Search results for: molecular docking and dynamics

Authors: Kanyaporn Sommeechai

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Air cadets who aspire to become military pilots upon graduation undergo rigorous training at military academies. As first-year cadets are akin to civilian freshmen, they encounter numerous challenges within the seniority-based military academy system. Imposed routines, such as mandatory morning runs and restrictions on mobile phone usage for two semesters, have the potential to impact their learning process and motivation to study, including second language (L2) acquisition. This study aims to investigate the motivational dynamics and L2 learning transitions experienced by air cadets. To achieve this, a Retrodictive Qualitative Modelling approach will be employed, coupled with the adaptation of the three-barrier structure encompassing institutional factors, situational factors, and dispositional factors. Semi-structured interviews will be conducted to gather rich qualitative data. By analyzing and interpreting the collected data, this research seeks to shed light on the motivational factors that influence air cadets' L2 learning journey. The three-barrier structure will provide a comprehensive framework to identify and understand the institutional, situational, and dispositional factors that may impede or facilitate their motivation and language learning progress. Moreover, the study will explore how these factors interact and shape cadets' motivation and learning experiences. The outcomes of this research will yield fundamental data that can inform strategies and interventions to enhance the motivation and language learning outcomes of air cadets. By better understanding their motivational dynamics and transitions, educators and institutions can create targeted initiatives, tailored pedagogical approaches, and supportive environments that effectively inspire and engage air cadets as L2 learners.

Keywords: second language, education, motivational dynamics, learning transitions

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Authors: Beata Jackowska-Zduniak

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We formulate and analyze a mathematical model describing dynamics of the hypothalamus-pituitary-thyroid homoeostatic mechanism in endocrine system. We introduce to this system two types of couplings and delay. In our model, feedback controls the secretion of thyroid hormones and delay reflects time lags required for transportation of the hormones. The influence of delayed feedback on the stability behaviour of the system is discussed. Analytical results are illustrated by numerical examples of the model dynamics. This system of equations describes normal activity of the thyroid and also a couple of types of malfunctions (e.g. hyperthyroidism).

Keywords: mathematical modeling, ordinary differential equations, endocrine system, delay differential equation

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Authors: Elias Akoury

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Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable technique used in structure determination of small and macromolecules to study their physical properties, elucidation of characteristic interactions, dynamics and thermodynamic processes. Quantum mechanics defines the theoretical description of NMR spectroscopy and treatment of the dynamics of nuclear spin systems. The phenomenon of residual dipolar coupling (RDCs) has become a routine tool for accurate structure determination by providing global orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. This offers accessibility of distance-independent angular information and insights to local relaxation. The measurement of RDCs requires an anisotropic orientation medium for the molecules to partially align along the magnetic field. This can be achieved by introduction of liquid crystals or attaching a paramagnetic center. Although anisotropic paramagnetic tags continue to mark achievements in the biomolecular NMR of large proteins, its application in small organic molecules remains unspread. Here, we propose a strategy for the synthesis of a lanthanide tag and the measurement of RDCs in organic molecules using paramagnetic lanthanide complexes.

Keywords: lanthanide tags, NMR spectroscopy, residual dipolar coupling, quantum mechanics of spin dynamics

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Authors: Junie B. Billones, Maria Constancia O. Carrillo, Voltaire G. Organo, Stephani Joy Y. Macalino, Inno A. Emnacen, Jamie Bernadette A. Sy

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The drug discovery and development process is generally known to be a very lengthy and labor-intensive process. Therefore, in order to be able to deliver prompt and effective responses to cure certain diseases, there is an urgent need to reduce the time and resources needed to design, develop, and optimize potential drugs. Computer-aided drug design (CADD) is able to alleviate this issue by applying computational power in order to streamline the whole drug discovery process, starting from target identification to lead optimization. This drug design approach can be predominantly applied to diseases that cause major public health concerns, such as tuberculosis. Hitherto, there has been no concrete cure for this disease, especially with the continuing emergence of drug resistant strains. In this study, CADD is employed for tuberculosis by first identifying a key enzyme in the mycobacterium’s metabolic pathway that would make a good drug target. One such potential target is the lipoate protein ligase B enzyme (LipB), which is a key enzyme in the M. tuberculosis metabolic pathway involved in the biosynthesis of the lipoic acid cofactor. Its expression is considerably up-regulated in patients with multi-drug resistant tuberculosis (MDR-TB) and it has no known back-up mechanism that can take over its function when inhibited, making it an extremely attractive target. Using cutting-edge computational methods, compounds from AnalytiCon Discovery Natural Derivatives database were screened and docked against the LipB enzyme in order to rank them based on their binding affinities. Compounds which have better binding affinities than LipB’s known inhibitor, decanoic acid, were subjected to in silico toxicity evaluation using the ADMET and TOPKAT protocols. Out of the 31,692 compounds in the database, 112 of these showed better binding energies than decanoic acid. Furthermore, 12 out of the 112 compounds showed highly promising ADMET and TOPKAT properties. Future studies involving in vitro or in vivo bioassays may be done to further confirm the therapeutic efficacy of these 12 compounds, which eventually may then lead to a novel class of anti-tuberculosis drugs.

