Search results for: single molecule

Authors: Nigar Kantarci Carsibasi

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Coarse-grained elastic network models, namely Gaussian network model (GNM) and Anisotropic network model (ANM), are utilized in order to investigate the fluctuation dynamics of Murine Double Minute 2 (MDM2), which is the native inhibitor of p53. Conformational dynamics of MDM2 are elucidated in unbound, p53 bound, and non-peptide small molecule inhibitor bound forms. With this, it is aimed to gain insights about the alterations brought to global dynamics of MDM2 by native peptide inhibitor p53, and two small molecule inhibitors (HDM201 and NVP-CGM097) that are undergoing clinical stages in cancer studies. MDM2 undergoes significant conformational changes upon inhibitor binding, carrying pieces of evidence of induced-fit mechanism. Small molecule inhibitors examined in this work exhibit similar fluctuation dynamics and characteristic mode shapes with p53 when complexed with MDM2, which would shed light on the design of novel small molecule inhibitors for cancer therapy. The results showed that residues Phe 19, Trp 23, Leu 26 reside in the minima of slowest modes of p53, pointing to the accepted three-finger binding model. Pro 27 displays the most significant hinge present in p53 and comes out to be another functionally important residue. Three distinct regions are identified in MDM2, for which significant conformational changes are observed upon binding. Regions I (residues 50-77) and III (residues 90-105) correspond to the binding interface of MDM2, including (α2, L2, and α4), which are stabilized during complex formation. Region II (residues 77-90) exhibits a large amplitude motion, being highly flexible, both in the absence and presence of p53 or other inhibitors. MDM2 exhibits a scattered profile in the fastest modes of motion, while binding of p53 and inhibitors puts restraints on MDM2 domains, clearly distinguishing the kinetically hot regions. Mode shape analysis revealed that the α4 domain controls the size of the cleft by keeping the cleft narrow in unbound MDM2; and open in the bound states for proper penetration and binding of p53 and inhibitors, which points to the induced-fit mechanism of p53 binding. P53 interacts with α2 and α4 in a synchronized manner. Collective modes are shifted upon inhibitor binding, i.e., second mode characteristic motion in MDM2-p53 complex is observed in the first mode of apo MDM2; however, apo and bound MDM2 exhibits similar features in the softest modes pointing to pre-existing modes facilitating the ligand binding. Although much higher amplitude motions are attained in the presence of non-peptide small molecule inhibitor molecules as compared to p53, they demonstrate close similarity. Hence, NVP-CGM097 and HDM201 succeed in mimicking the p53 behavior well. Elucidating how drug candidates alter the MDM2 global and conformational dynamics would shed light on the rational design of novel anticancer drugs.

Keywords: cancer, drug design, elastic network model, MDM2

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Authors: Valeria Butera, Norihisa Fukaya, Jun-Chu Choi, Kazuhiko Sato, Yoong-Kee Choe

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Several silicon dioxide sources can react with dimethyl carbonate (DMC) in presence of alkali bases catalysts to ultimately produce tetramethoxysilane (TMOS). Experimental findings suggested that the reaction proceeds through several steps in which the first molecule of DMC is converted to dimethylsilyloxide (DMOS) and CO₂. Following the same mechanistic steps, a second molecule of DMC reacts with the DMOS to afford the final product TMOS. Using a cluster model approach, a quantum-mechanical investigation of the first part of the reaction leading to DMOS formation is reported with a twofold purpose: (1) verify the viability of the reaction mechanism proposed on the basis of experimental evidences .(2) compare the behaviors of three different alkali hydroxides MOH, where M=Li, K and Cs, to determine whether diverse ionic radius and charge density can be considered responsible for the observed differences in reactivity. Our findings confirm the observed experimental trend and furnish important information about the effective role of the alkali hydroxides giving an explanation of the different catalytic activity of the three metal cations.

Keywords: Alcoxysilanes production, cluster model approach, DFT, DMC conversion

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

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Authors: A. Benhamena, L. Aminallah, A. Aid, M. Benguediab, A. Amrouche

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The goal of this work is to analyze the severity of interfacial stress distribution in the single lap adhesive joint under tensile loading. The three-dimensional and non-linear finite element method based on the computation of the peel and shear stresses was used to analyze the fracture behaviour of single lap adhesive joint. The effect of the loading magnitude and the overlap length on the distribution of peel and shear stresses was highlighted. A good correlation was found between the FEM simulations and the analytical results.

