Search results for: dimensionless binding

Authors: Jiya Mohammed, Ibrahim Ismail Giwa

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Unsteady squeezing flow of a viscous fluid between parallel plates is considered. The two plates are considered to be approaching each other symmetrically, causing the squeezing flow. Two-dimensional rectangular Cartesian coordinate is considered. The Navier-Stokes equation was reduced using similarity transformation to a single fourth order non-linear ordinary differential equation. The energy equation was transformed to a second order coupled differential equation. We obtained solution to the resulting ordinary differential equations via Homotopy Perturbation Method (HPM). HPM deforms a differential problem into a set of problem that are easier to solve and it produces analytic approximate expression in the form of an infinite power series by using only sixth and fifth terms for the velocity and temperature respectively. The results reveal that the proposed method is very effective and simple. Comparisons among present and existing solutions were provided and it is shown that the proposed method is in good agreement with Variation of Parameter Method (VPM). The effects of appropriate dimensionless parameters on the velocity profiles and temperature field are demonstrated with the aid of comprehensive graphs and tables.

Keywords: coupled differential equation, Homotopy Perturbation Method, plates, squeezing flow

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Authors: A. U. Haque, W. Asrar, A. A Omar, E. Sulaeman, J. S. M. Ali

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Buoyancy force applied on deformable symmetric bodies can be estimated by using Archimedes Principle. Such bodies like ellipsoidal bodies have high volume to surface ratio and are isometrically scaled for mass, length, area and volume to follow square cube law. For scaling up such bodies, it is worthwhile to find out the scaling relationship between the other physical quantities that represent thermodynamic, structural and inertial response etc. So, dimensionless similarities to find an allometric scale can be developed by using Bukingham π theorem which utilizes physical dimensions of important parameters. Base on this fact, physical dependencies of buoyancy system are reviewed to find the set of physical variables for deformable bodies of revolution filled with expandable gas like helium. Due to change in atmospheric conditions, this gas changes its volume and this change can effect the stability of elongated bodies on the ground as well as in te air. Special emphasis was given on the existing similarity parameters which can be used in the design of experiments of such bodies whose shape is affected by the external force like a drag, surface tension and kinetic loads acting on the surface. All these similarity criteria are based on non-dimensionalization, which also needs to be consider for scaling up such bodies.

Keywords: Bukhigham pi theorem, similitude, scaling, buoyancy

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Authors: Moulay Driss Mellaoui, Khadija Zaki, Khalid Abbiche, Abdallah Imjjad, Rachid Boutiddar, Abdelouahid Sbai, Aaziz Jmiai, Souad El Issami, Al Mokhtar Lamsabhi, Hanane Zejli

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This study presents a comprehensive analysis of six isoxazolidine and isoxazoline derivatives, leveraging a multifaceted approach that combines Density Functional Theory (DFT), AdmetSAR analysis, and molecular docking simulations to explore their electronic, pharmacokinetic, and anticancer properties. Through DFT analysis, using the B3LYP-D3BJ functional and the 6-311++G(d,p) basis set, we optimized molecular geometries, analyzed vibrational frequencies, and mapped Molecular Electrostatic Potentials (MEP), identifying key sites for electrophilic attacks and hydrogen bonding. Frontier Molecular Orbital (FMO) analysis and Density of States (DOS) plots revealed varying stability levels among the compounds, with 1b, 2b, and 3b showing slightly higher stability. Chemical potential assessments indicated differences in binding affinities, suggesting stronger potential interactions for compounds 1b and 2b. AdmetSAR analysis predicted favorable human intestinal absorption (HIA) rates for all compounds, highlighting compound 3b superior oral effectiveness. Molecular docking and molecular dynamics simulations were conducted on isoxazolidine and 4-isoxazoline derivatives targeting the EGFR receptor (PDB: 1JU6). Molecular docking simulations confirmed the high affinity of these compounds towards the target protein 1JU6, particularly compound 3b, among the isoxazolidine derivatives, compound 3b exhibited the most favorable binding energy, with a g score of -8.50 kcal/mol. Molecular dynamics simulations over 100 nanoseconds demonstrated the stability and potential of compound 3b as a superior candidate for anticancer applications, further supported by structural analyses including RMSD, RMSF, Rg, and SASA values. This study underscores the promising role of compound 3b in anticancer treatments, providing a solid foundation for future drug development and optimization efforts.

Keywords: isoxazolines, DFT, molecular docking, molecular dynamic, ADMET, drugs.

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Authors: Dong-Gi Lee, Suyeon Cha, Yong-Sun Bahn

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Sterol lipid is essential for cell membrane structure in eukaryotic cells. In mammalian cells, sterol regulatory element binding proteins (SREBPs) act as principal regulators of cellular cholesterol which is essential for proper cell membrane fluidity and structure. SREBP and sterol regulation are related to levels of cellular oxygen because it is a major substrate for sterol synthesis. Upon cellular sterol and oxygen levels are depleted, SREBP is translocated to the Golgi where it undergoes proteolytic cleavage of N terminus, then it travels to the nucleus to play a role as transcription factor. In yeast cells, synthesis of ergosterol is also highly oxygen consumptive, and Sre1 is a transcription factor known to play a central role in adaptation to growth under low oxygen condition and sterol homeostasis in Cryptococcus neoformans. In this study, we observed phenotypes in other strains of Cryptococcus species by constructing hob1Δ and sre1Δ mutants to confirm whether the functions of both genes are conserved in most serotypes. As a result, hob1Δ showed no noticeable phenotype under treatment of antifungal drugs and most environmental stresses in R265 (C. gattii) and XL280 (C. neoformans), suggesting that Hob1 is related to sterol regulation only in H99 (serotype A). On the other hand, the function of Sre1 was found to be conserved in most serotypes. Furthermore, mating experiment of hob1Δ or sre1Δ showed dramatic defects in serotype A (H99) and D (XL280). It revealed that Hob1 and Sre1 related to mating ability in Cryptococcus species, especially cell fusion efficiency. In conclusion, HOB1 and SRE1 play crucial role in regulating sterol-homeostasis and differentiation in C. neoformans, moreover, Hob1 is specific gene in Cryptococcus neoformans. It suggests that Hob1 is considered as potent factor-targeted new safety antifungal drug.

