Search results for: molecular dynamics

Authors: S. Ghalem, M. Mesmoudi, I. Daoudand, H. Allali

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The nitrogen-containing bisphosphonates (N-BPs) are well established as the treatments of choice for disorders of excessive bone resorption, myeloma and bone metastases, and osteoporosis. They inhibit farnesyl pyrophosphate synthase (FFPS), a key enzyme in the mevalonate pathway, resulting in inhibition of the prenylation of small GTP-binding proteins in osteoclasts and disruption of their cytoskeleton, adhesion/spreading, and invasion of cancer cells. A very few examples for synthesis of α-amino bisphosphonates based on several amino acids are known from the literature. In the present work, esters of aminoacid react with ketophsophonate (or their analog acid or acyl) to afford the desired products, α-iminophosphonates. The reaction of imine with dimethyl phosphate in the presence of catalytic amount of I2 give ester of α-aminobisphosphonate as sole product in good yield. Finally, we used computational docking methods to predict how several α-aminobisphosphonates bind to FPPS and how R and X influence. Pamidronate, β-aminobisphosphonate already marketed, was used as reference. These results are of interest since they represent a new and simple way to sythesize α-aminobisphosphonates with a free COOH group increased by R2 functionalisable and opening up the possibility of using the molecular docking to facilitate the design of other, novel FFPS inhibitors.

Keywords: drug research, cancer, α-amino bisphosphonates, molecular docking

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Authors: Paul Awolade, Parvesh Singh

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The global threat of pathogenic resistance to available therapeutic agents has become a menace to clinical practice, public health and man’s existence inconsequential. This has therefore led to an exigency in the development of new molecular scaffolds with profound activity profiles. In this vein, a versatile synthetic tool for accessing new molecules by incorporating two or more pharmacophores into a single entity with the unique ability to be recognized by multiple receptors hence leading to an improved bioactivity, known as molecular hybridization, has been explored with tremendous success. Accordingly, aware of the similarity in pharmacological activity spectrum of quinoline and 1,2,3-triazole pharmacophores such as; anti-Alzheimer, anticancer, anti-HIV, antimalarial and antimicrobial to mention but a few, the present study sets out to synthesize hybrids of quinoline and 1,2,3-triazole. The hybrids were accessed via click chemistry using copper catalysed azide-alkyne 1,3-dipolar cycloaddition reaction. All synthesized compounds were evaluated for their pharmaco-potential in an antimicrobial assay out of which the 3-OH derivative emerged as the most active with MIC value of 4 μg/mL against Cryptococcus neoformans; a value superior to standard Fluconazole and comparable to Amphotericin B. Structures of synthesized hybrids were elucidated using appropriate spectroscopic techniques (1H, 13C and 2D NMR, FT-IR and HRMS).

Keywords: bioisostere, click chemistry, molecular hybridization, quinoline, 1, 2, 3-triazole

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Authors: A. L. Balieiro, D. S. Silveira, R. A. Santos, L. S. Freitas, O. L. S. De Alsina, A. S. Lima, C. M. F. Soares

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The state of Sergipe has been emerging in milk production, mainly in the dairy basin located in the northeast of the state of the Brazil. However, this area concentrates the production of dairy, developing diverse products with higher aggregated value and scent and regional flavours. With this goal the present wok allows the development of dairy drinks with reduced lactose index, using kefir grains flavored with mangaba pulp. Initially, the removal of milk lactose was evaluated in adsorption columns completed with silica particles obtained by molecular impression technique, using sol ? gel method with the presence and absence of lactose biomolecule, molecular imprinted polymer (PIM) or pure matrix (MP), respectively. Then kefir grains were used for the development of dairy drinks flavored with regional fruits (mangaba). The products were analyzed sensorially, evaluated the probiotic potential and the removal of the lactose. Among the products obtained, the one that present best result in the sensorially was to the drink with removal PIM flavored of mangaba, for which around 60% of the testers indicated that would buy the new product.

Keywords: molecular imprinted polymer, milk, lactose, kefir

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Authors: Yunus Onur Yildiz, Mesut Kirca

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In this study, mechanical properties of a nanoporous metal coated with a different metallic material are studied through a new atomistic modelling technique and molecular dynamics (MD) simulations. This new atomistic modelling technique is based on the Voronoi tessellation method for the purpose of geometric representation of the ligaments. With the proposed technique, atomistic models of nanoporous metals which have randomly oriented ligaments with non-uniform mass distribution along the ligament axis can be generated by enabling researchers to control both ligament length and diameter. Furthermore, by the utilization of this technique, atomistic models of coated nanoporous materials can be numerically obtained for further mechanical or thermal characterization. In general, this study consists of two stages. At the first stage, we use algorithms developed for generating atomic coordinates of the coated nanoporous material. In this regard, coordinates of randomly distributed points are determined in a controlled way to be employed in the establishment of the Voronoi tessellation, which results in randomly oriented and intersected line segments. Then, line segment representation of the Voronoi tessellation is transformed to atomic structure by a special process. This special process includes generation of non-uniform volumetric core region in which atoms can be generated based on a specific crystal structure. As an extension, this technique can be used for coating of nanoporous structures by creating another volumetric region encapsulating the core region in which atoms for the coating material are generated. The ultimate goal of the study at this stage is to generate atomic coordinates that can be employed in the MD simulations of randomly organized coated nanoporous structures. At the second stage of the study, mechanical behavior of the coated nanoporous models is investigated by examining deformation mechanisms through MD simulations. In this way, the effect of coating on the mechanical behavior of the selected material couple is investigated.