Keywords: aluminum 2024-T3 alloy, single-lap adhesive joints, Interface stress distributions, material nonlinear analysis, adhesive, bending moment, finite element method

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Authors: Sujin Hong, Seokyoon Moon, Heejoong Kim, Yunseok Lee, Youngjune Park

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Gas hydrate is an inclusion compound in which a low-molecular-weight gas or organic molecule is trapped inside a three-dimensional lattice structure created by water-molecule via intermolecular hydrogen bonding. It is generally formed at low temperature and high pressure, and exists as crystal structures of cubic systems − structure I, structure II, and hexagonal system − structure H. Many efforts have been made to apply them to various energy and environmental fields such as gas transportation and storage, CO₂ capture and separation, and desalination of seawater. Particularly, studies on the behavior of gas hydrates by new organic materials for CO₂ storage and various applications are underway. In this study, thermodynamic and spectroscopic analyses of the gas hydrate system were performed focusing on cyclopentanol, an organic molecule that forms gas hydrate at relatively low pressure. The thermodynamic equilibria of CH₄ and CO₂ hydrate systems including cyclopentanol were measured and spectroscopic analyses of XRD and Raman were performed. The differences in thermodynamic systems and formation kinetics of CO₂ added cyclopentane, cyclopentanol and cyclopentanone hydrate systems were compared. From the thermodynamic point of view, cyclopentanol was found to be a hydrate promotor. Spectroscopic analyses showed that cyclopentanol formed a hydrate crystal structure of cubic structure II in the presence of CH₄ and CO₂. It was found that the differences in the functional groups among the organic guest molecules significantly affected the rate of hydrate formation and the total amounts of CO₂ stored in the hydrate systems. The total amount of CO₂ stored in the cyclopentanone hydrate was found to be twice that of the amount of CO₂ stored in the cyclopentane and the cyclopentanol hydrates. The findings are expected to open up new opportunity to develop the gas hydrate based wastewater desalination technology.

Keywords: gas hydrate, CO₂, separation, desalination, formation kinetics, thermodynamic equilibria

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Authors: Hossain A., Miah S., Ray P. K.

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Introduction: Single channel and tri-channel applicators are used in the traditional treatment of cervical cancer. Total reference air kerma (TRAK) and treatment outcomes in high-dose-rate brachytherapy for cervical cancer using single-channel and tri-channel applicators were the main objectives of this retrospective study. Material and Methods: Patients in the radiotherapy division who received brachytherapy, chemotherapy, and external radiotherapy (EBRT) using single and tri-channel applicators were the subjects of a retrospective cohort study from 2016 to 2020. All brachytherapy parameters, including TRAK, were calculated in accordance with the international protocol. The Kaplan Meier method was used to analyze survival rates using a log-rank test. Results and Discussions: Based on treatment times of 15.34 (10-20) days and 21.35 (6.5-28) days, the TRAK for the tri-channel applicator was 0.52 cGy.m² and for the single-channel applicator was 0.34 cGy.m². Based on TRAK, the rectum, bladder, and tumor had respective Pearson correlations of 0.082, 0.009, and 0.032. The 1-specificity and sensitivity were 0.70 and 0.30, respectively. At that time, AUC was 0.71. The log-rank test showed that tri-channel applicators had a survival rate of 95% and single-channel applicators had a survival rate of 85% (p=0.565). Conclusions: The relationship between TRAK and treatment duration and Pearson correlation for the tumor, rectum, and bladder suggests that TRAK should be taken into account for the proper operation of single channel and tri-channel applicators.

Keywords: single-channel, tri-channel, high dose rate brachytherapy, cervical cancer

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Authors: Zhengyi Kong, Seung-Eock Kim

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Single angle connections, which are bolted to the beam web and the column flange, are studied to investigate moment-rotation behavior. Elastic–perfectly plastic material behavior is assumed. ABAQUS software is used to analyze the nonlinear behavior of a single angle connection. The same geometric and material conditions with Yanglin Gong’s test are used for verifying finite element models. Since Kishi and Chen’s Power model and Lee and Moon’s Log model are accurate only for a limited range, simpler and more accurate hyperbolic function models are proposed. The equation for calculating rotation at ultimate moment is first proposed.

Keywords: finite element method, moment and rotation, rotation at ultimate moment, single-web angle connections

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Authors: Misa Nakao, Yuta Kurashina, Chikahiro Imashiro, Kenjiro Takemura

