Search results for: molecular simulations

Authors: Bilal Ahmad

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Alzheimer’s disease (AD) is one of the most common neurodegenerative illnesses. However, how Gut-microbiota plays a role in the pathogenesis of AD is not well elucidated. The purpose of this literature review is to summarize and understand the current findings that may elucidate the gut microbiota's role in the development of AD. Methods: A literature review of all the relevant papers known to the author was conducted. Relevant articles, abstracts and research papers were collected from well-accepted web sources like PubMed, PMC, and Google Scholar. Results: Recent studies have shown that Gut-microbiota has an important role in the progression of AD via Gut-Microbiota-Brain Axis. The onset of AD supports the ‘Hygiene Hypothesis’, which shows that AD might begin in the Gut, causing dysbiosis, which interferes with the intestinal barrier by releasing pro-inflammatory cytokines and making its way up to the brain via the blood-brain barrier (BBB). Molecular mechanisms lipopolysaccharides and serotonin kynurenine (tryptophan) pathways have a direct association with inflammation, the immune system, neurodegeneration, and AD. Conclusion: The studies helped to analyze the molecular basis of AD, other neurological conditions like depression, autism, and Parkinson's disease and how they are linked to Gut-microbiota. Further, studies to explore the therapeutic effects of probiotics in AD and cognitive enhancement should be warranted to provide significant clinical and practical value.

Keywords: gut-microbiota, Alzheimer’s disease, second brain aging, lipopolysaccharides, short-chain fatty acids

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Authors: Anjali Uday, Yuting Wang, Andres Alfonso Pena Olare

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The Discrete Element Method is a promising approach to modeling microscopic behaviors of granular materials. The quality of the simulations however depends on the model parameters utilized. The present study focuses on calibration and validation of the discrete element parameters for Cuxhaven sand based on the experimental data from triaxial and oedometer tests. A sensitivity analysis was conducted during the sample preparation stage and the shear stage of the triaxial tests. The influence of parameters like rolling resistance, inter-particle friction coefficient, confining pressure and effective modulus were investigated on the void ratio of the sample generated. During the shear stage, the effect of parameters like inter-particle friction coefficient, effective modulus, rolling resistance friction coefficient and normal-to-shear stiffness ratio are examined. The calibration of the parameters is carried out such that the simulations reproduce the macro mechanical characteristics like dilation angle, peak stress, and stiffness. The above-mentioned calibrated parameters are then validated by simulating an oedometer test on the sand. The oedometer test results are in good agreement with experiments, which proves the suitability of the calibrated parameters. In the next step, the calibrated and validated model parameters are applied to forecast the micromechanical behavior including the evolution of contact force chains, buckling of columns of particles, observation of non-coaxiality, and sample inhomogeneity during a simple shear test. The evolution of contact force chains vividly shows the distribution, and alignment of strong contact forces. The changes in coordination number are in good agreement with the volumetric strain exhibited during the simple shear test. The vertical inhomogeneity of void ratios is documented throughout the shearing phase, which shows looser structures in the top and bottom layers. Buckling of columns is not observed due to the small rolling resistance coefficient adopted for simulations. The non-coaxiality of principal stress and strain rate is also well captured. Thus the micromechanical behaviors are well described using the calibrated and validated material parameters.

Keywords: discrete element model, parameter calibration, triaxial test, oedometer test, simple shear test

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Authors: Harminder Kaur, Manpreet Kaur, Akanksha Kapila, Reenu

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Schiff base with general formula H₂L was derived from condensation of o-vanillin and 3-nitro-o-phenylenediamine. This Schiff base was used for the synthesis of organotin(IV) complexes with general formula R₂SnL [R=Phenyl or n-octyl] using equimolar quantities. Elemental analysis UV-Vis, FTIR, and multinuclear spectroscopic techniques (¹H, ¹³C, and ¹¹⁹Sn) NMR were carried out for the characterization of the synthesized complexes. These complexes were coloured and soluble in polar solvents. Computational studies have been performed to obtain the details of the geometry and electronic structures of ligand as well as complexes. Geometry of the ligands and complexes have been optimized at the level of Density Functional Theory with B3LYP/6-311G (d,p) and B3LYP/MPW1PW91 respectively followed by vibrational frequency analysis using Gaussian 09. Observed ¹¹⁹Sn NMR chemical shifts of one of the synthesized complexes showed tetrahedral geometry around Tin atom which is also confirmed by DFT. HOMO-LUMO energy distribution was calculated. FTIR, ¹HNMR and ¹³CNMR spectra were also obtained theoretically using DFT. Further IRC calculations were employed to determine the transition state for the reaction and to get the theoretical information about the reaction pathway. Moreover, molecular docking studies can be explored to ensure the anticancer activity of the newly synthesized organotin(IV) complexes.

Keywords: DFT, molecular docking, organotin(IV) complexes, o-vanillin, 3-nitro-o-phenylenediamine

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Authors: R. F. B. Gonçalves, E. N. Iwama, J. A. F. F. Rocco, K. Iha

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Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.