Keywords: pharmacophore, molecular docking, lipoate protein ligase B (LipB), ADMET, TOPKAT

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Authors: Silka Abyadati, Dadi Rusdiana, Enjang Akhmad Juanda

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This study aims to investigate the students’ mastery concepts enhancement between students who are studying by using Integrated Real-Life Video and Animation (IRVA) and students who are studying without using IRVA. The development of IRVA is conducted by five stages: Analyze, Design, Development, Implementation and Evaluation (ADDIE) based on constructivist for Rotational Dynamics material in Physics learning. A constructivist model-based learning used is Interpretation Construction (ICON), which has the following phases: 1) Observation, 2) Construction interpretation, 3) Contextualization prior knowledge, 4) Conflict cognitive, 5) Learning cognitive, 6) Collaboration, 7) Multiple interpretation, 8) Multiple manifestation. The IRVA is developed for the stages of observation, cognitive conflict and cognitive learning. The sample of this study consisted of 32 students experimental group and a control group of 32 students in class XI of the school year 2015/2016 in one of Senior High Schools Bandung. The study was conducted by giving the pretest and posttest in the form of 20 items of multiple choice questions to determine the enhancement of mastery concept of Rotational Dynamics. Hypothesis testing is done by using T-test on the value of N-gain average of mastery concepts. The results showed that there is a significant difference in an enhancement of students’ mastery concepts between students who are studying by using IRVA and students who are studying without IRVA. Students in the experimental group increased by 0.468 while students in the control group increased by 0.207.

Keywords: ADDIE, constructivist learning, Integrated Real-Life Video and Animation, mastery concepts, rotational dynamics

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Authors: Selma Bouasria, Mahi Abdelkader, Abbès Azzi, Herouz Keltoum

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This paper reports concept was used into the computational fluid dynamics (CFD) code cfx through user-defined functions to assess ventilation efficiency inside (forced-ventilation local). CFX is a simulation tool which uses powerful computer and applied mathematics, to model fluid flow situations for the prediction of heat, mass and momentum transfer and optimal design in various heat transfer and fluid flow processes to evaluate thermal comfort in a room ventilated (highly-glazed). The quality of the solutions obtained from CFD simulations is an effective tool for predicting the behavior and performance indoor thermo-aéraulique comfort.

Keywords: ventilation, thermal comfort, CFD, indoor environment, solar air heater

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Authors: Bohsiu Wu

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This study compares the differences in social dynamics between rural and urban areas in California to explain homicides involving family members. It is hypothesized that rural homicides are better explained by social isolation and lack of intervention resources, whereas urban homicides are attributed to social disadvantage factors. Several critical social dynamics including social isolation, social disadvantages, acculturation, and intervention resources were entered in a hierarchical linear model (HLM) to examine whether county-level factors affect how each specific dynamic performs at the ZIP code level, a proxy measure for communities. Homicide data are from the Supplementary Homicide Report for all 58 counties in California from 1997 to 1999. Predictors at both the county and ZIP code levels are derived from the 2000 US census. Preliminary results from a HLM analysis show that social isolation is a significant but moderate predictor to explain rural family homicide and various social disadvantage factors are significant factors accounting for urban family homicide. Acculturation has little impact. Rurality and urbanity appear to interact with various social dynamics in explaining family homicide. The implications for prevention at both the county and community level as well as directions for future study on the differences between rural and urban locales are explored in the paper.