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The Research Goal: With the growing demand for regenerative medicine, an effective mass cell culture process is required. In a repetitive subculture process for proliferating cells, preparing single cell suspension which does not contain any cell aggregates is highly required because cell aggregates often raise various undesirable phenomena, e.g., apoptosis and decrease of cell proliferation. Since cell aggregates often occur in cell suspension during conventional subculture processes, this study proposes a single cell sorter driven by a resonance vibration of a cell culture substrate. The Method and the Result: The single cell sorter is simply composed of a cell culture substrate and a glass pipe vertically placed against the cell culture substrate with a certain gap corresponding to a cell diameter. The cell culture substrate is made of biocompatible stainless steel with a piezoelectric ceramic disk glued to the bottom side. Applying AC voltage to the piezoelectric ceramic disk, an out-of-plane resonance vibration with a single nodal circle of the cell culture substrate can be excited at 5.5 kHz. By doing so, acoustic radiation force is emitted, and then cell suspension containing only single cells is pumped into the pipe and collected. This single cell sorter is effective to collect single cells selectively in spite of its quite simple structure. We collected C2C12 myoblast cell suspension by the single cell sorter with the vibration amplitude of 12 µmp-p and evaluated the ratio of single cells in number against the entire cells in the suspension. Additionally, we cultured the collected cells for 72 hrs and measured the number of cells after the cultivation in order to evaluate their proliferation. As a control sample, we also collected cell suspension by conventional pipetting, and evaluated the ratio of single cells and the number of cells after the 72-hour cultivation. The ratio of single cells in the cell suspension collected by the single cell sorter was 98.2%. This ratio was 9.6% higher than that collected by conventional pipetting (statistically significant). Moreover, the number of cells cultured for 72 hrs after the collection by the single cell sorter yielded statistically more cells than that collected by pipetting, resulting in a 13.6% increase in proliferated cells. These results suggest that the cell suspension collected by the single cell sorter driven by the resonance vibration hardly contains cell aggregates whose diameter is larger than the gap between the cell culture substrate and the pipe. Consequently, the cell suspension collected by the single cell sorter maintains high cell proliferation. Conclusions: In this study, we developed a single cell sorter capable of sorting and pumping single cells by a resonance vibration of a cell culture substrate. The experimental results show the single cell sorter collects single cell suspension which hardly contains cell aggregates. Furthermore, the collected cells show higher proliferation than that of cells collected by conventional pipetting. This means the resonance vibration of the cell culture substrate can benefit us with the increase in efficiency of mass cell culture process for clinical applications.

Keywords: acoustic radiation force, cell proliferation, regenerative medicine, resonance vibration, single cell sorter

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Authors: Manoj Kumar

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Ionization cross sections of molecules due to electron impact play an important role in chemical processes in various branches of applied physics, such as radiation chemistry, gas discharges, plasmas etching in semiconductors, planetary upper atmospheric physics, mass spectrometry, etc. In the present work, we have calculated the total ionization cross sections for Adenine (C₅H₅N₅), a biologically important molecule, by electron impact in the incident electron energy range from ionization threshold to 2 keV employing a well-known Jain-Khare semiempirical formulation based on Bethe and Möllor cross sections. In the non-availability of the experimental results, the present results are in good agreement qualitatively as well as quantitatively with available theoretical results. The present results drive our confidence for further investigation of complex bio-molecule with better accuracy. Notwithstanding, the present method can deduce reliable cross-sectional data for complex targets with adequate accuracy and may facilitate the acclimatization of calculated cross-sections into atomic molecular cross-section data sets for modeling codes and other applications.

Keywords: electron impact ionization cross-sections, oscillator strength, jain-khare semiempirical approach

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Authors: Evgeniya Popova, Vladimir Lesnikov, Nikolay Popov

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High yield complex coatings have been designed for thermally stressed cooled HP turbine blades from single crystal alloys ZHS32-VI-VI and ZHS36 with crystallographic orientation [001]. These coatings provide long-term protection of single crystal blades during operation. The three-layer coatings were prepared as follows: the diffusion barrier layer formation on the alloy surface, the subsequent deposition of the condensed bilayer coatings consisting of an inner layer based on Ni-Cr-Al-Y systems and an outer layer based on the alloyed β-phase. The structure, phase composition of complex coatings and reaction zone interaction with the single-crystal alloys ZHS32-VI and ZHS36-VI were investigated using scanning electron microscope (SEM). The effect of complex protective coatings on the properties of heat-resistant nickel alloys was studied.

Keywords: single crystal nickel alloys, complex heat-resistant coatings, structure, phase composition, properties

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Authors: S. H. Allehyani, H. S. Ibrahim, F. M. Ali, E. Sayd, T. Abou Aiad

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The present study aimed to analyse the radiation risk associated with the exposure of haemoglobin (Hb) of rat red blood cells (rbcs) exposed to a 50-Hz 6-kV/m electric field, a fast neutron dose of 1 mSv, and mixed radiation from fast neutrons and an electric field distributed over a period of three weeks at a rate of 5 days/week and 8 hours/day. The dielectric measurements and the absorption spectra for the haemoglobin molecule in the frequency range of 1 kHz to 5 MHz were measured for all of the samples. The dielectric relaxation results demonstrated an increase in the dielectric increment (∆ε) for the rbcs from all of the irradiated animals, which indicates an increase in the electric dipole. Moreover, the results revealed a decrease in the relaxation time (τ) and the molecular radius (r) of the irradiated molecules, which indicates that the increase in ∆ε is mainly due to a pronounced increase in the centre of mass of the charge on the electric dipole of the Hb molecule. The results from the absorption spectra indicate that the ratio of met-haemoglobin to oxy-haemoglobin is altered by irradiation. Moreover, the results from the delayed effect studies show that the structure and function of the newly generated Hb molecules are altered and dissimilar to that of healthy Hb.

