the piezoelectric moment at both ends of the actuator is also investigated and a reduced finite element model of the smart structure is created and verified. Finally, a linear controller is implemented and its ability to attenuate the vibration due to the first natural frequency is demonstrated.

Keywords: active linear control, lyapunov stability theorem, piezoelectricity, smart structure, static deflection

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Authors: Ali Raza, Rūta Rimašauskienė

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In the current work, the fused deposition modelling (FDM) technique is used to manufacture PLA reinforced with carbon fibre composite structures with two unique layer patterns, 0°\0° and 0°\90°. The purpose of the study is to investigate the dynamic characteristics of each fabricated composite structure. The Macro Fiber Composite (MFC) is embedded with 0°/0° and 0°/90° structures to investigate the effect of an MFC (M8507-P2 type) patch on vibration amplitude suppression under dynamic loading circumstances. First, modal analysis testing was performed using a Polytec 3D laser vibrometer to identify bending mode shapes, natural frequencies, and vibration amplitudes at the corresponding natural frequencies. To determine the stiffness of each structure, several loads were applied at the free end of the structure, and the deformation was recorded using a laser displacement sensor. The findings confirm that a structure with 0°\0° layers pattern was found to have more stiffness compared to a 0°\90° structure. The maximum amplitude suppression in each structure was measured using a laser displacement sensor at the first resonant frequency when the control voltage signal with optimal phase was applied to the MFC. The results confirm that the 0°/0° pattern's structure exhibits a higher displacement reduction than the 0°/90° pattern. Moreover, stiffer structures have been found to perform amplitude suppression more effectively.

Keywords: carbon fibre composite, MFC, modal analysis stiffness, stiffness

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Authors: Sinethemba Yakobi, Lindiwe Zuma, Ofentse Pooe

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Gonococcal infections present a notable public health issue, and the major approach for treatment involves using β-lactam antibiotics that specifically target penicillin-binding protein 2 (PBP2) in Neisseria gonorrhoeae. This study examines the influence of flavonoids, namely rutin, on the structural changes of PBP2 in both penicillin-resistant (FA6140) and penicillin-susceptible (FA19) strains. The research clarifies the structural effects of particular mutations, such as inserting an aspartate residue at position 345 (Asp-345a) in the PBP2 protein. The strain FA6140, which is resistant to penicillin, shows specific changes that lead to a decrease in penicillin binding. These mutations, namely P551S and F504L, significantly impact the pace at which acylation occurs and the stability of the strain under high temperatures. Molecular docking analyses investigate the antibacterial activities of rutin and other phytocompounds, emphasizing its exceptional binding affinity and potential as an inhibitor of PBP2. Quercetin and protocatechuic acid have encouraging antibacterial effectiveness, with quercetin displaying characteristics similar to those of drugs. Molecular dynamics simulations offer a detailed comprehension of the interactions between flavonoids and PBP2, highlighting rutin's exceptional antioxidant effects and strong affinity for the substrate binding site. The study's wider ramifications pertain to the pressing requirement for antiviral treatments in the context of the ongoing COVID-19 epidemic. Flavonoids have a strong affinity for binding to PBP2, indicating their potential as inhibitors to impair cell wall formation in N. gonorrhoeae. Ultimately, this study provides extensive knowledge on the interactions between proteins and ligands, the dynamics of the structure, and the ability of flavonoids to combat penicillin-resistant N. gonorrhoeae bacteria. The verified simulation outcomes establish a basis for creating potent inhibitors and medicinal therapies to combat infectious illnesses.

Keywords: phytochemicals, penicillin-binding protein 2, gonococcal infection, ligand-protein interaction, binding energy, neisseria gonorrhoeae FA19, neisseria gonorrhoeae FA6140, flavonoids