Keywords: cryptococcus neoformans, Hob1, Sre1, sterol regulatory element binding proteins

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Authors: Fadia Gafri, Kathryn Mckintosh, Louise Young, Alan Harvey, Simon Mackay, Andrew Paul, Robin Plevin

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Nuclear factor-kappa B (NF-κB) is a ubiquitous transcription factor found originally to play a key role in regulating inflammation. However considerable evidence links this pathway to the suppression of apoptosis, cellular transformation, proliferation and invasion (Aggarwal et al., 2006). Moreover, recent studies have also linked inflammation to cancer progression making NF-κB overall a promising therapeutic target for drug discovery (Dobrovolskaia & Kozlov, 2005). In this study we examined the effect of the natural product canthin-6-one (SU182) as part of a CRUK small molecule drug discovery programme for effects upon the NF-κB pathway. Initial studies demonstrated that SU182 was found to have good potency against the inhibitory kappa B kinases (IKKs) at 30M in vitro. However, at concentrations up to 30M, SU182 had no effect upon TNFα stimulated loss in cellular IκBα or p65 phosphorylation in the keratinocyte cell line NCTC2544. Nevertheless, 30M SU182 reduced TNF-α / PMA-induced NF-κB-linked luciferase reporter activity to (22.9 ± 5%) and (34.6± 3 %, P<0.001) respectively, suggesting an action downstream of IKK signalling. Indeed, SU182 neither decreased NF-κB-DNA binding as assayed by EMSA nor prevented the translocation of p65 (NF-κB) to the nucleus assessed by immunofluorescence and subcellular fractionation. In addition to the inhibition of transcriptional activity of TNFα-induced NF-κB reporter activity SU182 significantly reduced PMA-induced AP-1-linked luciferase reporter activity to about (48± 9% at 30M, P<0.001) . This mode of inhibition was not sufficient to prevent the activation of NF-κB dependent induction of other proteins such as COX-2 and iNOS, or activated MAP kinases (p38, JNK and ERK1/2) in LPS stimulated RAW 264.7 macrophages. Taken together these data indicate the potential for SU182 to interfere with the transcription factors NF-κB and AP-1 at transcriptional level. However, no potential anti-inflammatory effect was indicated, further investigation for other NF-κB dependent proteins linked to survival are also required to identify the exact mechanism of action.

Keywords: Canthin-6-one, NF-κB, AP-1, phosphorylation, Nuclear translocation, DNA-binding activity, inflammatory proteins.

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Authors: Luis F. Garcia, Julian E. Jaramillo, Jorge L. Chacón

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Colombia is a country where the benefits of wind power industry are barely used because of the geography in some areas does not allow the implementation of onshore horizontal axis wind turbines. Furthermore, exist rural areas without access to the electrical grid. Therefore, there is currently a deficit of energy supply in some towns. This research took place in one of those areas (i.e. Chicamocha Canyon-Santander) where the answer to the energy supply problems could be the use of vertical axis wind turbines, which can be used for turbulent flows. Hence, one task of this research is the analysis of the wind resources in the Chicamocha Canyon in order to implement the wind energy. The wind turbines must be designed in such a way that the blades take good advantage of the wind resources in the area of interest. Consequently, in the current research the analysis of two different airfoils (i.e. NACA0018 and DU 06-W-200) through a 2D CFD simulation is carried out by means of a free-software (OpenFOAM). Predicted results using the “Spalart-Allmaras” turbulence model are similar to the wind tunnel data published in the literature. Moreover, global parameters such as dimensionless lift and drag coefficients were calculated. Finally, this research encourages VAWT studies under wind turbulent flows in order to achieve the best use of natural resources in Colombia.

Keywords: airfoil, wind turbine, turbulence modelling, Chicamocha, CFD

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Authors: Ramy H. Mohammed

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In heat sinks, the flow within the core exhibits separation and hence does not lend itself to simple analytical boundary layer or duct flow analysis of the wall friction. In this paper, I present some findings from an experimental and numerical study aimed to obtain physical insight into the influence of the presence of the shield and its position on the hydraulic and thermal performance of square pin fin heat sink without top by-pass. The variations of the Nusselt number and friction factor are obtained under varied parameters, such as the Reynolds number and the shield position. The numerical code is validated by comparing the numerical results with the available experimental data. It is shown that, there is a good agreement between the temperature predictions based on the model and the experimental data. Results show that, as the presence of the shield, the heat transfer of fin array is enhanced and the flow resistance increased. The surface temperature distribution of the heat sink base is more uniform when the dimensionless shield position equals to 1/3 or 2/3. The comprehensive performance evaluation approach based on identical pumping power criteria is adopted and shows that the optimum shield position is at x/l=0.43 where energy is saved.