Keywords: rat red blood cell haemoglobin, dielectric properties, absorption spectra, biochemical analysis

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Authors: Sara Subhan

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Married couples tend to experience various bio-psycho-social issues that may eventually impact the quality of their marital relationship and mental wellbeing. This study aimed to find out the comparison between the single and dual-career couples’ personality, burnout and marital satisfaction. For that purpose Big Five Inventory, Couple Satisfaction Inventory, and Maslach Burnout Inventory-General Survey was used to measure the relationship between variables. The main study was carried out on 200 samples of single and dual-earner couples with the age range of 23-52 (mean= 34.58; standard deviation= 6.51) by using a purposive sampling strategy. The results showed that burnout tendencies like exhaustion, cynicism and professional efficacy are playing a mediation role between the personality and marital satisfaction of both single and dual career couples. Also, the results revealed that dual-career couples are more likely to have marital satisfaction as compared to single career couples. The results were further discussed in the light of its implications in its cultural context and counseling areas.

Keywords: dual career couples, marital satisfaction, burnout tendencies, personality

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Authors: Kabrambam D. Singh, Dinabandhu Sahoo, Yallappa Rajashekar

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Evolution has caused many insects to develop resistance to several synthetic insecticides. This problem along with the persisting concern regarding the health and environmental safety issues of the existing synthetic insecticides has urged the scientific fraternity to look for a new plant-based natural insecticide with inherent eco-friendly nature. Colocasia esculenta var. esculenta (L.) Schott (Araceae family) is widely grown throughout the South- East Asian Countries for its edible corms and leaves. Various physico-chemical and spectroscopic techniques (IR, 1H NMR, 13C NMR and Mass) were used for the isolation and characterization of isolated bioactive molecule named 2, 3-dimethylmaleic anhydride (3, 4-dimethyl-2, 5-furandione). This compound was found to be highly toxic, even at low concentration, against several storage grain pests when used as biofumigant. Experimental studies on the mode of action of 2, 3-dimethylmaleic anhydride revealed that the biofumigant act as inhibitor of acetylcholinesterase enzyme in cockroach and stored grain insects. The knockdown activity of bioactive compound is concurrent with in vivo inhibition of AChE; at KD99 dosage of bioactive molecule showed more than 90% inhibition of AChE activity in test insects. The molecule proved to affect the antioxidant enzyme system; superoxide dismutase (SOD), and catalase (CAT) and also found to decrease reduced glutathione (GSH) level in the treated insects. The above results indicate involvement of inhibition of AChE activity and oxidative imbalance as the potential mode of action of 2, 3-dimethylmaleic anhydride. In addition, the study reveals computational docking programs elaborate the possible interaction of 2, 3-dimethylmaleic anhydride with enzyme acetylcholinesterase (AChE) of Periplaneta americana. Finally, the results represent that toxicity of 2, 3-dimethylmaleic anhydride might be associated with inhibition of AChE activity and oxidative imbalance.

Keywords: 2, 3-dimethylmaleic anhydride, Colocasia esculenta var. esculenta (L.) Schott, Biofumigant, acetylcholinesterase, antioxidant enzyme, molecular docking

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Authors: Xingxin Wu, Fenli Shao, Tao Tan, Yang Tan, Yang Sun, Qiang Xu

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Psoriasis is a chronic inflammatory skin disease that affects about 2% of the world's population. IL-23 signaling plays a key role in the pathogenesis of psoriasis. Control of IL-23 release by small molecule compounds during developing psoriasis has not been well established. Here, we show that compound 1, a small molecule nature product, protected mice from imiquimod-induced psoriasis with improved skin lesions, reduced skin thickness, and reduced IL-23 mRNA expression in the skin tissue. FACS results showed compound 1 reduced the number of dendritic cells in the skin. Interestingly, compound 1 was not able to ameliorate IL-23-induced psoriasis-like skin inflammation in mice. Further, compound 1 inhibited MyD88-dependent IL-23 mRNA expression induced by LPS, CpG and imiquimod in BMDC cells, but not MyD88-independent CD80 and CD86 expression induced by LPS. The methods included real-time PCR, western blot, H & E staining, FACS and ELISA et al. In conclusion, compound 1 regulates MyD88-dependent signaling to control IL-23 release in dendritic cells, which improves imiquimod-induced psoriasis.

Keywords: dendritic cells, IL-23, toll-like receptor signaling, psoriasis

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Authors: S. F. H. Tasfy, N. A. M. Zabidi, M. S. Shaharun

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Carbon dioxide is highly thermochemical stable molecules where it is very difficult to activate the molecule and achieve higher catalytic conversion into alcohols or other hydrocarbon compounds. In this paper, series of the bimetallic Cu/ZnO-based catalyst supported by SBA-15 were systematically prepared via impregnation technique with different Cu: Zn ratio for hydrogenation of CO₂ to methanol. The synthesized catalysts were characterized by transmission electron microscopy (TEM), temperature programmed desorption, reduction, oxidation and pulse chemisorption (TPDRO), and surface area determination was also performed. All catalysts were tested with respect to the hydrogenation of CO₂ to methanol in microactivity fixed-bed reactor at 250^oC, 2.25 MPa, and H₂/CO₂ ratio of 3. The results demonstrate that the catalytic structure, activity, and methanol selectivity was strongly affected by the ratio between Cu: Zn, Where higher catalytic activity of 14 % and methanol selectivity of 92 % was obtained over Cu/ZnO-SBA-15 catalyst with Cu:Zn ratio of 7:3 wt. %. Comparing with the single catalyst, the synergetic between Cu and Zn provides additional active sites to adsorb more H₂ and CO₂ and accelerate the CO₂ conversion, resulting in higher methanol production under mild reaction conditions.