Keywords: communities, family, HLM, homicide, rural, urban

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Authors: Aemro Tazeze Terefe, Mengistu K. Aredo, Abule M. Workagegnehu, Wondimagegn M. Tesfaye

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Climate-induced shocks have been shown to reduce agricultural production and cause fluctuation in output in developing countries. When livelihoods depend on rain-fed agriculture, climate-induced shocks translate into consumption shocks. Despite the substantial improvements in household consumption, climate-induced shocks, and other factors adversely affect consumption dynamics at the household level in Ethiopia. Therefore, household consumption dynamics in the context of climate-induced shocks help to guide resilience capacity and establish appropriate interventions and programs. The research employed three-round panel data based on the Ethiopian Socioeconomic Survey with spatial rainfall data to define unique measures of rainfall variability. The linear dynamic panel model results show that the lagged value of consumption, market shocks, and rainfall variability positively affected consumption dynamics. In contrast, production shocks, temperature, and amount of rainfall had a negative relationship. Coping strategies mitigate adverse climate-induced shocks on consumption aftershocks that smooth consumption over time. Support to increase the resilience capacity of households can involve efforts to make existing livelihoods and forms of production or reductions in the vulnerability of households. Therefore, government interventions are mandatory for asset accumulation agendas that support household coping strategies and respond to shocks. In addition, the dynamic linkage between consumption and significant socioeconomic and institutional factors should be taken into account to minimize the effect of climate-induced shocks on consumption dynamics.

Keywords: climate shock, Ethiopia, fixed-effect model, food security

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Authors: Siddharth Ahuja, T. M. Muruganandam

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An analytical investigation is performed to study the unsteady response of a one-dimensional, non-linear dynamic shock system to external downstream pressure perturbations in a supersonic flow in a varying area duct. For a given pressure ratio across a wind tunnel, the normal shock's location can be computed as per one-dimensional steady gas dynamics. Similarly, for some other pressure ratio, the location of the normal shock will change accordingly, again computed using one-dimensional gas dynamics. This investigation focuses on the small-time interval between the first steady shock location and the new steady shock location (corresponding to different pressure ratios). In essence, this study aims to shed light on the motion of the shock from one steady location to another steady location. Further, this study aims to create the foundation of the Unsteady Gas Dynamics field enabling further insight in future research work. According to the new pressure ratio, a pressure pulse, generated at the exit of the tunnel which travels and perturbs the shock from its original position, setting it into motion. During such activity, other numerous physical phenomena also happen at the same time. However, three broad phenomena have been focused on, in this study - Traversal of a Wave, Fluid Element Interactions and Wave Interactions. The above mentioned three phenomena create, alter and kill numerous waves for different conditions. The waves which are created by the above-mentioned phenomena eventually interact with the shock and set it into motion. Numerous such interactions with the shock will slowly make it settle into its final position owing to the new pressure ratio across the duct, as estimated by one-dimensional gas dynamics. This analysis will be extremely helpful in the prediction of inlet 'unstart' of the flow in a supersonic engine intake and its prominence with the incoming flow Mach number, incoming flow pressure and the external perturbation pressure is also studied to help design more efficient supersonic intakes for engines like ramjets and scramjets.

Keywords: analytical investigation, compression and expansion waves, fluid element interactions, shock trajectory, supersonic flow, unsteady gas dynamics, varying area duct, wave interactions

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Authors: Hamza Javar Magnier, Robin Curtis

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There have been rapid advances in the upstream processing of protein therapeutics, which has shifted the bottleneck to downstream purification and formulation. Finding liquid formulations with shelf lives of up to two years is increasingly difficult for some of the newer therapeutics, which have been engineered for activity, but their formulations are often viscous, can phase separate, and have a high propensity for irreversible aggregation1. We explore means to develop improved predictive ability from a better understanding of how protein-protein interactions on formulation conditions (pH, ionic strength, buffer type, presence of excipients) and how these impact upon the initial steps in protein self-association and aggregation. In this work, we study the initial steps in the aggregation pathways using a minimal protein model based on square-well potentials and discontinuous molecular dynamics. The effect of model parameters, including range of interaction, stiffness, chain length, and chain sequence, implies that protein models fold according to various pathways. By reducing the range of interactions, the folding- and collapse- transition come together, and follow a single-step folding pathway from the denatured to the native state2. After parameterizing the model interaction-parameters, we developed an understanding of low-temperature conformational properties and fluctuations, and the correlation to the folding transition of proteins in isolation. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This implies that fluctuations at low-temperature can be correlated to the folding transition at the melting temperature. Because proteins “breath” at low temperatures, defining a native-state as a single structure with conserved contacts and a fixed three-dimensional structure is misleading. Rather, we introduce a new definition of a native-state ensemble based on our understanding of the core conservation, which takes into account the native fluctuations at low temperatures. This approach permits the study of a large range of length and time scales needed to link the molecular interactions to the macroscopically observed behaviour. In addition, these models studied are parameterized by fitting to experimentally observed protein-protein interactions characterized in terms of osmotic second virial coefficients.