Keywords: shield, fin array, performance evaluation, heat transfer, energy

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Authors: A. Gilewska, J. Masternak, K. Kazimierczuk, L. Turlej, J. Wietrzyk, B. Barszcz

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Platinum-based drugs are now widely used as chemotherapeutic agents. However the platinum complexes show the toxic side-effects: i) the development of platinum resistance; ii) the occurrence of severe side effects, such as nephro-, neuro- and ototoxicity; iii) the high toxicity towards human fibroblast. Therefore the development of new anticancer drugs containing different transition-metal ions, for example, ruthenium, rhodium, iridium is a valid strategy in cancer treatment. In this paper, we reported the synthesis, spectroscopic, structural and biological properties of complexes of ruthenium, rhodium, and iridium containing N,N-chelating ligand (2,2’-bisimidazole). These complexes were characterized by elemental analysis, UV-Vis and IR spectroscopy, X-ray diffraction analysis. These complexes exhibit a typical pseudotetrahedral three-legged piano-stool geometry, in which the aromatic arene ring forms the seat of the piano-stool, while the bidentate 2,2’-bisimidazole (ligand) and the one chlorido ligand form the three legs of the stool. The spectroscopy data (IR, UV-Vis) and elemental analysis correlate very well with molecular structures. Moreover, the cytotoxic activity of the complexes was carried out on human cancer cell lines: LoVo (colorectal adenoma), MV-4-11 (myelomonocytic leukaemia), MCF-7 (breast adenocarcinoma) and normal healthy mouse fibroblast BALB/3T3 cell lines. To predict a binding mode, a potential interaction of metal complexes with calf thymus DNA (CT-DNA) and protein (BSA) has been explored using UV absorption and circular dichroism (CD). It is interesting to note that the investigated complexes show no cytotoxic effect towards the normal BALB/3T3 cell line, compared to cisplatin, which IC₅₀ values was determined as 2.20 µM. Importantly, Ru(II) displayed the highest activity against HL-60 (IC₅₀ 4.35 µM). The biological studies (UV-Vis and circular dichroism) suggest that arene-complexes could interact with calf thymus DNA probably via an outside binding mode and interact with protein (BSA).

Keywords: ruthenium(II) complex, rhodium(III) complex, iridium(III) complex, biological activity

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Authors: Themistoklis Tzimas

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The proposed paper focuses on a triangular relationship, between human security, human development and responsibility to rebuild. This relationship constitutes the innovative contribution to the debate about human security. Human security constitutes a generic and legally binding notion, which orientates from an integrated approach the UN Charter principles and of the collective security system. Such an approach brings at the forefront of international law and of international relations not only states but non- state actors as well. Several doctrines attempt to implement the fore-mentioned approach among which the Responsibility to Protect- hereinafter R2P- doctrine and its aspect of Responsibility to Rebuild- hereinafter R2R. In this sense, R2P in general and R2R are supposed to be guided by human security imperatives. Human security because of its human- centered approach encompasses as an integral part of it, human development. Human development constitutes part of the backbone of human security, since it deals with the social and economic root- causes of the threats, which human security attempts to confront. In this sense, doctrines which orientate from human security, such as R2P and its R2R aspect should also take into account human development imperatives, in order to improve their efficiency. On the contrary though, R2R is more often linked with market- orientated policies, which are often imposed under transitional authorities, regardless of local needs. The implementation of such policies can be identified as a cause for striking failures in the framework of R2R. In addition it is a misinterpretation of the essence of human security and subsequently of R2P as well. The findings of the article, on the basis of the fore-mentioned argument is that a change must take place from a market- orientated misinterpretation of R2R to an approach attempting to implement human development doctrines, since the latter lie at the heart of human security and can be proven more effective in dealing with the root- causes of conflicts. Methodologically, the article begins with an examination of human security and of its binding nature on the basis of its orientation from the UN Charter. It also examines its significance in the framework of the collective security system. Then, follows the analysis of why and how human development constitutes an integral part of human security. At the next part it is proven that R2P in general and R2R more specifically constitute or should constitute an attempt to implement human security doctrines within the collective security system. Having built this triangular relationship it is argued that human development is proven to be the most suitable notion, so that the spirit of human security and the scopes of R2P are successfully implemented.

Keywords: human security, un charter, responsibility to protect, responsibility to rebuild, human development

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Authors: Salah Belaidi

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We have carried out extensive and in-depth research to search for bioactive compounds based on Algerian plants. A selection of 50 ligands from Algerian medicinal plants. Several compounds used in herbal medicine have been drawn using Marvin Sketch software. We determined the three-dimensional structures of the ligands with the MMFF94 force field in order to prepare these ligands for molecular docking. The 3D protein structure of the SARS-CoV-2 main protease was taken from the Protein Data Bank. We used AutoDockVina software to apply molecular docking. The hydrogen atoms were added during the molecular docking process, and all the twist bonds of the ligands were added using the (ligand) module in the AutoDock software. The COVID-19 main protease (Mpro) is a key enzyme that plays a vital role in viral transcription and mediating replication, so it is a very attractive drug target for SARS-CoV-2. In this work, an evaluation was carried out on the biologically active compounds present in these selected medicinal plants as effective inhibitors of the protease enzyme of COVID-19, with an in-depth computational calculation of the molecular docking using the Autodock Vina software. The top 7 ligands: Phloroglucinol, Afzelin, Myricetin-3-O- rutinosidTricin 7-neohesperidoside, Silybin, Silychristinthat and Kaempferol are selected among the 50 molecules studied which are Algerian medicinal plants, whose selection is based on the best binding energy which is relatively low compared to the reference molecule with binding affinities of -9.3, -9.3, -9, -8.9, -8 .5, 8.3 and -8.3 kcal mol-1 respectively. Then, we analyzed the ADME properties of the best7 ligands using the web server SwissADME. Two ligands (Silybin, Silychristin) were found to be potential candidates for the discovery and design of novel drug inhibitors of the protease enzyme of SARS-CoV-2. The stability of the two ligands in complexing with the Mpro protease was validated by molecular dynamics simulation; they revealed a stable trajectory in both techniques, RMSD and RMSF, by showing molecular properties with coherent interactions in molecular dynamics simulations. Finally, we conclude that the Silybin ligand forms a more stable complex with the Mpro protease compared to the Silychristin ligand.