Keywords: atomistic modelling, molecular dynamic, nanoporous metals, voronoi tessellation

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Authors: Rashida Rahmat Zohra, Afsheen Aman, Shah Ali Ul Qader

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Commercially important biopolymer, dextran, is enzymatically degraded into lower molecular weight fractions of vast industrial potential. Various organisms are associated with dextranase production, among which fungal, yeast and bacterial origins are used for commercial production. Dextranases are used to remove contaminating dextran in sugar processing industry and also used in oral care products for efficient removal of dental plaque. Among the hydrolytic products of dextran, isomaltooligosaccharides have prebiotic effect in humans and reduces the cariogenic effect of sucrose in oral cavity. Dextran derivatives produced by hydrolysis of high molecular polymer are also conjugated with other chemical and metallic compounds for usage in pharmaceutical, fine chemical industry, cosmetics, and food industry. Owing to the vast application of dextran and dextranases, current study focused on purification and analysis of kinetic parameters of dextranase from a newly isolated strain of Bacillus licheniformis KIBGE-IB25. Dextranase was purified up to 35.75 folds with specific activity of 1405 U/mg and molecular weight of 158 kDa. Analysis of kinetic parameters revealed that dextranase performs optimum cleavage of low molecular weight dextran (5000 Da, 0.5%) at 35ºC in 15 min at pH 4.5 with a Km and Vmax of 0.3738 mg/ml and 182.0 µmol/min, respectively. Thermal stability profiling of dextranase showed that it retained 80% activity up to 6 hours at 30-35ºC and remains 90% active at pH 4.5. In short, the dextranase reported here performs rapid cleavage of substrate at mild operational conditions which makes it an ideal candidate for dextran removal in sugar processing industry and for commercial production of low molecular weight oligosaccharides.

Keywords: Bacillus licheniformis, dextranase, gel permeation chromatograpy, enzyme purification, enzyme kinetics

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Authors: Rakesh C. Mathad, G. Y. Lokesh, Basavegowda

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In agriculture using quality seeds of improved varieties is very important to ensure higher productivity thereby food security and sustainability. To ensure good productivity, seeds should have characters as described by the breeder. To know whether the characters as described by the breeder are expressing in a variety such as genuineness or genetic purity, field grow out test (GOT) is done. In pigeon pea which is long durational crop, conducting a GOT may take very long time and expensive also. Since in pigeon pea flower character is a most distinguishing character from the contaminants, conducting a field grow out test require 120-130 days or till flower emergence, which may increase cost of storage and seed production. This will also delay the distribution of seed inventory to the pigeon pea growing areas. In this view during 2014-15 with financial support of Govt. of Karnataka, India, a project to develop a molecular genetic test for newly developed variety of pigeon pea cv.TS3R was commissioned at Seed Unit, UAS, Raichur. A molecular test was developed with the help SSR markers to identify pure variety from possible off types in newly released pigeon pea variety TS3R. In the investigation, 44 primer pairs were screened to identify the specific marker associated with this variety. Pigeon pea cv. TS3R could be clearly identified by using the primer CCM 293 based on the banding pattern resolved on gel electrophoresis and PCR reactions. However some of the markers like AHSSR 46, CCM 82 and CCM 57 can be used to test other popular varieties in the region like Asha, GRG-811 and Maruti respectively. Further to develop this in to a lab test, the seed sample size was standardized to 200 seeds and a grow out matrix was developed. This matrix was used to sample 12 days old leaves to extract DNA. The lab test results were validated with actual field GOT test results and found variations within the acceptable limit of 1%. This molecular method can now be employed to test the genetic purity in pigeon pea cv TS3R which reduces the time and can be a cheaper alternative method for field GOT.

Keywords: genuineness, grow-out matrix, molecular genetic purity, SSR markers

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Authors: Rouhollah Radjabi, Mojtaba Zarei, Elham Sanatgar, Hossein Shouhani

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RAPD molecular markers in order to discrimination of the Iranian native Bombyx mori silkworm breeds were used. DNA extraction using phenol - chloroform was and the qualitative and quantitative measurements of extracted DNA and its dilution, the obtained bands on agarose gel 1.5 percent were marked and analyzed. Results showed that the bands are observed between 250-2500 bp and most bands have been observed as Gilani-orange, the lowest bands observed are Khorasani-lemon. Primer 3 with 100% polymorphism with the highest polymorphism and primer 2 with 61.5 polymorphism had the lowest percentage of polymorphism. Cluster analysis of races and placed them in three main groups, races Gilani - orange, Baghdad and Khorasani -pink if the first group, camel's thorn, Herati - yellow race was alone in the second group and Khorasani – lemon was alone in the third group. The greatest similarity between the races, between Khorasani- pink and Baghdad (0.64). RAPD markers have been determined different silkworm races based on various morphological or economic characteristics except geographic origin.