Keywords: shelf-life, thermal analysis, Ozawa method, Kissinger method, LAMMPS software, thrust

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Authors: E. Yarar, E. A. Guven, S. Karabay

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In this study, a comprehensive simulation was made for the cold tube drawing with fixed plug. The cold tube drawing process is preferred due to its high surface quality and the high mechanical properties. In drawing processes applied to materials with low plastic deformability, cracks can occur on the surfaces and the process efficiency decreases. The aim of the work is to investigate the effects of different drawing parameters on drawing forces and stresses. In the simulations, optimum conditions were investigated for four different materials, Ti64Al4V, AA5052, AISI4140, and C365. One of the most important parameters for the cold drawing process is the die angle. Three dies were designed for the analysis with semi die angles of 5°, 10°, and 15°. Three different parameters were used for the friction coefficient between die and the material. In the simulations, reduction of area and the drawing speed is kept constant. Drawing is done in one pass. According to the simulation results, the highest drawing forces were obtained in Ti64Al4V. As the semi die angle increases, the drawing forces decrease. The change in semi die angle was most effective on Ti64Al4V. Increasing the coefficient of friction is another effect that increases the drawing forces. The increase in the friction coefficient has also increased in drawing stresses. The increase in die angle also increased the drawing stress distribution for the other three materials outside C365. According to the results of the analysis, it is found that the designed drawing die is suitable for drawing. The lowest drawing stress distribution and drawing forces were obtained for AA5052. Drawing die parameters have a direct effect on the results. In addition, lubricants used for drawing have a significant effect on drawing forces.

Keywords: cold tube drawing, drawing force, drawing stress, semi die angle

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Authors: Barsha Saha, Shouvik Chakravarty, Sukanta Ray, Kshaunish Das, Nidhan K. Biswas, Srikanta Goswami

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Pancreatic Ductal Adenocarcinoma is a well-recognised cause of cancer death with a five-year survival rate of about 9%, and its incidence in India has been found to be increased manifold in recent years. Due to delayed detection, this highly metastatic disease has a poor prognosis. Several molecular alterations happen during the progression of the disease from pre-cancerous conditions, and many such alterations could be investigated for their biomarker potential. MicroRNAs have been shown to be prognostic for PDAC patients in a variety of studies. We hereby used NGS technologies to evaluate the role of small RNA changes during pancreatic cancer development from chronic pancreatitis. Plasma samples were collected from pancreatic cancer patients (n=16), chronic pancreatitis patients (n=8), and also from normal individuals (n=16). Pancreatic tumour tissue (n=5) and adjacent normal tissue samples (n=5) were also collected. Sequencing of small RNAs was carried out after small RNAs were isolated from plasma samples and tissue samples. We find that certain microRNAs are highly deregulated in pancreatic cancer patients in comparison to normal samples. A combinatorial analysis of plasma and tissue microRNAs and subsequent exploration of their targets and altered molecular pathways could not only identify potential biomarkers for disease diagnosis but also help to understand the underlying mechanism.

Keywords: small RNA sequencing, pancreatic cancer, biomarkers, tissue sample

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Authors: Lynda Golea, Rachid Chebaki

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Schiff bases contain heterocyclic structural units with N and O donor atoms which plays an important role in coordination chemistry. Azomethine groups are a broad class of widely used compounds with applications in many fields, including analytical, inorganic chemistry and biological. Schiff's base is of promising research interest due to the widespread antibacterial resistance in medical science. In addition, the research is essential to generate Schiff base metal complexes with various applications. Schiff complexes have been used as drugs and have antibacterial, antifungal, antiviral, and anti-inflammatory properties. The various donor atoms they contain offer a special ability for metal binding. In this research on the physicochemical properties of azomethine groups, we synthesized and studied the Schiff base compounds by a condensation reaction of tryptamines and acetophenone in ethanol. The structure of the prepared compound was interpreted using 1H NMR, 13C NMR, UV-vis and FT-IR. A computational analysis at the level of DFT with functional B3LYP in conjunction with the base 6-311+G (d, p) was conducted to study its electronic and molecular structure. The biological study was performed on three bacterial strains usually causing infection, including Gram-positive and Gram-negative, for antibacterial activity. Results showed moderate biological activity and proportional activity with increasing concentration.

Keywords: azomethine, HOMO, LUMO, RMN, molecular docking

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Authors: Felix Platzer, Eric Fimbinger

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In Discrete Element Method (DEM) simulations, the breakage behavior of particles can be simulated based on different principles. In the case of large, complex-shaped particles that show various breakage patterns depending on the scenario leading to the failure and often only break locally instead of fracturing completely, some of these principles do not lead to realistic results. The reason for this is that in said cases, the methods in question, such as the Particle Replacement Method (PRM) or Voronoi Fracture, replace the initial particle (that is intended to break) into several sub-particles when certain breakage criteria are reached, such as exceeding the fracture energy. That is why those methods are commonly used for the simulation of materials that fracture completely instead of breaking locally. That being the case, when simulating local failure, it is advisable to pre-build the initial particle from sub-particles that are bonded together. The dimensions of these sub-particles consequently define the minimum size of the fracture results. This structure of bonded sub-particles enables the initial particle to break at the location of the highest local loads – due to the failure of the bonds in those areas – with several sub-particle clusters being the result of the fracture, which can again also break locally. In this project, different methods for the generation and calibration of complex-shaped particle conglomerates using bonded particle modeling (BPM) to enable the ability to depict more realistic fracture behavior were evaluated based on the example of filter cake. The method that proved suitable for this purpose and which furthermore allows efficient and realistic simulation of breakage behavior of complex-shaped particles applicable to industrial-sized simulations is presented in this paper.