Keywords: COVID-19, medicinal plants, molecular docking, ADME properties, molecular dynamics

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Authors: Axel Prettl

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This paper provides an overview of the different CFC rule settings in the OECD and 22 additional countries for the years 2004 to 2014 and compares them. In order to do so, it gives a summary of law amendments for every country, provides a comparison and afterwards all CFC rules are rated in their ”power of anti-avoidance” over time. For that rating of CFC rules, the largest common denominator of rule characteristics is used to keep it as abstract as necessary and possible. The paper points out that the CFC rules in the considered countries are very different in their specifications and they reach from very strict to very low binding. All in all these rules get more and more common and important; more countries implement a CFC legislation and the strictness of most of them rises over time.

Keywords: CFC rules, international taxation, corporate taxation, country comparison

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Authors: Md. Enamul Haque, Abdullah Al Kaisan, Mahmudur R. Saniat, Aminur Rahman

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In this paper, we have implemented both sequential and parallel version of fractal image compression algorithms using CUDA (Compute Unified Device Architecture) programming model for parallelizing the program in Graphics Processing Unit for medical images, as they are highly similar within the image itself. There is several improvements in the implementation of the algorithm as well. Fractal image compression is based on the self similarity of an image, meaning an image having similarity in majority of the regions. We take this opportunity to implement the compression algorithm and monitor the effect of it using both parallel and sequential implementation. Fractal compression has the property of high compression rate and the dimensionless scheme. Compression scheme for fractal image is of two kinds, one is encoding and another is decoding. Encoding is very much computational expensive. On the other hand decoding is less computational. The application of fractal compression to medical images would allow obtaining much higher compression ratios. While the fractal magnification an inseparable feature of the fractal compression would be very useful in presenting the reconstructed image in a highly readable form. However, like all irreversible methods, the fractal compression is connected with the problem of information loss, which is especially troublesome in the medical imaging. A very time consuming encoding process, which can last even several hours, is another bothersome drawback of the fractal compression.

Keywords: accelerated GPU, CUDA, parallel computing, fractal image compression

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Authors: E. Kilicay, Z. Karahaliloglu, B. Hazer, E. B. Denkbas

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In this study, we have prepared concanavaline A (ConA) functionalized curcumin (CUR) loaded PHBHHx (poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)) nanoparticles as a novel and efficient drug delivery system. CUR is a promising anticancer agent for various cancer types. The aim of this study was to evaluate therapeutic potential of curcumin loaded PHBHHx nanoparticles (CUR-NPs) and concanavaline A conjugated curcumin loaded NPs (ConA-CUR NPs) for ovarian cancer treatment. ConA was covalently connected to the carboxylic group of nanoparticles by EDC/NHS activation method. In the ligand attachment experiment, the binding capacity of ConA on the surface of NPs was found about 90%. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) analysis showed that the prepared nanoparticles were smooth and spherical in shape. The size and zeta potential of prepared NPs were about 228±5 nm and −21.3 mV respectively. ConA-CUR NPs were characterized by FT-IR spectroscopy which confirmed the existence of CUR and ConA in the nanoparticles. The entrapment and loading efficiencies of different polymer/drug weight ratios, 1/0.125 PHBHHx/CUR= 1.25CUR-NPs; 1/0.25 PHBHHx/CUR= 2.5CUR-NPs; 1/0.5 PHBHHx/CUR= 5CUR-NPs, ConA-1.25CUR NPs, ConA-2.5CUR NPs and ConA-5CUR NPs were found to be ≈ 68%-16.8%; 55%-17.7 %; 45%-33.6%; 70%-15.7%; 60%-17%; 51%-30.2% respectively. In vitro drug release showed that the sustained release of curcumin was observed from CUR-NPs and ConA-CUR NPs over a period of 19 days. After binding of ConA, the release rate was slightly increased due to the migration of curcumin to the surface of the nanoparticles and the matrix integrities was decreased because of the conjugation reaction. This functionalized nanoparticles demonstrated high drug loading capacity, sustained drug release profile, and high and long term anticancer efficacy in human cancer cell lines. Anticancer activity of ConA-CUR NPs was proved by MTT assay and reconfirmed by apoptosis and necrosis assay. The anticancer activity of ConA-CUR NPs was measured in ovarian cancer cells (SKOV-3) and the results revealed that the ConA-CUR NPs had better tumor cells decline activity than free curcumin. The nacked nanoparticles have no cytotoxicity against human ovarian carcinoma cells. Thus the developed functionalized nanoformulation could be a promising candidate in cancer therapy.