Keywords: protein folding, native-ensemble, conformational fluctuation, aggregation

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Authors: Manasa Kalla, Narasimha Raju Chebrolu, Ashok Chatterjee

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We have studied the quantum transport properties of a single molecular transistor in the presence of an external magnetic field using the Keldysh Green function technique. We also used the Anderson-Holstein-Caldeira-Leggett Model to describe the single molecular transistor that consists of a molecular quantum dot (QD) coupled to two metallic leads and placed on a substrate that acts as a heat bath. The phonons are eliminated by the Lang-Firsov transformation and the effective Hamiltonian is used to study the effect of an external magnetic field on the spectral density function, Tunneling Current, Differential Conductance and Spin polarization. A peak in the spectral function corresponds to a possible excitation. In the presence of a magnetic field, the spin-up and spin-down states are degenerate and this degeneracy is lifted by the magnetic field leading to the splitting of the central peak of the spectral function. The tunneling current decreases with increasing magnetic field. We have observed that even the differential conductance peak in the zero magnetic field curve is split in the presence electron-phonon interaction. As the magnetic field is increased, each peak splits into two peaks. And each peak indicates the existence of an energy level. Thus the number of energy levels for transport in the bias window increases with the magnetic field. In the presence of the electron-phonon interaction, Differential Conductance in general gets reduced and decreases faster with the magnetic field. As magnetic field strength increases, the spin polarization of the current is increasing. Our results show that a strongly interacting QD coupled to metallic leads in the presence of external magnetic field parallel to the plane of QD acts as a spin filter at zero temperature.

Keywords: Anderson-Holstein model, Caldeira-Leggett model, spin-polarization, quantum dots

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Authors: Anthony Albanese

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While much of the literature concerning Max Weber’s concept of charisma has addressed the importance of the follower’s recognition of and devotion to the charismatic leader, very little has been said about the processes that lead to the development of follower charisma. This article examines this largely overlooked aspect of the concept, as doing so (1) exacts the dynamics behind charisma’s transferability by moving beyond follower-centric models that focus on the recognition of the leader and toward one that emphasizes the follower’s generation and exhibition of charisma, (2) bridges a crucial gap between the rather wanting “losers of modernization” thesis and the social actor’s proclivity to produce stories and self-cast in said stories, (3) presents authoritarian dispositions as a reaction to the weakening effects everydayness have on charisma, and (4) complicates Weber’s formulation by reassessing the role of continually demonstrable mastery. To illustrate these dynamics, one should turn to the January 6th Capitol attack in the United States.

Keywords: max weber, extremism, right-wing populism, charisma

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Authors: Vishal Kumar Singh

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Bioprocess development is a time-constrained activity aimed at harnessing the full potential of culture performance in an ambience that is not natural to cells. Even with the use of chemically defined media and feeds, a significant amount of time is devoted in identifying the apt operating parameters. In addition, the scale-up of these processes is often accompanied by loss of antibody titer and product quality, which further delays the commercialization of the drug product. In such a scenario, the investigation of this disparity of culture performance is done by further experimentation at a smaller scale that is representative of at-scale production bioreactors. These scale-down model developments are also time-intensive. In this study, a computation fluid dynamics-based multi-objective scaling approach has been illustrated to speed up the process transfer. For the implementation of this approach, a transient multiphase water-air system has been studied in Ansys CFX to visualize the air bubble distribution and volumetric mass transfer coefficient (kLa) profiles, followed by the design of experiment based parametric optimization approach to define the operational space. The proposed approach is completely in silico and requires minimum experimentation, thereby rendering a high throughput to the overall process development.