Keywords: silkworm, molecular marker, RAPD, Iran

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Authors: Freddy Munzhelele

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Setting: the empirical research has shown that the life cycle theory has an impact on the firms’ financing decisions, particularly the dividend pay-outs. Accordingly, the life cycle theory posits that as a firm matures, it gets to a level and capacity where it distributes more cash as dividends. On the other hand, the young firms prioritise investment opportunities sets and their financing; thus, they pay little or no dividends. The research on firms’ financing decisions also demonstrated, among others, the adoption of trade-off and pecking order theories on the dynamics of firms capital structure. The trade-off theory talks to firms holding a favourable position regarding debt structures particularly as to the cost and benefits thereof; and pecking order is concerned with firms preferring a hierarchical order as to choosing financing sources. The case of life cycle hypothesis explaining the financial managers’ decisions as regards the firms’ capital structure dynamics appears to be an interesting link, yet this link has been neglected in corporate finance research. If this link is to be explored as an empirical research, the financial decision-making alternatives will be enhanced immensely, since no conclusive evidence has been found yet as to the dynamics of capital structure. Aim: the aim of this study is to examine the impact of life cycle theory on the capital structure dynamics trade-off and pecking order theories of firms listed in retail, industrial and mining sectors of the JSE. These sectors are among the key contributors to the GDP in the South African economy. Design and methodology: following the postpositivist research paradigm, the study is quantitative in nature and utilises secondary data obtainable from the financial statements of sampled firm for the period 2010 – 2022. The firms’ financial statements will be extracted from the IRESS database. Since the data will be in panel form, a combination of the static and dynamic panel data estimators will used to analyse data. The overall data analyses will be done using STATA program. Value add: this study directly investigates the link between the life cycle theory and the dynamics of capital structure decisions, particularly the trade-off and pecking order theories.

Keywords: life cycle theory, trade-off theory, pecking order theory, capital structure, JSE listed firms

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Authors: R. Hasterok, A. Betekhtin, N. Borowska, A. Braszewska-Zalewska, E. Breda, K. Chwialkowska, R. Gorkiewicz, D. Idziak, J. Kwasniewska, M. Kwasniewski, D. Siwinska, A. Wiszynska, E. Wolny

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In contrast to animals, the organisation of plant genomes at the cytomolecular level is still relatively poorly studied and understood. However, the Brachypodium genus in general and B. distachyon in particular represent exceptionally good model systems for such study. This is due not only to their highly desirable ‘model’ biological features, such as small nuclear genome, low chromosome number and complex phylogenetic relations, but also to the rapidly and continuously growing repertoire of experimental tools, such as large collections of accessions, WGS information, large insert (BAC) libraries of genomic DNA, etc. Advanced cytomolecular techniques, such as fluorescence in situ hybridisation (FISH) with evermore sophisticated probes, empowered by cutting-edge microscope and digital image acquisition and processing systems, offer unprecedented insight into chromatin organisation at various phases of the cell cycle. A good example is chromosome painting which uses pools of chromosome-specific BAC clones, and enables the tracking of individual chromosomes not only during cell division but also during interphase. This presentation outlines the present status of molecular cytogenetic analyses of plant genome structure, dynamics and evolution using B. distachyon and some of its relatives. The current projects focus on important scientific questions, such as: What mechanisms shape the karyotypes? Is the distribution of individual chromosomes within an interphase nucleus determined? Are there hot spots of structural rearrangement in Brachypodium chromosomes? Which epigenetic processes play a crucial role in B. distachyon embryo development and selective silencing of rRNA genes in Brachypodium allopolyploids? The authors acknowledge financial support from the Polish National Science Centre (grants no. 2012/04/A/NZ3/00572 and 2011/01/B/NZ3/00177)

Keywords: Brachypodium, B. distachyon, chromosome, FISH, molecular cytogenetics, nucleus, plant genome organisation

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Authors: Sedat Yayla, Mehmet Oruc, Shakhwan Yaseen

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Cavitation phenomena might rigorously impair machine parts such as pumps, propellers and impellers or devices as the pressure in the fluid declines under the liquid's saturation pressure. To evaluate the influence of cavitation, in this research two-dimensional computational fluid dynamics (CFD) venturi models with variety of inlet pressure values, throat lengths and vapor fluid contents were applied. In this research three different vapor contents (0%, 5% 10%), four inlet pressures (2, 4, 6, 8 and 10 atm) and two venturi models were employed at different throat lengths ( 5, 10, 15 and 20 mm) for discovering the impact of each parameter on the cavitation number. It is uncovered that there is a positive correlation between pressure inlet and vapor fluid content and cavitation number. Furthermore, it is unveiled that velocity remains almost constant at the inlet pressures of 6, 8,10atm, nevertheless increasing the length of throat results in the substantial escalation in the velocity of the throat at inlet pressures of 2 and 4 atm. Furthermore, velocity and cavitation number were negatively correlated. The results of the cavitation number varied between 0.092 and 0.495 depending upon the velocity values of the throat.