Keywords: curcumin, curcumin-PHBHHx nanoparticles, concanavalin A, concanavalin A-curcumin PHBHHx nanoparticles, PHBHHx nanoparticles, ovarian cancer cell

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Authors: Jihane Abdessadak, Hicham Achelhi, Kamal Reklaoui

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For any company or organization, change must be natural and binding in order to evolve its business, protect its durability and remain competitive. "Adapt or disappear". But how often managers, leaders or employees develop astonishing ideas that could improve several aspects of the organization and the feedback is less that encouraging and people give unrealistic judgments just to escape change. In this paper, we are going to discuss what we do know about change and resistance to change and what we can do to tame this phenomenon and, above all, the main steps that can follow an idea man in the delicate and decisive implementation of innovations.

Keywords: innovation, change, resistance to change/innovation, barriers to innovation, levers of innovation

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Authors: Hamid Ahmadi, Neda Azari Dodaran

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This paper aims to study the structural behavior of tubular KT-joints subjected to axial loading at fire induced elevated temperatures. At first, a finite element (FE) model was developed and validated against the data available from experimental tests. Then, a set of 810 FE analyses were performed to study the influence of temperature and dimensionless geometrical parameters (β, γ, θ, and τ) on the ultimate strength and initial stiffness. The joints were analyzed under two types of axial loading and five different temperatures (20 ºC, 200 ºC, 400 ºC, 550 ºC, and 700 ºC). Results show that the ultimate strength and initial stiffness of KT-joints decrease considerably by increasing the temperature. In the joints having bigger values of the β, the temperature elevation leads to less reduction in ultimate strength; while in the joints with bigger values of the γ, the temperature elevation results in more reduction in ultimate strength. The influence of the θ on the ultimate strength is independent from the temperature. To our knowledge, there is no design formula available for determining the ultimate strength of KT-joints at elevated temperatures. Hence, after parametric study, two equations were developed through nonlinear regression, for calculating the ultimate strength of KT-joints at elevated temperatures.

Keywords: axial loads, fire condition, parametric formula, static strength, tubular KT-joint

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Authors: Solene Masloh, Anne Chevrel, Maxime Culot, Leonardo Scapozza, Magali Zeisser-Labouebe

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The limited stability of clinically proven therapeutic antibodies limits their administration by the parenteral route. However, oral administration remains the best alternative as it is the most convenient and less invasive one. Obtaining a targeted treatment based on biologics, which can be orally administered, would, therefore, be an ideal situation to improve patient adherence and compliance. Nevertheless, the delivery of macromolecules through the intestine remains challenging because of their sensitivity to the harsh conditions of the gastrointestinal tract and their low permeability across the intestinal mucosa. To address this challenge, this project aims to demonstrate that targeting receptor-mediated endocytosis followed by transcytosis could maximize the intestinal uptake and transport of large molecules, such as Nanofitins. These affinity proteins of 7 kDa with binding properties similar to antibodies have already demonstrated retained stability in the digestive tract and local efficiency. However, their size does not allow passive diffusion through the intestinal barrier. Nanofitins having a controlled affinity for membrane receptors involved in the transcytosis mechanism used naturally for the transport of large molecules in humans were generated. Proteins were expressed using ribosome display and selected based on affinity to the targeted receptor and other characteristics. Their uptake and transport ex vivo across viable porcine intestines were investigated using an Ussing chambers system. In this paper, we will report the results achieved while addressing the different challenges linked to this study. To validate the ex vivo model, first, we proved the presence of the receptors targeted in humans on the porcine intestine. Then, after the identification of an optimal way of detection of Nanofitins, transport experiments were performed on porcine intestines with viability followed during the time of the experiment. The results, showing that the physiological process of transcytosis is capable of being triggered by the binding of Nanofitins on their target, will be reported here. In conclusion, the results show that Nanofitins can be transported across the intestinal barrier by triggering the receptor-mediated transcytosis and that the ex vivo model is an interesting technique to assess biologics absorption through the intestine.

Keywords: ex-vivo, Nanofitins, oral administration, transcytosis

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Authors: S. Behnia, S. Fathizadeh, A. Akhshani

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In the recent decades, DNA has increasingly interested in the potential technological applications that not directly related to the coding for functional proteins that is the expressed in form of genetic information. One of the most interesting applications of DNA is related to the construction of nanostructures of high complexity, design of functional nanostructures in nanoelectronical devices, nanosensors and nanocercuits. In this field, DNA is of fundamental interest to the development of DNA-based molecular technologies, as it possesses ideal structural and molecular recognition properties for use in self-assembling nanodevices with a definite molecular architecture. Also, the robust, one-dimensional flexible structure of DNA can be used to design electronic devices, serving as a wire, transistor switch, or rectifier depending on its electronic properties. In order to understand the mechanism of the charge transport along DNA sequences, numerous studies have been carried out. In this regard, conductivity properties of DNA molecule could be investigated in a simple, but chemically specific approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. In SSH model, the non-diagonal matrix element dependence on intersite displacements is considered. In this approach, the coupling between the charge and lattice deformation is along the helix. This model is a tight-binding linear nanoscale chain established to describe conductivity phenomena in doped polyethylene. It is based on the assumption of a classical harmonic interaction between sites, which is linearly coupled to a tight-binding Hamiltonian. In this work, the Hamiltonian and corresponding motion equations are nonlinear and have high sensitivity to initial conditions. Then, we have tried to move toward the nonlinear dynamics and phase space analysis. Nonlinear dynamics and chaos theory, regardless of any approximation, could open new horizons to understand the conductivity mechanism in DNA. For a detailed study, we have tried to study the current flowing in DNA and investigated the characteristic I-V diagram. As a result, It is shown that there are the (quasi-) ohmic areas in I-V diagram. On the other hand, the regions with a negative differential resistance (NDR) are detectable in diagram.