Keywords: bonded particle model, DEM, filter cake, particle breakage

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Authors: Roberta Gentry

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A mixed methods study that examined candidate’s perceptions of the use of computerized simulation as an effective tool to learn classroom management will be presented. The development, implementation, and assessment of the simulation and candidate data on the feasibility of the approach in comparison to other methods will be presented.

Keywords: behavior management, simulations, teacher preparation, teacher education

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Authors: Jessica C. Bannon, Cleso M. Jordao Jr., Mohammad Melebari, Carlos Leon-Velarde, Roger Johnson, Keith Warriner

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There has been an increased incidence of non-O157 Shiga Toxin Escherichia coli (STEC) with six serotypes (Top 6) being implicated in causing haemolytic uremic syndrome (HUS). Beef has been suggested to be a significant vehicle for non-O157 STEC although conclusive evidence has yet to be obtained. The following aimed to determine the prevalence of the Top 6 non-O157 STEC in beef processing using three different diagnostic platforms then characterize the recovered isolates. Hide, carcass and environmental swab samples (n = 60) were collected from a beef processing facility over a 12 month period. Enriched samples were screened using Biocontrol GDS, BAX or PALLgene molecular diagnostic tests. Presumptive non-O157 STEC positive samples were confirmed using conventional PCR and serology. STEC was detected by GDS (55% positive), BAX (85% positive), and PALLgene (93%). However, during confirmation testing only 8 of the 60 samples (13%) were found to harbour STEC. Interestingly, the presence of virulence factors in the recovered isolates was unstable and readily lost during subsequent sub-culturing. There is a low prevalence of Top 6 non-O157 STEC associated with beef although other serotypes are encountered. Yet, the instability of the virulence factors in recovered strains would question their clinical relevance.

Keywords: beef, food microbiology, shiga toxin, STEC

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Authors: Siva K. Bathina, Sudheer Siddapureddy

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Pool fires are formed when the flammable liquid accidentally spills on the ground or water and ignites. Pool fire is a kind of buoyancy-driven and diffusion flame. There have been many pool fire accidents caused during processing, handling and storing of liquid fuels in chemical and oil industries. Such kind of accidents causes enormous damage to property as well as the loss of lives. Pool fires are complex in nature due to the strong interaction among the combustion, heat and mass transfers and pyrolysis at the fuel surface. Moreover, the experimental study of such large complex fires involves fire safety issues and difficulties in performing experiments. In the present work, large eddy simulations are performed to study such complex fire scenarios using fire dynamic simulator. A 1 m diesel pool fire is considered for the studied cases, and diesel is chosen as it is most commonly involved fuel in fire accidents. Fire simulations are performed by specifying two different boundary conditions: one the fuel is in liquid state and pyrolysis model is invoked, and the other by assuming the fuel is initially in a vapor state and thereby prescribing the mass loss rate. A domain of size 11.2 m × 11.2 m × 7.28 m with uniform structured grid is chosen for the numerical simulations. Grid sensitivity analysis is performed, and a non-dimensional grid size of 12 corresponding to 8 cm grid size is considered. Flame properties like mass burning rate, irradiance, and time-averaged axial flame temperature profile are predicted. The predicted steady-state mass burning rate is 40 g/s and is within the uncertainty limits of the previously reported experimental data (39.4 g/s). Though the profile of the irradiance at a distance from the fire along the height is somewhat in line with the experimental data and the location of the maximum value of irradiance is shifted to a higher location. This may be due to the lack of sophisticated models for the species transportation along with combustion and radiation in the continuous zone. Furthermore, the axial temperatures are not predicted well (for any of the boundary conditions) in any of the zones. The present study shows that the existing models are not sufficient enough for modeling blended fuels like diesel. The predictions are strongly dependent on the experimental values of the soot yield. Future experiments are necessary for generalizing the soot yield for different fires.

Keywords: burning rate, fire accidents, fire dynamic simulator, pyrolysis

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Authors: Maria Bercea, Bernhard A. Wolf

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The thermodynamic behavior for solutions of poly (methyl methacrylate-ran-t-butyl methacrylate) of variable composition as compared with the corresponding homopolymers was investigated by light scattering measurements carried out for dilute solutions and vapor pressure measurements of concentrated solutions. The complex dependencies of the Flory Huggins interaction parameter on concentration and copolymer composition in solvents of different polarity (toluene and chloroform) can be understood by taking into account the ability of the polymers to rearrange in a response to changes in their molecular surrounding. A recent unified thermodynamic approach was used for modeling the experimental data, being able to describe the behavior of the different solutions by means of two adjustable parameters, one representing the effective number of solvent segments and another one accounting for the interactions between the components. Thus, it was investigated how the solvent quality changes with the composition of the copolymers through the Gibbs energy of mixing as a function of polymer concentration. The largest reduction of the Gibbs energy at a given composition of the system was observed for the best solvent. The present investigation proves that the new unified thermodynamic approach is a general concept applicable to homo- and copolymers, independent of the chain conformation or shape, molecular and chemical architecture of the components and of other dissimilarities, such as electrical charges.