Keywords: cavitation number, computational fluid dynamics, mixture of fluid, two-phase flow, velocity of throat

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Authors: Muzna Tariq, Ihtzaz Qamar

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In most engineering cases, the working temperatures inside a combustion chamber are high enough that they lie beyond the operational range of thermocouples. Furthermore, design and manufacturing limitations restrict the use of internal thermocouples in many applications. Heat transfer inside a combustion chamber is caused due to interaction of the post-combustion hot fluid with the chamber wall. Heat transfer that involves an interaction between the fluid and solid is categorized as Conjugate Heat Transfer (CHT). Therefore, to satisfy the needs of CHT, CHT Analysis is performed by using ANSYS CFD tool to estimate theoretically precise thermocouple positions at the combustion chamber wall where excessive temperatures (beyond thermocouple range) can be avoided. In accordance with these Computational Fluid Dynamics (CFD) results, a combustion chamber is designed, and a prototype is manufactured with multiple thermocouple ports positioned at the specified distances so that the temperature of hot gases can be measured on the chamber wall where the temperatures do not exceed the thermocouple working range.

Keywords: computational fluid dynamics, conduction, conjugate heat transfer, convection, fluid flow, thermocouples

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Authors: Yusuf Jundi Sado

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Changes in land use are mostly credited to human actions that result in negative impacts on biodiversity and ecosystem functions. This study aims to analyze the dynamics of land use and land cover changes for sustainable natural resources planning and management. Chilalo-Galama Mountain Range, Ethiopia. This study used Thematic Mapper 05 (TM) for 1986, 2001 and Landsat 8 (OLI) data 2017. Additionally, data from the Central Statistics Agency on human population growth were analyzed. Semi-Automatic classification plugin (SCP) in QGIS 3.2.3 software was used for image classification. Global positioning system, field observations and focus group discussions were used for ground verification. Land Use Land Cover (LU/LC) change analysis was using maximum likelihood supervised classification and changes were calculated for the 1986–2001 and the 2001–2017 and 1986-2017 periods. The results show that agricultural land increased from 27.85% (1986) to 44.43% and 51.32% in 2001 and 2017, respectively with the overall accuracies of 92% (1986), 90.36% (2001), and 88% (2017). On the other hand, forests decreased from 8.51% (1986) to 7.64 (2001) and 4.46% (2017), and grassland decreased from 37.47% (1986) to 15.22%, and 15.01% in 2001 and 2017, respectively. It indicates for the years 1986–2017 the largest area cover gain of agricultural land was obtained from grassland. The matrix also shows that shrubland gained land from agricultural land, afro-alpine, and forest land. Population dynamics is found to be one of the major driving forces for the LU/LU changes in the study area.

Keywords: Landsat, LU/LC change, Semi-Automatic classification plugin, population dynamics, Ethiopia

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Authors: Khaled Bahgat

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In the present work, the characterization of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione (APTT) molecule was carried out by quantum chemical method and vibrational spectral techniques. The FT-IR (4000–400 cm_1) and FT-Raman (4000–100 cm_1) spectra of APTT were recorded in solid phase. The UV–Vis absorption spectrum of the APTT was recorded in the range of 200–400 nm. The molecular geometry, harmonic vibrational frequencies and bonding features of APTT in the ground state have been calculated by HF and DFT methods using 6-311++G(d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO) and natural localized molecular orbital (NLMO) analysis. The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by time depended DFT (TD-DFT) approach. The 1H and 13C nuclear magnetic resonance chemical shift of the molecule were calculated using the gauge-including atomic orbital (GIAO) method and compared with experimental results. Finally, the calculation results were analyzed to simulate infrared, FT-Raman and UV spectra of the title compound which shows better agreement with observed spectra.

Keywords: 4-amino-3-phenyl-1H-1, 2, 4-triazole-5(4H)-thione, vibrational assignments, normal coordinate analysis, quantum mechanical calculations

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Authors: Sebastian Gerber, Julian Fesel, Christian Zimmer, Pauline Yzombard, Daniel Comparat, Michael Doser

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Molecular anions play a central role in a wide range of fields: from atmospheric and interstellar science, anionic superhalogens to the chemistry of highly correlated systems. However, up to now the synthesis of negative ions in a controlled manner at ultracold temperatures, relevant for the processes in which they are involved, is currently limited to a few Kelvin by supersonic beam expansion followed by resistive, buffer gas or electron cooling in cryogenic environments. We present a realistic scheme for laser cooling of C2- molecules to sub-Kelvin temperatures, which has so far only been achieved for a few neutral diatomic molecules. The generation of a pulsed source of C2- and subsequent laser cooling techniques of C2- molecules confined in a Penning trap are reviewed. Further, laser cooling of one anionic species would allow to sympathetically cool other molecular anions, electrons and antiprotons that are confined in the same trapping potential. In this presentation the status of the experiment and the feasibility of C2- sympathetic Doppler laser cooling, photo-detachment cooling and AC-Stark Sisyphus cooling will be reviewed.