Keywords: hydrogenation of carbon dioxide, methanol synthesis, Cu/ZnO-based catalyst, mesoporous silica (SBA-15), metal ratio

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Authors: K. Youssef, Ç. Hüseyin

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The blades of a wind turbine have the most important job of any wind turbine component; they must capture the wind and convert it into usable mechanical energy. The objective of this work is to determine the mechanical power of single big C-section of vertical wind turbine for wind car in a two-dimensional model. The wind car has a vertical axis with 3 single big C-section blades mounted at an angle of 120°. Moreover, the three single big C-section blades are directly connected to wheels by using various kinds of links. Gears are used to convert the wind energy to mechanical energy to overcome the load exercised on the main shaft under low speed. This work allowed a comparison of drag characteristics and the mechanical power between the single big C-section blades with the previous work on 3 C-section and 3 double C-section blades for wind car. As a result obtained from the flow chart the torque and power curves of each case study are illustrated and compared with each other. In particular, drag force and torque acting on each types of blade was taken at an airflow speed of 4 m/s, and an angular velocity of 13.056 rad/s.

Keywords: blade, vertical wind turbine, drag characteristics, mechanical power

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Authors: Ernesto Linan, Linda Cruz, Lucero Becerra

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In this paper, a new hybridized algorithm based on Chemical Reaction Optimization and Simulated Annealing is proposed to solve the alignment sequence Problem. The Chemical Reaction Optimization is a population-based meta-heuristic algorithm based on the principles of a chemical reaction. Simulated Annealing is applied to solve a large number of combinatorial optimization problems of general-purpose. In this paper, we propose hybridization between Chemical Reaction Optimization algorithm and Simulated Annealing in order to solve the Sequence Alignment Problem. An initial population of molecules is defined at beginning of the proposed algorithm, where each molecule represents a sequence alignment problem. In order to simulate inter-molecule collisions, the process of Chemical Reaction is placed inside the Metropolis Cycle at certain values of temperature. Inside this cycle, change of molecules is done due to collisions; some molecules are accepted by applying Boltzmann probability. The results with the hybrid scheme are better than the results obtained separately.

Keywords: chemical reaction optimization, sequence alignment problem, simulated annealing algorithm, metaheuristics

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Authors: Nuridayanti Che Khalib, Kaliyaperumal Thanigaimani, Suhana Arshad, Ibrahim Abdul Razak

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The 1:1 co-crystal of 2-amino-4-chloro-6-methylpyrimidine (2A4C6MP) with 4-methylbenzoic acid (4MBA) (I) has been prepared by slow evaporation method in methanol, which was crystallized in monoclinic C2/c space group, Z = 8, a = 28.431 (2) Å, b = 7.3098 (5) Å, c = 14.2622 (10) Å, and β = 109.618 (3)°. The presence of unionized –COOH functional group in co-crystal I was identified both by spectral methods (1H and 13C NMR, FTIR) and X-ray diffraction structural analysis. The 2A4C6MP molecule interact with the carboxylic group of the respective 4MBA molecule through N—H⋯O and O—H⋯N hydrogen bonds, forming a cyclic hydrogen –bonded motif R22(8). The crystal structure was stabilized by Npyrimidine-H⋯O=C and C=O-H⋯Npyrimidine types hydrogen bonding interactions. Theoretical investigations have been computed by HF and density function (B3LYP) method with 6-311+G(d,p) basis set. The vibrational frequencies together with 1H and 13C NMR chemical shifts have been calculated on the fully optimized geometry of co-crystal I. Theoretical calculations are in good agreement with the experimental results. Solvent-free formation of this co-crystal I is confirmed by powder X-ray diffraction analysis.

Keywords: supramolecular co-crystal, 2-amino-4-chloro-6-methylpyrimidine, Harthree-Fock and DFT studies, spectroscopic analysis

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Authors: Rajesh Kumar Gautam, Debabrata Seth