Keywords: bioprocess development, scale up, scale down, computation fluid dynamics, multi-objective, Ansys CFX, design of experiment

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Authors: Wu Di, Yeo Khoon Seng, Lim Tee Tai

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The typical insects employ a flapping-wing mode of flight. The numerical simulations on free flight of a model fruit fly (Re=143) including hovering and are presented in this paper. Unsteady aerodynamics around a flapping insect is studied by solving the three-dimensional Newtonian dynamics of the flyer coupled with Navier-Stokes equations. A hybrid-grid scheme (Generalized Finite Difference Method) that combines great geometry flexibility and accuracy of moving boundary definition is employed for obtaining flow dynamics. The results show good points of agreement and consistency with the outcomes and analyses of other researchers, which validate the computational model and demonstrate the feasibility of this computational approach on analyzing fluid phenomena in insect flight. The present modeling approach also offers a promising route of investigation that could complement as well as overcome some of the limitations of physical experiments in the study of free flight aerodynamics of insects. The results are potentially useful for the design of biomimetic flapping-wing flyers.

Keywords: free hovering flight, flapping wings, fruit fly, insect aerodynamics, leading edge vortex (LEV), computational fluid dynamics (CFD), Navier-Stokes equations (N-S), fluid structure interaction (FSI), generalized finite-difference method (GFD)

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Authors: Hanik Park, Kyungsook Jeon, Suchul Shin, Youngchul Park

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The air vent head prevents the inflow of seawater into the cargo holds when it is used for the ballast tank on heavy weather. In this study, the flow characteristics and the grid size were created by the application of Computational Fluid Dynamics by taking into the consideration of comparison of test results. Then, the accuracy of the analysis was verified by comparing with experimental results. Based on this analysis, accurate turbulence model and grid size can be selected. Thus, the design characteristic of air vent head for bulk carrier contributes the reliability based on the research results.

Keywords: bulk carrier, FEM, SST, vent

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Authors: Wiwat Chumai, Perawit Boonsomchua, Kanjana Ongkasin

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The ball bouncing problem is a well-known problem in physics involving a ball dropped from a height to the ground. In this paper, the work investigates the theoretical and experimental setup that describes the dynamics of a rigid body on a chaotic elastic surface under air-damp conditions. Examination of four different types of balls is made, including marble, metal ball, tennis ball, and ping-pong ball. In this experiment, the effect of impact velocities is not considered; the ball is dropped from a fixed height. The method in this work employs the Rayleigh Dissipation Function to specify the effects of dissipative forces in Lagrangian mechanics. Our discoveries reveal that the dynamics of the ball exhibit horizontal motion while damping oscillation occurs, forming the destabilization in vertical pinch-off motion. Moreover, rotational motion is studied. According to the investigation of four different balls, the outcomes illustrate that greater mass results in more frequent dynamics, and the experimental results at some points align with the theoretical model. This knowledge contributes to our understanding of the complex fluid system and could serve as a foundation for further developments in water droplet simulation.

Keywords: droplet, damping oscillation, nonlinear damping oscillation, bouncing ball problem, elastic surface

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Authors: Keltoum Chahour, Mickael Binois

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Due to a lack of standardization during the invasive fractional flow reserve (FFR) procedure, the index is subject to many sources of uncertainties. In this paper, we investigate -through simulation- the effect of the (FFR) device position and configuration on the obtained value of the (FFR) fraction. For this purpose, we use computational fluid dynamics (CFD) in a 3D domain corresponding to a diseased arterial portion. The (FFR) pressure captor is introduced inside it with a given length and coefficient of bending to capture the (FFR) value. To get over the computational limitations, basically, the time of the simulation is about 2h 15min for one (FFR) value; we generate a Gaussian Process (GP) model for (FFR) prediction. The (GP) model indicates good accuracy and demonstrates the effective error in the measurement created by the random configuration of the pressure captor.

Keywords: fractional flow reserve, Gaussian processes, computational fluid dynamics, drift

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Authors: Sayanti Kar, Amitava Ghosh, Pritam Aitch, Gupinath Bhandari

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An extensive seasonal analysis of wastewater had been done from outfalls of river Ganga in Howrah, Hooghly, 24 PGS (N) District, West Bengal, India during 2017. The morphological parameters of Bitter gourd (Momordica charantia L.) were estimated under wastewater treatment. An approach to study the activity within the range of low molecular weight peptide 3-0.5 kDa were taken through its extraction and purification by ion exchange resin column, cation, and anion exchanger. HPLC analysis had been done for both in wastewater treated and untreated plants. The antioxidant activity by using DPPH and germination percentage in control and treated plants were also determined in relation to wastewater effect. The inhibition of growth and its parameters were maximum in pre-monsoon in comparing to post-monsoon and monsoon season. The study also helped to explore the effect of wastewater on the peptidome of Bitter gourd (Momordica charantia L.). Some of these low molecular weight peptide(s) (3-0.5 kDa) also inhibited during wastewater treatment. Expression of particular peptide(s) or absence of some peptide(s) in chromatogram indicated the adverse effects on plants which may be the indication of stressful condition. Pre monsoon waste water was found to create more impact than other two.