Keywords: DNA conductivity, Landauer resistance, negative dierential resistance, Chaos theory, mean Lyapunov exponent

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Authors: Sweta Pandey, Samridhi Dhyani, Susmita Chaudhuri

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Klebsiella pneumoniae causes a wide range of infections, including urinary tract infections, sepsis, bacteremia, pneumonia, and liver abscesses. The emergence of multi-drug resistance in this bacterium led to a major setback for clinical management. WHO also endorsed a need for finding alternative therapy to antibiotics for the treatment of these infections. Development of vaccines and passive antibody therapy has been proven as a potent alternative to antibiotics in the case of MDR, XDR, and PDR Klebsiella infections. Siderophore receptors have been demonstrated to be overexpressed for the internalization of iron siderophore complexes during infections in most Gram-negative bacteria. For the present study, immune response to siderophore receptors to establish this protein as a potential immunogen for the development of therapeutic leads was explored. Clinical strains of Klebsiella pneumoniae were grown in iron-deficient conditions, and the iron-regulated outer membrane proteins were extracted and characterized through mass spectrometry for specific identification. The gene for identified protein was cloned in pET- 28a vector and expressed in E. coli. The native protein and the recombinant protein were isolated and purified and used as antigens for the generation of immune response in BALB/c mice. The native protein of Klebsiella pneumoniae grown in iron-deficient conditions was identified as FepA (Ferrienterobactin receptor) and other siderophore receptors. This 80 kDa protein generated an immune response in BALB/c mice. The antiserum from mice after subsequent booster doses was collected and showed binding with FepA protein in western blot and phagocytic uptake of the K. pneumoniae in the presence antiserum from immunized mice also observed from the animal studies after bacterial challenge post immunisation in mice have shown bacterial clearance. The antiserum from mice showed binding and clearance of the Klebsiella pneumoniae bacteria in vitro and in vivo. These antigens used for generating an active immune response in mice can further be used for therapeutic monoclonal antibody development against Klebsiella pneumoniae infections.

Keywords: antiserum, FepA, Klebsiella pneumoniae, multi drug resistance, siderophore receptor

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Neda Azari Dodaran, Hamid Ahmadi

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Results of 405 finite element (FE) analyses were used in the present research to study the effect of the joint geometry on the ultimate strength and initial stiffness of tubular K-joints subjected to axial loading at fire-induced elevated temperatures. The FE models were validated against the data available from experimental tests. Structural behavior under different temperatures (200ºC, 400ºC, 500ºC, and 700ºC) was investigated and compared to the behavior at ambient temperature (20ºC). A parametric study was conducted to investigate the effect of dimensionless geometrical parameters (β, γ, θ, and τ) on the ultimate strength and initial stiffness. Afterwards, ultimate strength data extracted from the FE analyses were compared with the values calculated from the equations proposed by available design codes in which the ultimate strength of the joint at elevated temperatures is obtained by replacing the yield stress of the steel at ambient temperature with the corresponding value at elevated temperature. It was indicated that this method may not have acceptable accuracy for K-joints under axial loading. Hence, a design formula was developed, through nonlinear regression analyses, to determine the ultimate strength of K-joints subjected to balanced axial loads at elevated temperatures.

Keywords: axial loading, elevated temperature, parametric equation, static strength, tubular K-joint

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from x-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for x-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across x-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: biomacromolecular structure, coenzyme, electron density discrepancy analysis, x-ray crystallography

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Authors: Ekta, G. K. Darbha

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Nanotechnology offers the potential of simultaneously increasing efficiency as compared to their bulk material as well as reducing harmful environmental impacts of pesticides in field of agriculture. The term nanopesticide covers different pesticides that are cumulative of several surfactants, polymers, metal ions, etc. of nanometer size ranges from 1-1000 nm and exhibit abnormal behavior (high efficacy and high specific surface area) of nanomaterials. Commercial formulations of pesticides used by farmers nowadays cannot be used effectively due to a number of problems associated with them. For example, more than 90% of applied formulations are either lost in the environment or unable to reach the target area required for effective pest control. Around 20−30% of pesticides are lost through emissions. A number of factors (application methods, physicochemical properties of the formulations, and environmental conditions) can influence the extent of loss during application. It is known that among various formulations, polymer-based formulations show the greatest potential due to their greater efficacy, slow release and protection against premature degradation of active ingredient as compared to other commercial formulations. However, the nanoformulations can have a significant effect on the fate of active ingredient as well as may release some new ingredients by reacting with existing soil contaminants. Environmental fate of these newly generated species is still not explored very well which is essential to field scale experiments and hence a lot to be explored in the field of environmental fate, nanotoxicology, transport properties and stability of such formulations. In our preliminary work, we have synthesized polymer based nanoformulation of commercially used weedicide atrazine. Atrazine belongs to triazine class of herbicide, which is used in the effective control of seed germinated dicot weeds and grasses. It functions by binding to the plastoquinone-binding protein in PS-II. Plant death results from starvation and oxidative damage caused by breakdown in electron transport system. The stability of the suspension of nanoformulation containing herbicide has been evaluated by considering different parameters like polydispersity index, particle diameter, zeta-potential under different environmental relevance condition such as pH range 4-10, temperature range from 25°C to 65°C and stability of encapsulation also have been studied for different amount of added polymer. Morphological characterization has been done by using SEM.