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Thioflavin-T (ThT) play a key role of an important biologically active fluorescent sensor for amyloid fibrils. ThT molecule has been developed a method to detect the analysis of different type of diseases such as neurodegenerative disorders, Alzheimer’s, Parkinson’s, and type II diabetes. ThT was used as a fluorescent marker to detect the formation of amyloid fibril. In the presence of amyloid fibril, ThT becomes highly fluorescent. ThT undergoes twisting motion around C-C bonds of the two adjacent benzothiazole and dimethylaniline aromatic rings, which is predominantly affected by the micro-viscosity of the local environment. The present study articulates photophysics and torsional dynamics of biologically active molecule ThT in the presence of deep-eutectic solvents (DESs). DESs are environment-friendly, low cost and biodegradable alternatives to the ionic liquids. DES resembles ionic liquids, but the constituents of a DES include a hydrogen bond donor and acceptor species, in addition to ions. Due to the presence of the H-bonding network within a DES, it exhibits structural heterogeneity. Herein, we have prepared two different DESs by mixing urea with choline chloride and N, N-diethyl ethanol ammonium chloride at ~ 340 K. It was reported that deep eutectic mixture of choline chloride with urea gave a liquid with a freezing point of 12°C. We have experimented by taking two different concentrations of ThT. It was observed that at higher concentration of ThT (50 µM) it forms aggregates in DES. The photophysics of ThT as a function of temperature have been explored by using steady-state, and picoseconds time-resolved fluorescence emission spectroscopic techniques. From the spectroscopic analysis, we have observed that with rising temperature the fluorescence quantum yields and lifetime values of ThT molecule gradually decreases; this is the cumulative effect of thermal quenching and increase in the rate of the torsional rate constant. The fluorescence quantum yield and fluorescence lifetime decay values were always higher for DES-II (urea & N, N-diethyl ethanol ammonium chloride) than those for DES-I (urea & choline chloride). This was mainly due to the presence of structural heterogeneity of the medium. This was further confirmed by comparison with the activation energy of viscous flow with the activation energy of non-radiative decay. ThT molecule in less viscous media undergoes a very fast twisting process and leads to deactivation from the photoexcited state. In this system, the torsional motion increases with increasing temperature. We have concluded that beside bulk viscosity of the media, structural heterogeneity of the medium play crucial role to guide the photophysics of ThT in DESs. The analysis of the experimental data was carried out in the temperature range 288 ≤ T = 333K. The present articulate is to obtain an insight into the DESs as media for studying various photophysical processes of amyloid fibrils sensing molecule of ThT.

Keywords: deep eutectic solvent, photophysics, Thioflavin T, the torsional rate constant

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Authors: A. Kojah, A. Nacaroğlu

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Single phase transmission lines are used to transfer data or energy between two users. Transient conditions such as switching operations and short circuit faults cause the generation of the fluctuation on the waveform to be transmitted. Spatial voltage distribution on the single phase transmission line may change owing to the position and duration of the short circuit fault in the system. In this paper, the state space representation of the single phase transmission line for short circuit fault and for various types of terminations is given. Since the transmission line is modeled in time domain using distributed parametric elements, the mathematical representation of the event is given in state space (time domain) differential equation form. It also makes easy to solve the problem because of the time and space dependent characteristics of the voltage variations on the distributed parametrically modeled transmission line.

Keywords: energy transmission, transient effects, transmission line, transient voltage, RLC short circuit, single phase

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Authors: Dinda A. Utami, Muhammad N. Alfarizi

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The purpose of this study was to determine the ability of zeolite catalyst for the trans- esterification reaction in biodiesel production from animal fat. The ability of the zeolite as a catalyst is determined by the structure and composition of the zeolite. An important factor that determines the properties of zeolites in catalysis includes adsorption capability to the compound of the reactants. Zeolites with a pore size of specific properties selectively adsorbing molecules. A molecule can be adsorbed by either the zeolite cavities if the size and shape of the molecule in accordance with the size and shape of the cavity in the zeolite. At this time, it is common to use homogeneous catalysts for biodiesel. We know these catalysts have some disadvantages in its use. Such as the difficulty of separation of the product with the catalyst, the generation of waste that is harmful to the environment due to residual catalysts can’t be reused, and the difficulty of handling and storage. But nowadays, solid catalyst developed technically to improve the efficiency of biodiesel production. In this case of study, we used trans-esterification process wherein the triglyceride is reacted with an alcohol with zeolite as a solid catalyst and it will produce biodiesel and glycerol as a byproduct. Development of solid catalyst seems to be the perfect solution to address the problems associated with homogeneous catalysts.

Keywords: biodiesel, animal fat, trans esterification, zeolite catalyst

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Authors: Kazuyoshi Mori

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In this paper, we consider the parametrization of the discrete-time systems without the unit-delay element within the framework of the factorization approach. In the parametrization, we investigate the number of required parameters. We consider single-input single-output systems in this paper. By the investigation, we find, on the discrete-time systems without the unit-delay element, three cases that are (1) there exist plants which require only one parameter and (2) two parameters, and (3) the number of parameters is at most three.

Keywords: factorization approach, discrete-time system, parameterization of stabilizing controllers, system without unit-delay

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Authors: Xiaocong He

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Self-pierce riveting (SPR) is a new high-speed mechanical fastening technique which is suitable for point joining dissimilar sheet materials, as well as coated and pre-painted sheet materials. Mechanical structures assembled by SPR are expected to possess a high damping capacity. In this study, experimental measurement techniques were proposed for the prediction of vibration behavior of single-lap cantilevered SPR beams. The dynamic test software and the data acquisition hardware were used in the experimental measurement of the dynamic response of the single-lap cantilevered SPR beams. Free and forced vibration behavior of the single-lap cantilevered SPR beams was measured using the LMS CADA-X experimental modal analysis software and the LMS-DIFA Scadas II data acquisition hardware. The frequency response functions of the SPR beams of different rivet number were compared. The main goal of the paper is to provide a basic measuring method for further research on vibration based non-destructive damage detection in single-lap cantilevered SPR beams.