Keywords: random copolymers, Flory Huggins interaction parameter, Gibbs energy of mixing, chemical architecture

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Authors: Mansi Srivastava, Uzma Saqib, Adnan Naim, Anjali Roy, Dongfang Liu, Deepak Bhatnagar, Ravinder Ravinder, Mirza S. Baig

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Macrophages polarize to proinflammatory M1 or anti-inflammatory M2 states with distinct physiological functions. This transition within the M1 to M2 phenotypes decides the nature, duration, and severity of an inflammatory response. However, inspite of a substantial understanding of the fate of these phenotypes, the underlying molecular mechanisms are not well understood. We have investigated the role of Neuronal nitric oxide synthase (NOS1) mediated regulation of Activator protein 1 (AP-1) transcription factor in macrophages as a critical effector of macrophage phenotypic change. Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of jun, Fos, and ATF family proteins. We determined that NOS1-derived nitric oxide (NO) facilitate Fos and jun interaction which induces IL12 & IL23 expression. Pharmacological inhibition of NOS1 inhibits Fos and jun interaction but increases ATF2 and Fos dimerization. Switching of Fos and jun dimer to ATF2 and jun dimerization switches phenotype from IL–12high IL-23high IL-10low to IL–12low IL-23lowIL-10high phenotype, respectively. Together, these findings highlight a key role of the TLR4-NOS1-AP1 signaling axis in regulating macrophage polarization.

Keywords: inflammation, macrophage, lipopolysaccharide (LPS), proinflammatory cytokines, activator protein 1 (AP-1), neuronal nitric oxide synthase (NOS1)

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Authors: Jonmichael Weaver, David Miller

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Dyneema is an ultra-high molecular weight polyethylene (UHMWPE) fiber created by DSM. This fiber has many applications due to the high tensile strength, low weight, and inability to absorb water. DSM manufactures a non-woven unidirectional cross-ply [0,90]2 lamina, using the Dyneema fiber. Using this lamina system, various thickness panels are created for a 40% lighter weight alternative to Kevlar for the same ballistics protection. Environmental effects on the ply/laminate system alter the material properties, resulting in diminished ultimate performance. Understanding the specific environmental parameters and characterizing the resulting material property degradation is essential for determining the safety and reliability of Dyneema in service. Two laminas were contrasted for their response to accelerated aging by UV, humidity, and temperature cycling. Both lamina contain the same fiber, SK-99, but differ in matrix composition, Dyneema HB-210 employs a polyurethane (PUR) based matrix, and HB-212 contains a rubber-based matrix. Each system was inspected using a scanning electron microscope (SEM) and evaluated by dynamic mechanical analysis (DMA) to characterize the material property changes alongside the corresponding composite damage and matrix failure mode over the aging parameters. Overall, resulting in the HB-212 degrading faster compared with the HB-210.

Keywords: dyneema, accelerated aging, polymers, ballistics protection, armor, DSM, kevlar, composites

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Authors: Manoj Sarda, Abhishek Agarwal, Juhi Kaushik, Vatsal Sanjay, Arup Kumar Das

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Railways in India remain primary mode of transport having one of the largest networks in the world and catering to billions of transits yearly. Catastrophic economic damage and loss to life is encountered over the past few decades due to fire to locomotives. Study of fire dynamics and fire propagation plays an important role in evacuation planning and reducing losses. Simulation based study of propagation of fire and soot inside an air conditioned coach of Indian locomotive is done in this paper. Finite difference based solver, Fire Dynamic Simulator (FDS) version 6 has been used for analysis. A single air conditioned 3 tier coupe closed to ambient surroundings by glass windows having occupancy for 8 people is the basic unit of the domain. A system of three such coupes combined is taken to be fundamental unit for the entire study to resemble effect to an entire coach. Analysis of flame and soot contours and concentrations is done corresponding to variations in heat release rate per unit volume (HRRPUA) of fire source, variations in conditioned air velocity being circulated inside coupes by vents and an alternate fire initiation and propagation mechanism via ducts. Quantitative results of fractional area in top and front view of the three coupes under fire and smoke are obtained using MATLAB (IMT). Present simulations and its findings will be useful for organizations like Commission of Railway Safety and others in designing and implementing safety and evacuation measures.