Keywords: atrazine, nanoformulation, nanopesticide, nanotoxicology

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Authors: Rubén Bãnos, José Arcos, Oscar Bautista, Federico Méndez

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The Oscillatory electroosmotic flow (OEOF) in power law fluids through a microchannel is studied numerically. A time-dependent external electric field (AC) is suddenly imposed at the ends of the microchannel which induces the fluid motion. The continuity and momentum equations in the x and y direction for the flow field were simplified in the limit of the lubrication approximation theory (LAT), and then solved using a numerical scheme. The solution of the electric potential is based on the Debye-H¨uckel approximation which suggest that the surface potential is small,say, smaller than 0.025V and for a symmetric (z : z) electrolyte. Our results suggest that the velocity profiles across the channel-width are controlled by the following dimensionless parameters: the angular Reynolds number, Reω, the electrokinetic parameter, ¯κ, defined as the ratio of the characteristic length scale to the Debye length, the parameter λ which represents the ratio of the Helmholtz-Smoluchowski velocity to the characteristic length scale and the flow behavior index, n. Also, the results reveal that the velocity profiles become more and more non-uniform across the channel-width as the Reω and ¯κ are increased, so oscillatory OEOF can be really useful in micro-fluidic devices such as micro-mixers.

Keywords: low zeta potentials, non-newtonian, oscillatory electroosmotic flow, power-law model

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Authors: Jillian M. Hagel, Joseph E. Tucker, Peter J. Facchini

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With the aim of establishing a holistic approach for the treatment of central nervous system (CNS) disorders, we are pursuing a drug development program rapidly progressing through discovery and characterization phases. The drug candidates identified in this program are referred to as neuroplastogens owing to their ability to mediate neuroplasticity, which can be beneficial to patients suffering from anxiety, depression, or posttraumatic stress disorder. These and other related neuropsychiatric conditions are associated with the onset of neuronal atrophy, which is defined as a reduction in the number and/or productivity of neurons. The stimulation of neuroplasticity results in an increase in the connectivity between neurons and promotes the restoration of healthy brain function. We have synthesized a substantial catalogue of proprietary indolethylamine derivatives based on the general structures of serotonin (5-hydroxytryptamine) and psychedelic molecules such as N,N-dimethyltryptamine (DMT) and psilocin (4-hydroxy-DMT) that function as neuroplastogens. A primary objective in our screening protocol is the identification of derivatives associated with a significant reduction in hallucination, which will allow administration of the drug at a dose that induces neuroplasticity and triggers other efficacious outcomes in the treatment of targeted CNS disorders but which does not cause a psychedelic response in the patient. Both neuroplasticity and hallucination are associated with engagement of the 5HT2A receptor, requiring drug candidates differentially coupled to these two outcomes at a molecular level. We use novel and proprietary artificial intelligence algorithms to predict the mode of binding to the 5HT2A receptor, which has been shown to correlate with the hallucinogenic response. Hallucination is tested using the mouse head-twitch response model, whereas mouse marble-burying and sucrose preference assays are used to evaluate anxiolytic and anti-depressive potential. Neuroplasticity is assays using dendritic outgrowth assays and cell-based ELISA analysis. Pharmacokinetics and additional receptor-binding analyses also contribute the selection of lead candidates. A summary of the program is presented.

Keywords: neuroplastogen, non-hallucinogenic, drug development, anxiety, depression, PTSD, indolethylamine derivatives, psychedelic-inspired, 5-HT2A receptor, computational chemistry, head-twitch response behavioural model, neurite outgrowth assay

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Authors: Anas El Amraoui, Abdelkhalek Cheddadi, Mohammed Touhami Ouazzani

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Laminar natural convection in a cylindrical annular cavity filled with air and provided with two fins is studied numerically using the discretization of the governing equations with the Centered Finite Difference method based on the Alternating Direction Implicit (ADI) scheme. The fins are attached to the inner cylinder of radius r_i (hot wall of temperature T_i). The outer cylinder of radius r_o is maintained at a temperature T_o (T_o < T_i). Two values of the dimensionless thickness of the fins are considered: 0.015 and 0.203. We consider a low fin height equal to 0.078 and medium fin heights equal to 0.093 and 0.203. The position of the fin is 0.82π and the radius ratio is equal to 2. The effect of Rayleigh number, Ra, on the flow structure and heat transfer is analyzed for a range of Ra from 10³ to 10⁴. The results for established flow structures and heat transfer at low height indicate that the flow regime that occurs is unicellular for all Ra and fin thickness; in addition, the heat transfer rate increases with increasing Rayleigh number and is the same for both thicknesses. At median fin heights 0.093 and 0.203, the increase of Rayleigh number leads to transitions of flow structure which correspond to significant variations of the heat transfer. The critical Rayleigh numbers, Ra_c.app and Ra_c.disp corresponding to the appearance of the bicellular flow regime and its disappearance, are determined and their influence on the change of heat transfer rate is analyzed.