Keywords: antiprotons, anions, cooling of ions and molecules, Doppler cooling, photo-detachment, penning trap, Sisyphus cooling, sympathetic cooling

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Authors: Guanyu Jiang, Donghai Xu, Huanteng Liu

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After the Fukushima-Daiichi accident, the development of accident tolerant fuel cladding materials to improve reactor safety has become a hot topic in the field of nuclear industry. ZrO₂ has a satisfactory neutron economy and can guarantee the fission chain reaction process, which enables it to be a promising coating for zirconium alloy cladding. Maintaining a good corrosion resistance in primary coolant loop during normal operations of Pressurized Water Reactors is a prerequisite for ZrO₂ as a protective coating on zirconium alloy cladding. Research on the corrosion performance of ZrO₂ coating in nuclear water chemistry is relatively scarce, and existing reports failed to provide an in-depth explanation for the failure causes of ZrO₂ coating. Herein, a detailed corrosion process of ZrO₂ coating in lithiated water at 360 °C and 18.5 MPa was proposed based on experimental research and molecular dynamics simulation. Lithiated water with different LiOH solutions in the present work was deaerated and had a dissolved oxygen concentration of < 10 ppb. The concentration of Li (as LiOH) was determined to be 2.3 ppm, 70 ppm, and 500 ppm, respectively. Corrosion tests were conducted in a static autoclave. Modeling and corresponding calculations were operated on Materials Studio software. The calculation of adsorption energy and dynamics parameters were undertaken by the Energy task and Dynamics task of the Forcite module, respectively. The protective effect and failure mechanism of ZrO₂ coating on Zry-4 under varied LiOH concentrations was further revealed by comparison with the coating corrosion performance in pure water (namely 0 ppm Li). ZrO₂ coating provided a favorable corrosion protection with the occurrence of localized corrosion at low LiOH concentrations. Factors influencing corrosion resistance mainly include pitting corrosion extension, enhanced Li+ permeation, short-circuit diffusion of O²⁻ and ZrO₂ phase transformation. In highly-concentrated LiOH solutions, intergranular corrosion, internal oxidation, and perforation resulted in coating failure. Zr ions were released to coating surface to form flocculent ZrO₂ and ZrO₂ clusters due to the strong diffusion and dissolution tendency of α-Zr in the Zry-4 substrate. Considering that primary water of Pressurized Water Reactors usually includes 2.3 ppm Li, the stability of ZrO₂ make itself a candidate fuel cladding coating material. Under unfavorable conditions with high Li concentrations, more boric acid should be added to alleviate caustic corrosion of ZrO₂ coating once it is used. This work can provide some references to understand the service behavior of nuclear coatings under variable water chemistry conditions and promote the in-pile application of ZrO₂ coating.

Keywords: ZrO₂ coating, Zry-4, corrosion behavior, failure mechanism, LiOH concentration

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Authors: Worrapol Koranuntachai, Tonkid Chantrasmi, Udomkiat Nontakaew

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Medical latex gloves are made from the latex compound in production lines. Latex dipping is considered one of the most important processes that directly affect the final product quality. In a continuous production line, a chain conveyor carries the formers through the process and partially submerges them into an open channel flow in a latex dipping tank. In general, the conveyor speed is determined by the desired production capacity, and the latex-dipping tank can then be designed accordingly. It is important to understand the flow behavior in the dipping tank in order to achieve high quality in the process. In this work, Computational Fluid Dynamics (CFD) was used to simulate the flow past an array of formers in a simplified latex dipping process. The computational results showed both the flow structure and the vortex generation between two formers. The maximum shear stress over the surface of the formers was used as the quality metric of the latex-dipping process when adjusting operation parameters.

Keywords: medical latex gloves, latex dipping, dipping tank, computational fluid dynamics

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Authors: Lidija R. Jevrić, Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević

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Quantitative structure-retention relationship (QSRR) analysis was used to predict the chromatographic behavior of s-triazine derivatives by using theoretical descriptors computed from the chemical structure. Fundamental basis of the reported investigation is to relate molecular topological descriptors with chromatographic behavior of s-triazine derivatives obtained by reversed-phase (RP) thin layer chromatography (TLC) on silica gel impregnated with paraffin oil and applied ethanol-water (φ = 0.5-0.8; v/v). Retention parameter (RM0) of 14 investigated s-triazine derivatives was used as dependent variable while simple connectivity index different orders were used as independent variables. The best QSRR model for predicting RM0 value was obtained with simple third order connectivity index (3χ) in the second-degree polynomial equation. Numerical values of the correlation coefficient (r=0.915), Fisher's value (F=28.34) and root mean square error (RMSE = 0.36) indicate that model is statistically significant. In order to test the predictive power of the QSRR model leave-one-out cross-validation technique has been applied. The parameters of the internal cross-validation analysis (r2CV=0.79, r2adj=0.81, PRESS=1.89) reflect the high predictive ability of the generated model and it confirms that can be used to predict RM0 value. Multivariate classification technique, hierarchical cluster analysis (HCA), has been applied in order to group molecules according to their molecular connectivity indices. HCA is a descriptive statistical method and it is the most frequently used for important area of data processing such is classification. The HCA performed on simple molecular connectivity indices obtained from the 2D structure of investigated s-triazine compounds resulted in two main clusters in which compounds molecules were grouped according to the number of atoms in the molecule. This is in agreement with the fact that these descriptors were calculated on the basis of the number of atoms in the molecule of the investigated s-triazine derivatives.

Keywords: s-triazines, QSRR, chemometrics, chromatography, molecular descriptors

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Authors: Sunita Gakkhar, Arti Mishra

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In this paper, a nonlinear host vector model has been proposed and analyzed for the two strain dengue dynamics incorporating ADE effect. The model considers that the asymptomatic infected people are more responsible for secondary infection than that of symptomatic ones and differentiates between them. The existence conditions are obtained for various equilibrium points. Basic reproduction number has been computed and analyzed to explore the effect of secondary infection enhancement parameter on dengue infection. Stability analyses of various equilibrium states have been performed. Numerical simulation has been done for the stability of endemic state.