Keywords: air conditioned coaches, fire propagation, flame contour, soot flow, train fire

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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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: Giang Tran Thi Huong, Hieu Dong Van, Tung Dao Duy, Saadanov Iskender, Isakeev Mairambek, Tsutomu Omatsu, Yukie Katayama, Tetsuya Mizutani, Yuki Ozeki, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Newcastle disease virus (NDV) is a contagious viral disease of the poultry industry and other birds throughout the world. At present, very little is known about molecular epidemiological data regarding the causes of ND outbreak in commercial poultry farms in Kyrgyzstan. In the current study, the NDV isolated from the one out of three samples from the unvaccinated flock was confirmed as NDV. Phylogenetic analysis indicated that this NDV strain is clustered in the Class II subgenotype VIId, and closely related to the Chinese NDV isolate. Phylogenetic analyses revealed that the isolated NDV strain has an origin different from the 4 NDV strains previously identified in Kyrgyzstan. According to the mean death time (MDT: 61.1 h) and a multibasic amino acid (aa) sequence at the F0 proteolytic cleavage site (¹¹²R-R-Q-K-R-F¹¹⁷), the NDV isolate was determined as mesogenic strain. Several mutations in the neutralizing epitopes (notably, ³⁴⁷E→K) and the global head were observed in the hemagglutinin-neuraminidase (HN) protein of the current isolate. The present study represents the molecular characterization of the coding gene region of NDV in Kyrgyzstan. Additionally, further study will be investigated on the antigenic characterization using monoclonal antibody.

Keywords: Kyrgyzstan, Newcastle disease, genotype, genome characterization

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Authors: Syed Asif Hassan, Tabrej Khan

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Tuberculosis (TB) caused by bacillus Mycobacterium tuberculosis (Mtb) continues to take a disturbing toll on human life and healthcare facility worldwide. The global burden of TB remains enormous. The alarming rise of multi-drug resistant strains of Mycobacterium tuberculosis calls for an increase in research efforts towards the development of new target specific therapeutics against diverse strains of M. tuberculosis. Therefore, the discovery of new molecular scaffolds targeting new drug sites should be a priority for a workable plan for fighting resistance in Mycobacterium tuberculosis (Mtb). Mtb non-acylated lipoprotein LprG (Rv1411c) has a Toll-like receptor 2 (TLR2) agonist actions that depend on its association with triacylated glycolipids binding specifically with the hydrophobic pocket of Mtb LprG lipoprotein. The detection of a glycolipid carrier function has important implications for the role of LprG in Mycobacterial physiology and virulence. Therefore, considering the pivotal role of glycolipids in mycobacterial physiology and host-pathogen interactions, designing competitive antagonist (chemotherapeutics) ligands that competitively bind to glycolipid binding domain in LprG lipoprotein, will lead to inhibition of tuberculosis infection in humans. In this study, a unified approach involving ligand-based virtual screening protocol USRCAT (Ultra Shape Recognition) software and molecular docking studies using Auto Dock Vina 1.1.2 using the X-ray crystal structure of Mtb LprG protein was implemented. The docking results were further confirmed by DSX (DrugScore eXtented), a robust program to evaluate the binding energy of ligands bound to the Ligand binding domain of the Mtb LprG lipoprotein. The ligand, which has the higher hypothetical affinity, also has greater negative value. Based on the USRCAT, Lipinski’s values and molecular docking results, [(2R)-2,3-di(hexadecanoyl oxy)propyl][(2S,3S,5S,6R)-3,4,5-trihydroxy-2,6-bis[[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6 (hydroxymethyl)tetrahydropyran-2-yl]oxy]cyclohexyl] phosphate (XPX) was confirmed as a promising drug-like lead compound (antagonist) binding specifically to the hydrophobic domain of LprG protein with affinity greater than that of PIM2 (agonist of LprG protein) with a free binding energy of -9.98e+006 Kcal/mol and binding affinity of -132 Kcal/mol, respectively. A further, in vitro assay of this compound is required to establish its potency in inhibiting molecular evasion mechanism of MTB within the infected host macrophages. These results will certainly be helpful in future anti-TB drug discovery efforts against Multidrug-Resistance Tuberculosis (MDR-TB).

Keywords: antagonist, agonist, binding affinity, chemotherapeutics, drug-like, multi drug resistance tuberculosis (MDR-TB), RV1411c protein, toll-like receptor (TLR2)

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Authors: Yessengali Ussenbekov, Valery Terletskiy, Orik Zhanserkenova, Shynar Kasymbekova, Indira Beyshova, Aitkali Imanbayev, Almas Serikov

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Currently, there are 46 hereditary diseases afflicting cattle with known molecular genetic diagnostic methods developed for them. Genetic anomalies frequently occur in the Holstein cattle breeds from American and Canadian bloodlines. The data on the incidence of BLAD, CVM, DUMPS and BC autosomal recessive lethal mutations in pedigree animals are discordant, the detrimental allele incidence rates are high for the Holstein cattle breed, whereas the incidence rates of these mutations are low in some breeds or they are completely absent. Data were obtained on the basis of frozen semen of stud bulls. DNA was extracted from the semen with the DNA-Sorb-B extraction kit. The lethal mutation in the genes CD18, SLC35A3, UMP and ASS of Alatau stud bulls (N=124) was detected by polymerase chain reaction and RFLP analysis. It was established that stud bulls of the local Alatau breed were not carriers of the BLAD, CVM, DUMPS, and BC detrimental mutations. However, with a view to preventing the dissemination of hereditary diseases it is recommended to monitor the pedigree stock using molecular genetic methods.