Keywords: bitter gourd (Momordica charantia l.), low molecular weight peptide, river ganga, waste water

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Authors: Deni̇z Ezgi̇ Gülmez, Mesut Kirca

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Nanoporous (np) metals have attracted considerable attention owing to their cellular morphological features at atomistic scale which yield ultra-high specific surface area awarding a great potential to be employed in diverse applications such as catalytic, electrocatalytic, sensing, mechanical and optical. As one of the carbon based nanostructures, fullerenes are also another type of outstanding nanomaterials that have been extensively investigated due to their remarkable chemical, mechanical and optical properties. In this study, the idea of improving the mechanical behavior of nanoporous metals by inclusion of the fullerenes, which offers a new metal-carbon nanocomposite material, is examined and discussed. With this motivation, tensile mechanical behavior of nanoporous metals reinforced with carbon fullerenes is investigated by classical molecular dynamics (MD) simulations. Atomistic models of the nanoporous metals with ultrathin ligaments are obtained through a stochastic process simply based on the intersection of spherical volumes which has been used previously in literature. According to this technique, the atoms within the ensemble of intersecting spherical volumes is removed from the pristine solid block of the selected metal, which results in porous structures with spherical cells. Following this, fullerene units are added into the cellular voids to obtain final atomistic configurations for the numerical tensile tests. Several numerical specimens are prepared with different number of fullerenes per cell and with varied fullerene sizes. LAMMPS code was used to perform classical MD simulations to conduct uniaxial tension experiments on np models filled by fullerenes. The interactions between the metal atoms are modeled by using embedded atomic method (EAM) while adaptive intermolecular reactive empirical bond order (AIREBO) potential is employed for the interaction of carbon atoms. Furthermore, atomic interactions between the metal and carbon atoms are represented by Lennard-Jones potential with appropriate parameters. In conclusion, the ultimate goal of the study is to present the effects of fullerenes embedded into the cellular structure of np metals on the tensile response of the porous metals. The results are believed to be informative and instructive for the experimentalists to synthesize hybrid nanoporous materials with improved properties and multifunctional characteristics.

Keywords: fullerene, intersecting spheres, molecular dynamic, nanoporous metals

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Authors: O. B. Iskender, K. V. Ling, V. Dubanchet, L. Simonini

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This paper discusses the recent advances and future prospects of spacecraft position and attitude control using Model Predictive Control (MPC). First, the challenges of the space missions are summarized, in particular, taking into account the errors, uncertainties, and constraints imposed by the mission, spacecraft and, onboard processing capabilities. The summary of space mission errors and uncertainties provided in categories; initial condition errors, unmodeled disturbances, sensor, and actuator errors. These previous constraints are classified into two categories: physical and geometric constraints. Last, real-time implementation capability is discussed regarding the required computation time and the impact of sensor and actuator errors based on the Hardware-In-The-Loop (HIL) experiments. The rationales behind the scenarios’ are also presented in the scope of space applications as formation flying, attitude control, rendezvous and docking, rover steering, and precision landing. The objectives of these missions are explained, and the generic constrained MPC problem formulations are summarized. Three key design elements used in MPC design: the prediction model, the constraints formulation and the objective cost function are discussed. The prediction models can be linear time invariant or time varying depending on the geometry of the orbit, whether it is circular or elliptic. The constraints can be given as linear inequalities for input or output constraints, which can be written in the same form. Moreover, the recent convexification techniques for the non-convex geometrical constraints (i.e., plume impingement, Field-of-View (FOV)) are presented in detail. Next, different objectives are provided in a mathematical framework and explained accordingly. Thirdly, because MPC implementation relies on finding in real-time the solution to constrained optimization problems, computational aspects are also examined. In particular, high-speed implementation capabilities and HIL challenges are presented towards representative space avionics. This covers an analysis of future space processors as well as the requirements of sensors and actuators on the HIL experiments outputs. The HIL tests are investigated for kinematic and dynamic tests where robotic arms and floating robots are used respectively. Eventually, the proposed algorithms and experimental setups are introduced and compared with the authors' previous work and future plans. The paper concludes with a conjecture that MPC paradigm is a promising framework at the crossroads of space applications while could be further advanced based on the challenges mentioned throughout the paper and the unaddressed gap.