Keywords: self-piercing riveting, dynamic response, experimental measurement, frequency response functions

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Authors: Jessie Rapoza, Petr Moroshkin, Jimmy Xu

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Chirality is omnipresent, in nature, in life, and in the field of physics. One intriguing example is the homochirality that has remained a great secret of life. Another is the pairs of mirror-image molecules – enantiomers. They are identical in atomic composition and therefore indistinguishable in the scalar physical properties. Yet, they can be either therapeutic or toxic, depending on their chirality. Recent studies suggest a potential link between abnormal levels of certain D-amino acids and some serious health impairments, including schizophrenia, amyotrophic lateral sclerosis, and potentially cancer. Although indistinguishable in their scalar properties, the chirality of a molecule reveals itself in interaction with the surrounding of a certain chirality, or more generally, a broken mirror-symmetry. In this work, we report on a system for chiral molecule detection, in which the mirror-symmetry is doubly broken, first by asymmetric structuring a nanopatterned plasmonic surface than by the incidence of circularly polarized light (CPL). In this system, the incident circularly-polarized light induces a surface plasmon polariton (SPP) wave, propagating along the asymmetric plasmonic surface. This SPP field itself is chiral, evanescently bound to a near-field zone on the surface (~10nm thick), but with an amplitude greatly intensified (by up to 104) over that of the incident light. It hence probes just the molecules on the surface instead of those in the volume. In coupling to molecules along its path on the surface, the chiral SPP wave favors one chirality over the other, allowing for chirality detection via the change in an optical rectification current measured at the edges of the sample. The asymmetrically structured surface converts the high-frequency electron plasmonic-oscillations in the SPP wave into a net DC drift current that can be measured at the edge of the sample via the mechanism of optical rectification. The measured results validate these design concepts and principles. The observed optical rectification current exhibits a clear differentiation between a pair of enantiomers. Experiments were performed by focusing a 1064nm CW laser light at the sample - a gold grating microchip submerged in an approximately 1.82M solution of either L-arabinose or D-arabinose and water. A measurement of the current output was then recorded under both rights and left circularly polarized lights. Measurements were recorded at various angles of incidence to optimize the coupling between the spin-momentums of the incident light and that of the SPP, that is, spin-momentum locking. In order to suppress the background, the values of the photocurrent for the right CPL are subtracted from those for the left CPL. Comparison between the two arabinose enantiomers reveals a preferential signal response of one enantiomer to left CPL and the other enantiomer to right CPL. In sum, this work reports on the first experimental evidence of the feasibility of chiral molecule detection via optical rectification in a metal meta-grating. This nanoscale interfaced electrical detection technology is advantageous over other detection methods due to its size, cost, ease of use, and integration ability with read-out electronic circuits for data processing and interpretation.

Keywords: Chirality, detection, molecule, spin

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Authors: Hamza Zidoum

Abstract:

This paper investigates the impact of human genetic variation on the function of human proteins using machine-learning algorithms. Single-Nucleotide Polymorphism represents the most common form of human genome variation. We focus on the single amino-acid polymorphism located in the coding region as they can affect the protein function leading to pathologic phenotypic change. We use several supervised Machine Learning methods to identify structural properties correlated with increased risk of the missense mutation being damaging. SVM associated with Principal Component Analysis give the best performance.

Keywords: single-nucleotide polymorphism, machine learning, feature selection, SVM

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Authors: R. Reshma srilakshmi, S. Shalini, P. Yogeeswari, D. Sriram

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Lysine aminotransferase is a crucial enzyme for dormancy in M. tuberculosis. It is involved in persistence and antibiotic resistance. In present work, we attempted to develop benzthiazole derivatives as lysine aminotransferase inhibitors. In our attempts, we also unexpectedly arrived at an interesting compound 21 (E)-4-(5-(2-(benzo[d]thiazol-2-yl)-2-cyanovinyl)thiophen-2-yl)benzoic acid which even though has moderate activity against persistent phase of mycobacterium, it has significant potency against active phase. In the entire series compound 22 (E)-4-(5-(2-(benzo[d]thiazol-2-yl)-2-cyanovinyl)thiophen-2-yl)isophthalic acid emerged as potent molecule with LAT IC50 of 2.62 µM. It has a significant log reduction of 2.9 and 2.3 fold against nutrient starved and biofilm forming mycobacteria. It was found to be inactive in MABA assay and M.marinum induced zebra fish model. It is also devoid of cytotoxicity. Compound 22 was also found to possess bactericidal effect which is independent of concentration and time. It was found to be effective in combination with Rifampicin in 3D granuloma model. The results are very encouraging as the hit molecule shows activity against active as well as persistent forms of tuberculosis. The identified hit needs further more pharmacokinetic and dynamic screening for development as new drug candidate.