Keywords: PCR, autosomal recessive point mutation, BLAD, CVM, DUMPS, BC, stud bulls

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Authors: Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Yung Fu Chang

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For the identification of bovine mastitic pathogen, an economical, rapid and sensitive molecular diagnostic assay is developed by PCR multiplexing of gene and pathogenic species specific DNA sequences. The multiplex PCR assay is developed for detecting nine important bacterial pathogens causing mastitis Worldwide. The bacterial species selected for this study are Streptococcus agalactiae, Streptococcus dysagalactiae, Streptococcus uberis, Staphylococcus aureus, Escherichia coli, Staphylococcus haemolyticus, Staphylococcus chromogenes Mycoplasma bovis and Staphylococcus epidermidis. A single reaction assay was developed and validated by 27 reference strains and further tested on 276 bacterial strains obtained from culturing mastitic milk. The multiplex PCR assay developed here is further evaluated by applying directly on genomic DNA isolated from 200 mastitic milk samples. It is compared with bacterial culturing method and proved to be more sensitive, rapid, economical and can specifically identify 9 bacterial pathogens in a single reaction. It has detected the pathogens in few culture negative mastitic samples. Recognition of disease is the foundation of disease control and prevention. This assay can be very helpful for maintaining the udder health and milk monitoring.

Keywords: multiplex PCR, bacteria, mastitis, milk

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Authors: Sujoy Das, M. M. Ghosh

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The thermal conductivity of a fluid can be significantly enhanced by dispersing nano-sized particles in it, and the resultant fluid is termed as "nanofluid". A theoretical model for estimating the thermal conductivity of a nanofluid has been proposed here. It is based on the mechanism that evenly dispersed nanoparticles within a nanofluid undergo Brownian motion in course of which the nanoparticles repeatedly collide with the heat source. During each collision a rapid heat transfer occurs owing to the solid-solid contact. Molecular dynamics (MD) simulation of the collision of nanoparticles with the heat source has shown that there is a pulse-like pick up of heat by the nanoparticles within 20-100 ps, the extent of which depends not only on thermal conductivity of the nanoparticles, but also on the elastic and other physical properties of the nanoparticle. After the collision the nanoparticles undergo Brownian motion in the base fluid and release the excess heat to the surrounding base fluid within 2-10 ms. The Brownian motion and associated temperature variation of the nanoparticles have been modeled by stochastic analysis. Repeated occurrence of these events by the suspended nanoparticles significantly contributes to the characteristic thermal conductivity of the nanofluids, which has been estimated by the present model for a ethylene glycol based nanofluid containing Cu-nanoparticles of size ranging from 8 to 20 nm, with Gaussian size distribution. The prediction of the present model has shown a reasonable agreement with the experimental data available in literature.

Keywords: brownian dynamics, molecular dynamics, nanofluid, thermal conductivity

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

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There are several methods for determination of the lipophilicity of biologically active compounds, however chromatography has been shown as a very suitable method for this purpose. Chromatographic (C18-RP-HPLC) analysis of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives was carried out. The obtained retention indices (logk, methanol (90%) / water (10%)) were correlated with calculated physicochemical and lipophilicity descriptors. The QSRR analysis was carried out applying principal component regression (PCR) and partial least squares regression (PLS). The PCR and PLS model were selected on the basis of the highest variance and the lowest root mean square error of cross-validation. The obtained PCR and PLS model successfully correlate the calculated molecular descriptors with logk parameter indicating the significance of the lipophilicity of compounds in chromatographic process. On the basis of the obtained results it can be concluded that the obtained logk parameters of the analyzed androstane derivatives can be considered as their chromatographic lipophilicity. These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1105.

Keywords: androstane derivatives, chromatography, molecular structure, principal component regression, partial least squares regression

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Authors: Wilmer Esteban Vallejo Narváez, Serguei Fomine

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The theoretical investigation of Si-doped graphene nanoflakes (NFs) was conducted to understand their catalytic impact on CO₂ reduction using molecular hydrogen at the Density Functional Theory (DFT) level. The introduction of silicon by substituting carbon induces defects in the NF structure, resulting in a polyradical ground state. This silicon defect significantly boosts reactivity towards substrates, making Si-doped graphene NFs more catalytically active in CO₂ reduction to formic acid compared to silicene. Notably, Si-doped graphene demonstrates a preference for formic acid over carbon monoxide, mirroring the behavior of silicene. Furthermore, investigations into formic acid-to-formaldehyde and formaldehyde-to-methanol conversions reveal instances where Si-doped graphene outperforms silicene in terms of efficacy. In the final reduction step, the methanol-to-methane reaction unfolds in four stages, with the rate-determining step involving hydrogen transfer from silicon to methyl. Notably, the activation energy for this step is lower in Si-doped graphene compared to silicene. Consequently, Si-doped graphene NFs emerge as superior catalysts with lower activation energies overall. Remarkably, throughout these catalytic processes, Si-doped graphene maintains environmental stability, further highlighting its enhanced catalytic activity without compromising graphene's inherent stability.