Keywords: dengue, ade, stability, threshold, asymptomatic, infection

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Authors: O. J. Jesumoroti, Faridoon, R. Klein, K. A. Iobb, D. Mnkadhla, H. C. Hoppe, P. T. Kaye

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The 1, 3-aryl diketo acids (DKA) based agents represent an important class of HIV integrase (IN) strand transfer inhibitors. In other to study the chelating role of the divalent metal ion in the inhibition of IN strand transfer, we designed and synthesized a series of 2-hydroxy-3-oxo-3-phenyl propionate derivatives with the notion that such compounds could interact with the divalent ion in the active site of IN. The synthetic sequence to the desired compounds involves the concept of Doebner knoevenagel condensation, Fischer esterification and ketohydroxylation using neuclophilic re-oxidant; compounds were characterized by their IR, IHNMR, 13CNMR, HRMS spectroscopic data and melting point determination. Also, molecular docking was employed in this study and it was revealed that there is interaction with the active site of the enzyme. However, there is disparity in the corresponding anti-HIV activity determined by the experimental bioassay. These compounds lack potency at low micromolar concentration when compared to the results of the docking studies. Nevertheless, the results of the study suggest modification of the aryl ring with one or two hydroxyl groups to improve the inhibitory activity.

Keywords: anti-HIV-1 integrase, ketohydroxylation, molecular docking, propionate derivatives

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Authors: Supannika Klangphukhiew, Roongnapa Srichana, Rina Patramanon

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Cortisol has been used as a well-known commercial stress biomarker. A homeostasis response to psychological stress is indicated by an increased level of cortisol produced in hypothalamus-pituitary-adrenal (HPA) axis. Chronic psychological stress contributing to the high level of cortisol relates to several health problems. In this study, the cortisol biosensor was fabricated that mimicked the natural receptors. The artificial antibodies were prepared using molecular imprinted polymer technique that can imitate the performance of natural anti-cortisol antibody with high stability. Cortisol-molecular imprinted polymer (cortisol-MIP) was obtained using the multi-step swelling and polymerization protocol with cortisol as a target molecule combining methacrylic acid:acrylamide (2:1) with bisacryloyl-1,2-dihydroxy-1,2-ethylenediamine and ethylenedioxy-N-methylamphetamine as cross-linkers. Cortisol-MIP was integrated to the sensor. It was coated on the disposable screen-printed carbon electrode (SPCE) for portable electrochemical analysis. The physical properties of Cortisol-MIP were characterized by means of electron microscope techniques. The binding characteristics were evaluated via covalent patterns changing in FTIR spectra which were related to voltammetry response. The performance of cortisol-MIP modified SPCE was investigated in terms of detection range, high selectivity with a detection limit of 1.28 ng/ml. The disposable cortisol biosensor represented an application of MIP technique to recognize steroids according to their structures with feasibility and cost-effectiveness that can be developed to use in point-of-care.

Keywords: stress biomarker, cortisol, molecular imprinted polymer, screen-printed carbon electrode

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Authors: Giulio Mangano, Alberto De Marco, Giovanni Zenezini

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The concept of City Logistics (CL) has emerged to improve the impacts of last mile freight distribution in urban areas. In this paper, a System Dynamics (SD) model exploring the dynamics of the diffusion of a ICT platform for CL management across different populations is proposed. For the development of the model two sources have been used. On the one hand, the major diffusion variables and feedback loops are derived from a literature review of existing diffusion models. On the other hand, the parameters are represented by the value propositions delivered by the platform as a response to some of the users’ needs. To extract the most important value propositions the Business Model Canvas approach has been used. Such approach in fact focuses on understanding how a company can create value for her target customers. These variables and parameters are thus translated into a SD diffusion model with three different populations namely municipalities, logistics service providers, and own account carriers. Results show that, the three populations under analysis fully adopt the platform within the simulation time frame, highlighting a strong demand by different stakeholders for CL projects aiming at carrying out more efficient urban logistics operations.

Keywords: city logistics, simulation, system dynamics, business model

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Authors: Y. Yang, Dian Ming Xing, Qiu Hua Du

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Based on the Motorized Momentum Exchange Tether (MMET), with the principle of momentum exchange, the three dimension flexible dynamics of continuous cislunar payloads transferring system (CCPTS) is built by Lagrange method and its numerical solution is solved by Mathematica software. In the derivation precession of potential energy, this paper uses the Tylor expansion method to simplify the Lagrange equation. Furthermore, the tension coming from the centripetal load is considered in the elastic potential energy. The comparison simulation results between the 3D rigid model and 3D flexible model of CCPTS shows that the tether flexibility has important influence on CCPTS’s orbital parameters (such as radius of CCPTS’s COM and the true anomaly) and the tether’s rotational movement, the relative deviation of radius and the true anomaly between the two dynamic models is about 0.00678% and 0.00259%, the relative deviation of the angle of tether-span and local gravity gradient is about 3.55%. Additionally, the external torque has an apparent influence on the tether’s axial vibration.