Keywords: benzothiazole, latent tuberculosis, LAT, nutrient starvation

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Authors: Reinhard Neck, Guido Schäfer

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In this paper, we explore the macroeconomic effects of the European Single Market on Austria by simulating the McKibbin-Sachs Global Model. Global interdependence and the impact of long-run effects on short-run adjustments are taken into account. We study the sensitivity of the results with respect to different assumptions concerning monetary and fiscal policies for the countries and regions of the world economy. The consequences of different assumptions about budgetary policies in Austria are also investigated. The simulation results are contrasted with ex-post evaluations of the actual impact of Austria’s membership in the Single Market. As a result, it can be concluded that the Austrian participation in the European Single Market entails considerable long-run gains for the Austrian economy with nearly no adverse side-effects on any macroeconomic target variable.

Keywords: macroeconomics, European Union, simulation, sensitivity analysis

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Authors: Maheen Zia

Abstract:

Near the early twenty-first century, LEGO decided to diversify its product range which resulted in more specific and single-outcome sets occupying the store shelves than classic kits having fairly all-purpose bricks. Earlier, LEGOs came with more bricks and lesser instructions. Today, there are more single kits being produced and sold, which come with a strictly defined set of guidelines. If one set is used to make a car, the same bricks cannot be put together to produce any other article. Earlier, multiple bricks gave children a chance to be imaginative, think of new items and construct them (by just putting the same pieces differently). The new products are less open-ended and offer a limited possibility for players in both designing and realizing those designs. The article reviews (in the light of existing research) how classic LEGO sets could help enhance a child’s creativity in comparison with single sets, which allow a player to interact (not experiment) with the bricks.

Keywords: constructive play, creativity, LEGO, play-based learning

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Authors: Temesgen Geremew

Abstract:

ZnS/glass and CdS/glass single layers and ZnS/CdS and CdS/ZnS heterojunction thin films were deposited by the chemical bath deposition method using zinc acetate and cadmium acetate as the metal ion sources and thioacetamide as a nonmetallic ion source in acidic medium. Na2EDTA was used as a complexing agent to control the free cation concentration. +e single layer and heterojunction thin films were characterized with X-ray diffraction (XRD), a scanning electron microscope (SEM), energy dispersive X-ray (EDX), and a UV-VIS spectrometer. +e XRD patterns of the CdS/glass thin film deposited on the soda lime glass substrate crystalized in the cubic structure with a single peak along the (111) plane. +e ZnS/CdS heterojunction and ZnS/glass single layer thin films were crystalized in the hexagonal ZnS structure. +e CdS/ZnS heterojunction thin film is nearly amorphous.The optical analysis results confirmed single band gap values of 2.75 eV and 2.5 eV for ZnS/CdS and CdS/ZnS heterojunction thin films, respectively. +e CdS/glass and CdS/ZnS thin films have more imaginary dielectric components than the real part. The optical conductivity of the single layer and heterojunction films is in the order of 1015 1/s. +e optical study also confirmed refractive index values between 2 and 2.7 for ZnS/glass, ZnS/CdS, and CdS/ZnS thin films for incident photon energies between 1.2 eV and 3.8 eV. +e surface morphology studies revealed compacted spherical grains covering the substrate surfaces with few cracks on ZnS/glass, ZnS/CdS, and CdS/glass and voids on CdS/ZnS thin films. +e EDX result confirmed nearly 1 :1 metallic to nonmetallic ion ratio in the single-layered thin films and the dominance of Zn ion over Cd ion in both ZnS/CdS and CdS/ZnS heterojunction thin films.

Keywords: SERS, sensor, Hg2+, water detection, polythiophene

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Authors: Kyung-Jin You, Kiwon Rhee, Marc H. Schieber, Nitish V. Thakor, Hyun-Chool Shin

Abstract:

It remains unknown whether M1 neurons encode multi-finger movements independently or as a certain neural network of single finger movements although multi-finger movements are physically a combination of single finger movements. We present an evidence of correlation between single and multi-finger movements and also attempt a challenging task of semi-blind decoding of neural data with minimum training of the neural decoder. Data were collected from 115 task-related neurons in M1 of a trained rhesus monkey performing flexion and extension of each finger and the wrist (12 single and 6 two-finger-movements). By exploiting correlation of temporal firing pattern between movements, we found that correlation coefficient for physically related movements pairs is greater than others; neurons tuned to single finger movements increased their firing rate when multi-finger commands were instructed. According to this knowledge, neural semi-blind decoding is done by choosing the greatest and the second greatest likelihood for canonical candidates. We achieved a decoding accuracy about 60% for multiple finger movement without corresponding training data set. this results suggest that only with the neural activities on single finger movements can be exploited to control dexterous multi-fingered neuroprosthetics.

Keywords: finger movement, neural activity, blind decoding, M1

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