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Authors: Mona G. Alharbi

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A new family of methionine-sulfoxide reductase (Msr) was recently discovered and was named free methionine sulfoxide reductase (fRMsr). This family includes enzymes with a reductase activity toward the free R isomer of a methionine sulfoxide substrate. The fRMsrs have a GAF domain topology, a domain, which was previously identified as having in some cases a cyclic nucleotide phosphodiesterase activity. The classification of fRMsrs as GAF domains revealed a new function can be added to the GAF domain family. Interestingly the four members identified in the fRMsr family share the GAF domain structure and the presence of three conserved cysteines in the active site with free R methionine sulfoxide substrate specificity. This thesis presents the crystal structures of reduced, free Met-SO substrate-bound and MES-bound forms of a new fRMsr from Burkholderia pseudomallei (BPSL2418). BPSL2418 was cloned, overexpressed and purified to enable protein crystallization. The crystallization trials for reduced, Met-SO-bound and MES-bound forms of BPSL2418 were prepared and reasonable crystals of each form were produced. The crystal structures of BPSL2418MES, BPSL2418Met-SO and BPSL2418Reduced were solved at 1.18, 1.4 and 2.0Å, respectively by molecular replacement. The BPSL2418MES crystal belongs to space group P 21 21 21 while BPSL2418Met-SO and BPSL2418Reduced crystals belong to space group P 1 21 1. All three forms share the GAF domain structure of six antiparallel β-strands and four α-helices with connecting loops. The antiparallel β-strands (β1, β2, β5 and β6) are located in the center of the BPSL2418 structure flanked on one side by a three α-helices (α1, α2 and α4) and on the other side by a (loop1, β3, loop2, α3, β4 loop4) unit where loop4 forms a capping flap and covers the active site. The structural comparison of the three forms of BPSL2418 indicates that the catalytically important cysteine is CYS109, where the resolving cysteine is CYS75, which forms a disulfide bond with CYS109. They also suggest that the third conserved cysteine in the active site, CYS85, which is located in α3, is a non-essential cysteine for the catalytic function but it may play a role in the binding of the substrate. The structural comparison of the three forms reveals that conformational changes appear in the active site particularly involving loop4 and CYS109 during catalysis. The 3D structure of BPSL2418 shows strong structure similarity to fRMsrs enzymes, which further suggests that BPSL2418 acts as a free Met-R-SO reductase and shares the catalytic mechanism of fRMsr family.

Keywords: Burkholderia pseudomallei, GAF domain protein, methionine sulfoxide reductase, protein crystallization

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Authors: Mayank, Navneet Kaur, Narinder Singh

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The V599 mutations in the BRAF protein are extremely oncogenic, responsible for countless of malignant conditions. Along with wild type, V599E, V599D, and V599R are the important mutated variants of the BRAF proteins. The BRAF inhibitory anticancer agents are continuously developing, and sorafenib is a BRAF inhibitor that is under clinical use. The crystal structure of sorafenib bounded to wild type, and V599 is known, showing a similar interaction pattern in both the case. The mutated 599th residue, in both the case, is also found not interacting directly with the co-crystallized sorafenib molecule. However, the IC50 value of sorafenib was found extremely different in both the case, i.e., 22 nmol/L for wild and 38 nmol/L for V599E protein. Molecular docking study and MMGBSA binding energy results also revealed a significant difference in the binding pattern of sorafenib in both the case. Therefore, to explore the role of distinctively situated 599th residue, we have further conducted comprehensive computational studies. The molecular dynamics simulation, residue interaction network (RIN) analysis, and residue correlation study results revealed the importance of the 599th residue on the therapeutic outcome and overall dynamic of the BRAF protein. Therefore, although the position of 599th residue is very much distinctive from the ligand-binding cavity of BRAF, still it has exceptional control over the overall functional outcome of the protein. The insight obtained here may seem extremely important and guide us while designing ideal BRAF inhibitory anticancer molecules.

Keywords: BRAF, oncogenic, sorafenib, computational studies

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Authors: Ehsan Sadie

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Developments in the field of damping technology and advances in the area of dampers in equipping many structures have been the result of efforts and testing by researchers in this field. In this paper, a sample of a two-story building is simulated with the help of SAP2000 software, and the effect of a viscous damper on the performance of the structure is explained. The effect of dampers on the response of the structure is investigated. This response involves the horizontal displacement of floors. In this case, the structure is modeled once without a damper and again with a damper. In this regard, the results are presented in the form of tables and graphs. Since the seismic behavior of the structure is studied, the responses show the appropriate effect of viscous dampers in reducing the displacement of floors, and also the energy dissipation in the structure with dampers compared to structures without dampers is significant. Therefore, it is economical to use viscous dampers in areas that have a higher relative earthquake risk.

Keywords: bending frame, displacement criterion, dynamic response spectra, earthquake, non-linear history spectrum, SAP2000 software, structural response, viscous damper

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Authors: Shogo Kato, Daisuke Okamoto, Satoko Tsuru, Yoshinori Iizuka, Ryoko Shimono

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Healthcare safety has been perceived important. It is essential to prevent troubles in healthcare processes for healthcare safety. Trouble prevention is based on trouble prediction using accumulated knowledge on processes, troubles, and countermeasures. However, information on troubles has not been accumulated in hospitals in the appropriate structure, and it has not been utilized effectively to prevent troubles. In the previous study, though a detailed knowledge acquisition process for trouble prediction was proposed, the knowledgebase for countermeasures was not involved. In this paper, we aim to propose the structure of the knowledgebase for countermeasures in the knowledge acquisition process for trouble prediction in healthcare process. We first design the structure of countermeasures and propose the knowledge representation form on countermeasures. Then, we evaluate the validity of the proposal, by applying it into an actual hospital.