Keywords: cislunar transfer, dynamics, momentum exchange, tether

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Authors: Desta Gebretekle Shiferaw, Balakrishna Kalluraya

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Oxadiazoles and their derivatives with thioether functionalities represent a new and exciting class of physiologically active heterocyclic compounds. Several molecules with these moieties play a vital role in pharmaceuticals because of their diverse biological activities. This paper describes a new class of 1,3,4- oxadiazole-2-thioethers with acetophenone, coumarin, and N-phenyl acetamide residues (S-alkylation), with the hope that the addition of various biologically active molecules will have a synergistic effect on anticancer activity. The structure of the synthesized title compounds was determined by the combined methods of IR, proton-NMR, carbon-13-NMR, and mass spectrometry. Further, all the newly prepared molecules were assessed against their antioxidant activity. Furthermore, four compounds were assessed for their molecular docking interactions and cytotoxicity activity. The synthesized derivatives have shown moderate antioxidant activity compared to the standard BHA. The IC50 of the tilted molecules (11b, 11c, 13b, and 14b) observed for in vitro anti-cancer activities were 11.20, 15.73, 59.61, and 27.66 g/ml at 72-hour treatment time against the A549 cell lines, respectively. The tested compounds' biological evaluation showed that 11b is the most effective molecule in the series.

Keywords: antioxidant activity, cytotoxicity activity, molecular docking, 1, 3, 4-Oxadiazole-2 thioether derivatives

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Authors: Janne Engblom, Elias Oikarinen

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The understanding of housing price dynamics is of importance to a great number of agents: to portfolio investors, banks, real estate brokers and construction companies as well as to policy makers and households. A panel dataset is one that follows a given sample of individuals over time, and thus provides multiple observations on each individual in the sample. Panel data models include a variety of fixed and random effects models which form a wide range of linear models. A special case of panel data models is dynamic in nature. A complication regarding a dynamic panel data model that includes the lagged dependent variable is endogeneity bias of estimates. Several approaches have been developed to account for this problem. In this paper, the panel models were estimated using the Common Correlated Effects estimator (CCE) of dynamic panel data which also accounts for cross-sectional dependence which is caused by common structures of the economy. In presence of cross-sectional dependence standard OLS gives biased estimates. In this study, U.S housing price dynamics were examined empirically using the dynamic CCE estimator with first-difference of housing price as the dependent and first-differences of per capita income, interest rate, housing stock and lagged price together with deviation of housing prices from their long-run equilibrium level as independents. These deviations were also estimated from the data. The aim of the analysis was to provide estimates with comparisons of estimates between 1980-1999 and 2000-2012. Based on data of 50 U.S cities over 1980-2012 differences of short-run housing price dynamics estimates were mostly significant when two time periods were compared. Significance tests of differences were provided by the model containing interaction terms of independents and time dummy variable. Residual analysis showed very low cross-sectional correlation of the model residuals compared with the standard OLS approach. This means a good fit of CCE estimator model. Estimates of the dynamic panel data model were in line with the theory of housing price dynamics. Results also suggest that dynamics of a housing market is evolving over time.

Keywords: dynamic model, panel data, cross-sectional dependence, interaction model

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Authors: Timothy Onyenobi

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Accidental fires and its dynamic as it relates to building compartmentation and the impact of the compartment morphology, is still an on-going area of study; especially with the use of computational fluid dynamics (CFD) modeling methods. With better knowledge on this subject come better solution recommendations by fire engineers. Interviews were carried out for this study where it was identified that the response perspectives to accidental fire were different with the fire engineer providing qualitative data which is based on “what is expected in real fires” and the fire fighters provided information on “what actually obtains in real fires”. This further led to a study and analysis of two real and comprehensively instrumented fire experiments: the Open Plan Office Project by National Institute of Standard and Technology (NIST) USA (to study time to flashover) and the TF2000 project by the Building Research Establishment (BRE) UK (to test for conformity with Building Regulation requirements). The findings from the analysis of the experiments revealed the relative yet critical weakness of fire prediction using a CFD model (usually used by fire engineers) as well as explained the differences in response perspectives of the fire engineers and firefighters from the interview analysis.

Keywords: CFD, compartment fire, experiment, fire fighters, fire engineers

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Authors: Mojtaba Mirmontazemi, Habibollah Dadgar

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Bone is the most common metastasis site in some advanced malignancies, such as prostate and breast cancer. Bone metastasis generally indicates fewer prognostic factors in these patients. Different radiological and molecular imaging modalities are used for detecting bone lesions. Molecular imaging including computed tomography, magnetic resonance imaging, planar bone scintigraphy, single-photon emission tomography, and positron emission tomography as noninvasive visualization of the biological occurrences has the potential to exact examination, characterization, risk stratification and comprehension of human being diseases. Also, it is potent to straightly visualize targets, specify clearly cellular pathways and provide precision medicine for molecular targeted therapies. These advantages contribute implement personalized treatment for each patient. Currently, NaF PET/CT has significantly replaced standard bone scintigraphy for the detection of bone metastases. On one hand, 68Ga-PSMA PET/CT has gained high attention for accurate staging of primary prostate cancer and restaging after biochemical recurrence. On the other hand, FDG PET/CT is not commonly used in osseous metastases of prostate and breast cancer as well as its usage is limited to staging patients with aggressive primary tumors or localizing the site of disease. In this article, we examine current studies about FDG, NaF, and PSMA PET/CT images in bone metastases diagnostic utility and assess response to treatment in patients with breast and prostate cancer.