Keywords: silicon-doped graphene, CO₂ reduction, DFT, catalysis

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Authors: A. S. Vidyashree, C. M. Kalleshwaraswamy, R. Asokan, H. M. Mahadevaswamy

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Termites are very vital ecological thespians in tropical ecosystem, having been designated as “ecosystem engineers”, due to their significant role in providing soil ecosystem services. Despite their importance, our understanding of a number of their basic biological processes in termites is extremely limited. Developing a better understanding of termite biology is closely dependent upon consistent species identification. At present, identification of termites is relied on soldier castes. But for many species, soldier caste is not reported, that creates confusion in identification. The use of molecular markers may be helpful in estimating phylogenetic relatedness between the termite species and estimating genetic differentiation among local populations within each species. To understand this, termites samples were collected from various places of Western Ghats covering four states namely Karnataka, Kerala, Tamil Nadu, Maharashtra during 2013-15. Termite samples were identified based on their morphological characteristics, molecular characteristics, or both. Survey on the termite fauna in Karnataka, Kerala, Maharashtra and Tamil Nadu indicated the presence of a 16 species belongs to 4 subfamilies under two families viz., Rhinotermitidae and Termitidae. Termititidae was the dominant family which was belonging to 4 genera and four subfamilies viz., Macrotermitinae, Amitermitinae, Nasutitermitinae and Termitinae. Amitermitinae had three species namely, Microcerotermes fletcheri, M. pakistanicus and Speculitermes sinhalensis. Macrotermitinae had the highest number of species belonging two genera, namely Microtermes and Odontotermes. Microtermes genus was with only one species i.e., Microtermes obesi. The genus Odontotermes was represented by the highest number of species (07), namely, O. obesus was the dominant (41 per cent) and the most widely distributed species in Karnataka, Karala, Maharashtra and Tamil nadu followed by O. feae (19 per cent), O.assmuthi (11 per cent) and others like O. bellahunisensis O. horni O. redemanni, O. yadevi. Nasutitermitinae was represented by two genera namely Nasutitermes anamalaiensis and Trinervitermes biformis. Termitinae subfamily was represented by Labiocapritermes distortus. Rhinotermitidae was represented by single subfamily Heterotermetinae. In Heterotermetinae, two species namely Heterotermes balwanthi and H. malabaricus were recorded. Genetic relationship among termites collected from various locations of Western Ghats of India was characterized based on mitochondrial DNA sequences (12S, 16S, and COII). Sequence analysis and divergence among the species was assessed. These results suggest that the use of both molecular and morphological approaches is crucial in ensuring accurate species identification. Efforts were made to understand their evolution and to address the ambiguities in morphological taxonomy. The implication of the study in revising the taxonomy of Indian termites, their characterization and molecular comparisons between the sequences are discussed.

Keywords: isoptera, mitochondrial DNA sequences, rhinotermitidae, termitidae, Western ghats

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

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

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

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Authors: F. Q. Shao, W. Q. Wang, Y. Yin, T. P. Yu, D. B. Zou, J. M. Ouyang

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The Radiation Pressure Acceleration (RPA) mechanism is very promising in laser-driven ion acceleration because of high laser-ion energy conversion efficiency. Although some experiments have shown the characteristics of RPA, the energy of ions is quite limited. The ion energy obtained in experiments is only several MeV/u, which is much lower than theoretical prediction. One possible limiting factor is the transverse instability incited in the RPA process. The transverse instability is basically considered as the Rayleigh-Taylor (RT) instability, which is a kind of interfacial instability and occurs when a light fluid pushes against a heavy fluid. Multi-dimensional particle-in-cell (PIC) simulations show that the onset of transverse instability will destroy the acceleration process and broaden the energy spectrum of fast ions during the RPA dominant ion acceleration processes. The evidence of the RT instability driven by radiation pressure has been observed in a laser-foil interaction experiment in a typical RPA regime, and the dominant scale of RT instability is close to the laser wavelength. The development of transverse instability in the radiation-pressure-acceleration dominant laser-foil interaction is numerically examined by two-dimensional particle-in-cell simulations. When a laser interacts with a foil with modulated surface, the internal instability is quickly incited and it develops. The linear growth and saturation of the transverse instability are observed, and the growth rate is numerically diagnosed. In order to optimize interaction parameters, a method of information entropy is put forward to describe the chaotic degree of the transverse instability. With moderate modulation, the transverse instability shows a low chaotic degree and a quasi-monoenergetic proton beam is produced.