Keywords: trouble prevention, knowledge structure, structured knowledge, reusable knowledge

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Authors: Elif Tugce Aksun Tumerkan, Chris Lowe, Hannah Krupa

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Fluorescent proteins are self-sufficient in forming chromophores with a visible wavelength from 3 amino acids sequence within their own polypeptide structure. This chromophore – a molecule that absorbs a photon of light and exhibits an energy transition equal to the energy of the absorbed photon. Fluorescent proteins (FPs) consisted of a chain of 238 amino acid residues and composed of 11 beta strands shaped in a cylinder surrounding an alpha helix structure. A better understanding of the system of the chromospheres and the increasing advance in protein engineering in recent years, the properties of FPs offers the potential for new applications. They have used sensors and probes in molecular biology and cell-based research that giving a chance to observe these FPs tagged cell localization, structural variation and movement. For clarifying functional uses of fluorescent proteins, electrophoretic properties of these proteins are one of the most important parameters. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is used for determining electrophoretic properties commonly. While there are many techniques are used for determining the functionality of protein-based research, SDS-PAGE analysis can only provide a molecular level assessment of the proteolytic fragments. Before SDS-PAGE analysis, fluorescent proteins need to successfully purified. Due to directly purification of the target, FPs is difficult from the animal, gene expression is commonly used which must be done by transformation with the plasmid. Furthermore, used gel within electrophoresis and staining agents properties have a key role. In this review, the different factors that have the impact on the electrophoretic properties of fluorescent proteins explored. Fluorescent protein separation and purification are the essential steps before electrophoresis that should be done very carefully. For protein purification, gene expression process and following steps have a significant function. For successful gene expression, the properties of selected bacteria for expression, used plasmid are essential. Each bacteria has own characteristics which are very sensitive to gene expression, also used procedure is the important factor for fluorescent protein expression. Another important factors are gel formula and used staining agents. Gel formula has an effect on the specific proteins mobilization and staining with correct agents is a key step for visualization of electrophoretic bands of protein. Visuality of proteins can be changed depending on staining reagents. Apparently, this review has emphasized that gene expression and purification have a stronger effect than electrophoresis protocol and staining agents.

Keywords: cell biology, gene expression, staining agents, SDS-page

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Authors: Bo Keun Lee, Doo Yeon Kwon, Ji Hoon Park, Gun Hee Lee, Ji Hye Baek, Heung Jae Chun, Young Joo Koh, Moon Suk Kim

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Thermo-responsive materials are viscoelastic materials that undergo a sol-to-gel phase transition at a specific temperature and many materials have been developed. MPEG-b-PCL (MPC) as a thermo-responsive material contained hydrophilic and hydrophobic segments and it formed an ordered crystalline structure of hydrophobic PCL segments in aqueous solutions. The ordered crystalline structure packed tightly or aggregated and finally induced an aggregated gel through intra- and inter-molecular interactions as a function of temperature. Thus, we introduced anionic and cationic groups into the end positions of the PCL chain to alter the hydrophobicity of the PCL segment. Introducing anionic and cationic groups into the PCL end position altered their solubility by changing the crystallinity and hydrophobicity of the PCL block domains. These results indicated that the properties of the end group in the hydrophobic PCL blockand the balance between hydrophobicity and hydrophilicity affect thermo-responsivebehavior of the copolymers in aqueous solutions. Thus, we concluded that determinant of the temperature-dependent thermo-responsive behavior of MPC depend on the ionic end group in the PCL block. So, we introduced zwitterionic end groups to investigate the thermo-responsive behavior of MPC. Methoxypoly(ethylene oxide) and ε-caprolactone (CL) were randomly copolymerized that introduced varying hydrophobic PCL lengths and an MPC featuring a zwitterionic sulfobetaine (MPC-ZW) at the chain end of the PCL segment. The MPC and MPC-ZW copolymers were obtained formed sol-state at room temperature when prepared as 20-wt% aqueous solutions. The solubility of MPC decreased when the PCL block was increased from molecular weight. The solubilization time of MPC-2.4k was around 20 min and MPC-2.8k, MPC-3.0k increased to 30 min and 1 h, respectively. MPC-3.6k was not solubilized. In case of MPC-ZW 3.6k, However, the zwitterion-modified MPC copolymers were solubilized in 3–5 min. This result indicates that the zwitterionic end group of the MPC-ZW diblock copolymer increased the aqueous solubility of the diblock copolymer even when the length of the hydrophobic PCL segment was increased. MPC and MPC-ZW diblock copolymers that featuring zwitterionic end groups were synthesized successfully. The sol-to-gel phase-transition was formed that specific temperature depend on the length of the PCL hydrophobic segments introduced and on the zwitterion groups attached to the MPC chain end. This result indicated that the zwitterionic end groups reduced the hydrophobicity in the PCL block and changed the solubilization. The MPC-ZW diblock copolymer can be utilized as a potential injectable drug and cell carrier.

Keywords: thermo-responsive material, zwitterionic, hydrophobic, crystallization, phase transition

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