Keywords: natural convection, fins, critical Rayleigh number, heat transfer, fluid flow regime, horizontal annulus

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Authors: Marina Passero, Tianhua Zhai, Zuyi (Jacky) Huang

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Alzheimer’s disease has become a major public health issue, as indicated by the increasing populations of Americans living with Alzheimer’s disease. After decades of extensive research in Alzheimer’s disease, only seven drugs have been approved by Food and Drug Administration (FDA) to treat Alzheimer’s disease. Five of these drugs were designed to treat the dementia symptoms, and only two drugs (i.e., Aducanumab and Lecanemab) target the progression of Alzheimer’s disease, especially the accumulation of amyloid-b plaques. However, controversial comments were raised for the accelerated approvals of either Aducanumab or Lecanemab, especially with concerns on safety and side effects of these two drugs. There is still an urgent need for further drug discovery to target the biological processes involved in the progression of Alzheimer’s disease. Excessive cholesterol has been found to accumulate in the brain of those with Alzheimer’s disease. Cholesterol can be synthesized in both the blood and the brain, but the majority of biosynthesis in the adult brain takes place in astrocytes and is then transported to the neurons via ApoE. The blood brain barrier separates cholesterol metabolism in the brain from the rest of the body. Various proteins contribute to the metabolism of cholesterol in the brain, which offer potential targets for Alzheimer’s treatment. In the astrocytes, SREBP cleavage-activating protein (SCAP) binds to Sterol Regulatory Element-binding Protein 2 (SREBP2) in order to transport the complex from the endoplasmic reticulum to the Golgi apparatus. Cholesterol is secreted out of the astrocytes by ATP-Binding Cassette A1 (ABCA1) transporter. Lipoprotein receptors such as triggering receptor expressed on myeloid cells 2 (TREM2) internalize cholesterol into the microglia, while lipoprotein receptors such as Low-density lipoprotein receptor-related protein 1 (LRP1) internalize cholesterol into the neuron. Cytochrome P450 Family 46 Subfamily A Member 1 (CYP46A1) converts excess cholesterol to 24S-hydroxycholesterol (24S-OHC). Cholesterol has been approved for its direct effect on the production of amyloid-beta and tau proteins. The addition of cholesterol to the brain promotes the activity of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), secretase, and amyloid precursor protein (APP), which all aid in amyloid-beta production. The reduction of cholesterol esters in the brain have been found to reduce phosphorylated tau levels in mice. In this work, a computational pipeline was developed to identify the protein targets involved in cholesterol regulation in brain and further to identify chemical compounds as the inhibitors of a selected protein target. Since extensive evidence shows the strong correlation between brain cholesterol regulation and Alzheimer’s disease, a detailed literature review on genes or pathways related to the brain cholesterol synthesis and regulation was first conducted in this work. An interaction network was then built for those genes so that the top gene targets were identified. The involvement of these genes in Alzheimer’s disease progression was discussed, which was followed by the investigation of existing clinical trials for those targets. A ligand-protein docking program was finally developed to screen 1.5 million chemical compounds for the selected protein target. A machine learning program was developed to evaluate and predict the binding interaction between chemical compounds and the protein target. The results from this work pave the way for further drug discovery to regulate brain cholesterol to combat Alzheimer’s disease.

Keywords: Alzheimer’s disease, drug discovery, ligand-protein docking, gene-network analysis, cholesterol regulation

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Authors: Rachid Zentar, Mokrane Bala, Pascal Boustingorry

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The prediction of the rheological behavior of concrete is at the center of current concerns of the concrete industry for different reasons. The shortage of good quality standard materials combined with variable properties of available materials imposes to improve existing models to take into account these variations at the design stage of concrete. The main reasons for improving the predictive models are, of course, saving time and cost at the design stage as well as to optimize concrete performances. In this study, we will highlight the different properties of the granular mixtures that affect the rheological properties of concrete. Our objective is to identify the intrinsic parameters of the aggregates which make it possible to predict the yield stress of concrete. The work was done using two typologies of grains: crushed and rolled aggregates. The experimental results have shown that the rheology of concrete is improved by increasing the packing density of the granular mixture using rolled aggregates. The experimental program realized allowed to model the yield stress of concrete by a modified model of Chateau et al. through a dimensionless parameter following Krieger-Dougherty law. The modelling confirms that the yield stress of concrete depends not only on the properties of cement paste but also on the packing density of the granular skeleton and the shape of grains.

Keywords: crushed aggregates, intrinsic viscosity, packing density, rolled aggregates, slump, yield stress of concrete

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Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

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The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

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Authors: Thomas Okechukwu Onah, Onyekachi Marcel Egwuagu

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Zero-surface temperature, which controlled the cooling profile, was modeled and used to investigate the effect of process parameters on the hot-rolled steel plates. The parameters include impingement gaps of 40mm to 70mm; pipe diameters of 20mm to 45mm feeding jet nozzle with 30 holes of 8mm diameters each; and flow rates within 2.896x10-⁶m³/s and 3.13x10-⁵m³/s. The developed simulation model of the Zero-Surface Temperature, upon validation, showed 99% prediction accuracy with dimensional homogeneity established. The evaluated Zero-Surface temperature of Controlled Water Jet Impingement Steel plates showed a high cooling rate of 36.31 Celsius degree/sec at an optimal cooling nozzle diameter of 20mm, impingement gap of 70mm and a flow rate of 1.77x10-⁵m³/s resulting in Reynold's number 2758.586, in the turbulent regime was obtained. It was also deduced that as the nozzle diameter was increasing, the impingement gap was reducing. This achieved a faster rate of cooling to an optimum temperature of 300oC irrespective of the starting surface cooling temperature. The results additionally showed that with a tested-plate initial temperature of 550oC, a controlled cooling temperature of about 160oC produced a film and nucleated boiling heat extraction that was particularly beneficial at the end of controlled cooling and influenced the microstructural properties of the test plates.

Keywords: temperature, mechanistic-model, plates, impingements, dimensionless-numbers

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