Keywords: information entropy, radiation pressure acceleration, Rayleigh-Taylor instability, transverse instability

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Authors: M. Khorshed Alam, H. Takaba

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The catalytic properties of metal usually change by intermixturing with another metal in polymer electrolyte fuel cells. Pt-Ru alloy is one of the much-talked used alloy to enhance the CO oxidation. In this work, we have investigated the CO coverage on the Pt2Ru3 nanoparticle with different atomic conformation of Pt and Ru using a combination of material informatics with computational chemistry. Density functional theory (DFT) calculations used to describe the adsorption strength of CO and H with different conformation of Pt Ru ratio in the Pt2Ru3 slab surface. Then through the Monte Carlo (MC) simulations we examined the segregation behaviour of Pt as a function of surface atom ratio, subsurface atom ratio, particle size of the Pt2Ru3 nanoparticle. We have constructed a regression equation so as to reproduce the results of DFT only from the structural descriptors. Descriptors were selected for the regression equation; xa-b indicates the number of bonds between targeted atom a and neighboring atom b in the same layer (a,b = Pt or Ru). Terms of xa-H2 and xa-CO represent the number of atoms a binding H2 and CO molecules, respectively. xa-S is the number of atom a on the surface. xa-b- is the number of bonds between atom a and neighboring atom b located outside the layer. The surface segregation in the alloying nanoparticles is influenced by their component elements, composition, crystal lattice, shape, size, nature of the adsorbents and its pressure, temperature etc. Simulations were performed on different size (2.0 nm, 3.0 nm) of nanoparticle that were mixing of Pt and Ru atoms in different conformation considering of temperature range 333K. In addition to the Pt2Ru3 alloy we also considered pure Pt and Ru nanoparticle to make comparison of surface coverage by adsorbates (H2, CO). Hence, we assumed the pure and Pt-Ru alloy nanoparticles have an fcc crystal structures as well as a cubo-octahedron shape, which is bounded by (111) and (100) facets. Simulations were performed up to 50 million MC steps. From the results of MC, in the presence of gases (H2, CO), the surfaces are occupied by the gas molecules. In the equilibrium structure the coverage of H and CO as a function of the nature of surface atoms. In the initial structure, the Pt/Ru ratios on the surfaces for different cluster sizes were in range of 0.50 - 0.95. MC simulation was employed when the partial pressure of H2 (PH2) and CO (PCO) were 70 kPa and 100-500 ppm, respectively. The Pt/Ru ratios decrease as the increase in the CO concentration, without little exception only for small nanoparticle. The adsorption strength of CO on the Ru site is higher than the Pt site that would be one of the reason for decreasing the Pt/Ru ratio on the surface. Therefore, our study identifies that controlling the nanoparticle size, composition, conformation of alloying atoms, concentration and chemical potential of adsorbates have impact on the steadiness of nanoparticle alloys which ultimately and also overall catalytic performance during the operations.

Keywords: anode catalysts, fuel cells, material informatics, Monte Carlo

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Authors: Khalid Alhudaib

Abstract:

Potato is considered as one of the most important and potential vegetable crops in Saudi Arabia. Alfalfa mosaic virus (AMV), genus Alfamovirus, family Bromoviridae is among the broad spread of viruses in potato. During spring and fall growing seasons of potato in 2015 and 2016, several field visits were conducted in the four major growing areas of potato cultivation (Riyadh-Qaseem-Hail-Hard). The presence of AMV was detected in samples using ELISA, dot blot hybridization and/or RT-PCR. The highest occurrence of AMV was observed as 18.6% in Qaseem followed by Riyadh with 15.2% while; the lowest infection rates were recorded in Hard and Hail, 8.3 and 10.4%, respectively. The sequences of seven isolates of AMV obtained in this study were determined and the sequences were aligned with the other sequences available in the GenBank database. Analyses confirmed the low variability among AMV isolated in this study, which means that all AMV isolates may originate from the same source. Due to high incidence of AMV, other economic susceptible crops may become affected by high incidence of this virus in potato crops. This requires accurate examination of potato seed tubers to prevent the spread of the virus in Saudi Arabia. The obtained results indicated that the hybridization and ELISA are suitable techniques in the routine detection of AMV in a large number of samples while RT-PCR is more sensitive and essential for molecular characterization of AMV.

Keywords: Alfamovirus, AMV, Alfalfa mosaic virus, PCR, potato

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Authors: Acheampong Addo, Emmanuel Odartei Armah, Seth Koranteng Agyakwah, Ruby Asmah, Emmanuel Tetteh-Doku Mensah, Rhoda Lims Diyie, Sena Amewu, Catherine Ragasa, Edward Kofi Abban, Mike Yaw Osei-Atweneboana

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The study investigated genetic variation and relationships among populations of Nile tilapia cultured in small-scale fish farms in selected regions of Ghana. A total of 700 samples were collected. All samples were screened with five microsatellite markers and results were analyzed using (Genetic Analysis in Excel), (Molecular and Evolutionary Genetic Analysis software, and Genpop on the web for Heterozygosity and Shannon diversity, (Analysis of Molecular Variance), and (Principal Coordinate Analysis). Fish from the 16 populations (made up of 14 farms and 2 selectively bred populations) clustered into three groups: 7 populations clustered with the GIFT-derived strain, 4 populations clustered with the Akosombo strain, and three populations were in a separate cluster. The clustering pattern indicated groups of different strains of Nile tilapia cultured. Mantel correlation test also showed low genetic variations among the 16 populations hence the need to boost seed quality in order to accelerate aquaculture production in Ghana.

Keywords: microsatellites, small- scale, Nile tilapia, akosombo strain, GIFT strain

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