Keywords: skeletal metastases, fluorodeoxyglucose, sodium fluoride, molecular imaging, precision medicine, prostate cancer (68Ga-PSMA-11)

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Authors: Hind O. Osman, Tilal Elsaman, Bashir A. Yousef, Esraa Elhadi, Aimun A. E. Ahmed, Eyman Mohamed Eltayib, Malik Suliman Mohamed, Magdi Awadalla Mohamed

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Epilepsy is the most common neurological condition and cause of substantial morbidity and mortality. In the present study, the molecular hybridization tool was adopted to obtain six Schiff bases of isatin and adamantane-1-carbohydrazide (18–23). Then, their anticonvulsant activity was evaluated using a pentylenetetrazole- (PTZ-) induced seizure model using phenobarbitone as a positive control. Our findings showed that compounds 18–23 provided significant protection against PTZ-induced seizure, and maximum activities were associated with compound 23. Moreover, all investigated compounds increased the latency of induced convulsion and reduced the duration of epilepsy, with compound 23 being the best. Interestingly, most of the synthesized molecules showed a reduction in neurological symptoms and severity of the seizure. Molecular docking studies suggest GABA-A receptor as a potential target, and in silico ADME screening revealed that the pharmaceutical properties of compound 23 are within the specified limit. Thus, compound 23 was identified as a promising candidate that warrants further drug discovery processes.

Keywords: isatin and adamantane, anticonvulsant activity, PTZ-induced seizure, molecular docking

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Authors: Xinyi Xu

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This study conducts a detailed examination of Asian stock markets over the period from 2008 to 2023, with a focus on the dynamics of cointegration and their relevance for long-term investment strategies. Specifically, we assess the co-movement and potential for pairs trading—a strategy where investors take opposing positions on two stocks, indices, or financial instruments that historically move together. For example, we explore the relationship between the Nikkei 225 (N225), Japan’s benchmark stock index, and the Straits Times Index (STI) of Singapore, as well as the relationship between the Korea Composite Stock Price Index (KS11) and the STI. The methodology includes tests for normality, stationarity, cointegration, and the application of Vector Error Correction Modeling (VECM). Our findings reveal significant long-term relationships between these pairs, indicating opportunities for pairs trading strategies. Furthermore, the research underscores the challenges posed by model instability and the influence of major global incidents, which are identified as structural breaks. These findings pave the way for further exploration into the intricacies of financial market dynamics.

Keywords: normality tests, stationarity, cointegration, VECM, pairs trading

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Authors: Dong Xie, Jun Zhao, Yiming Weng

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One of the challenges in dental cement biomaterials is how to make a restorative with mechanical strengths and wear resistance that are comparable to contemporary dental resin composites. Currently none of the dental cement restoratives has been used in high stress-bearing sites due to their low mechanical strengths and poor wear-resistance. The objective of this study was to synthesize and characterize the poly(alkenoic acid)s with different molecular structures, use these polymers to formulate a dental cement restorative, and study the effect of molecular structures on reaction kinetics, viscosity, and mechanical strengths of the formed polymers and cement restoratives. In this study, poly(alkenoic acid)s with different molecular structures were synthesized. The purified polymers were formulated with commercial Fuji II LC glass fillers to form the experimental cement restoratives. The reaction kinetics was studied via 1HNMR spectroscopy. The formed restoratives were evaluated using compressive strength, diametral tensile strength, flexural strength, hardness and wear-resistance tests. Specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. Fuji II LC restorative was used as control. The results show that the higher the arm number and initiator concentration, the faster the reaction was. It was also found that the higher the arm number and branching that the polymer had, the lower the viscosity of the polymer in water and the lower the mechanical strengths of the formed restorative. The experimental restoratives were 31-53% in compressive strength, 37-55% in compressive modulus, 80-126% in diametral tensile strength, 76-94% in flexural strength, 4-21% in fracture toughness and 53-96% in hardness higher than Fuji II LC. For wear test, the experimental restoratives were only 5.4-13% of abrasive and 6.4-12% of attritional wear depths of Fuji II LC in each wear cycle. The aging study also showed that all the experimental restoratives increased their strength continuously during 30 days, unlike Fuji II LC. It is concluded that polymer molecular structures have significant and positive impact on mechanical properties of dental cement restoratives.

Keywords: dental materials, polymers, strength, biomaterials

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Authors: Miroslava Marković, Renata Gagić, Serdar, Aleksandar Lučić, Ljubinko Rakonjac

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Forest dieback that comes in waves since the early 20th century has lately grown into an epidemic, in particular in oak stands. For this reason, research was conducted of the population dynamics of early oak defoliators, which represent a grave danger in oak stands due to their gradogenic attributes. The research was carried out over a 5-year period in oak forests in the area of forest administrations Kragujevac and Gornji Milanovac. The samples used in the research were collected from bottom branches, where Geometridae were found in the largest numbers, as well as from the mid and upper parts of the crowns, where other species were found. Population levels of these pests were presented in laboratory conditions on winter branch samples and in newly foliated stands on site, depending on the basic parameters of the climatic conditions. The greatest deviation of the population level of early oak defoliators was noted in 2018 on all 6 presented localities through the analysis of winter branches and the analysis of their presence in newly foliated stands on site, and it was followed by the highest average air temperature.

Keywords: defoliators, oak, population level, population dynamics

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