Keywords: convex optimization, model predictive control, rendezvous and docking, spacecraft autonomy

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Authors: Sehrish Jalal, Choon-Mee Kim, Dong-Min Kim

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Background: Many pathogens causing hemorrhagic fevers of medical and veterinary importance have been identified and isolated from rodents in the Republic of Korea (ROK). Objective: We investigated the prevalence of emerging viruses causing hemorrhagic fevers, such as hemorrhagic fever with renal syndrome (HFRS), severe fever with thrombocytopenia syndrome (SFTS) and flaviviruses, from wild rodents. Methods: Striped field mice, Apodemus agrarius, (n=39) were captured during 2014-2015 in the south-west of ROK. Using molecular methods, lung samples were evaluated for SFTS virus, HFRS virus and flavivirus, and seropositivity was evaluated in the blood. Results: A high positive rate of Hantavirus (46.2%) was detected in A.agrarius lungs by reverse transcription-nested polymerase chain reaction (RT-N-PCR). The monthly prevalence of HFRS virus was 16.7% in October, 86.7% in November and 25% in August of the following year (p < 0.001). Moreover, 17.9% of blood samples were serologically positive for Hantavirus antibodies. The most prevalent strain in A. agrarius was Hantaan virus. All samples were positive for neither SFTS nor flavivirus. Conclusion: Hantan virus was detected in 86.7% of A. agrarius in November (autumn), and thus, virus shedding from A. agrarius can increase the risk of humans contracting HFRS. These findings may help to predict and prevent disease outbreaks in ROK.

Keywords: hemorrhagic fever virus, molecular diagnostic technique, rodents, Korea

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Authors: Moreblessings Shoko

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Polymersomes are materials which are considered as artificial counterparts of natural vesicles. The nanotechnology of such smart nanovesicles is very useful to enhance the efficiency of many therapeutic and diagnostic drugs. Those compounds show a higher stability, flexibility, and mechanical strength to the membrane compared to natural liposomes. Also, they can be designed in detail, the permeability of the membrane can be controlled by different stimuli, and the surface can be functionalized with different biological molecules to facilitate monitoring and target. For this purpose, this study demonstrates the formation of multifunctional and pH sensitive polymersomes and their functionalization with different reactive groups or biomolecules inside and outside of polymersomes´ membrane providing by crossing the membrane and docking/undocking processes for biomedical applications. Overall, they are highly versatile and thus present new opportunities for the design of targeted and selective recognition systems, for example, in mimicking cell functions and in synthetic biology.

Keywords: women, geomatics, challenges, capacity building

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Authors: Atena Sadat Hosseini, Mohammadhossein Habibi

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Acute myeloid leukemia (AML) is the most typically diagnosed leukemia. In older adults, AML imposes a dismal outcome. AML originates with a dominant mutation, then adds collaborative, transformative mutations leading to myeloid transformation and clinical/biological heterogeneity. Several chemotherapeutic drugs are used for this cancer. These drugs are naturally associated with several side effects, and finding a more accurate molecular mechanism of these drugs can have a significant impact on the selection and better candidate of drugs for treatment. In this study, we evaluated bortezomibin myeloma cells using bioinformatics analysis and evaluation of RNA-Seq data. Then investigated the molecular pathways proteins- proteins interactions associated with this chemotherapy drug. A total of 658upregulated genes and 548 downregulated genes were sorted.AUF1 (hnRNP D0) binds and destabilizes mRNA, degradation of GLI2 by the proteasome, the role of GTSE1 in G2/M progression after G2 checkpoint, TCF dependent signaling in response to WNT demonstrated in upregulated genes. Besides insulin resistance, AKT phosphorylates targets in the nucleus, cytosine methylation, Longevity regulating pathway, and Signal Transduction of S1P Receptor were related to low expression genes. With respect to this results, HIST2H2AA3, RP11-96O20.4, ZED9, PRDX1, and DOK2, according to node degrees and betweenness elements candidates from upregulated genes. in the opposite side, PYURF, NRSN1, FGF23, UPK3BL, and STAG3 were a prominent role in downregulated genes. Sum up, Using in silico analysis in the present study, we conducted a precise study ofbortezomib molecular mechanisms in myeloma cells. so that we could take further evaluation to discovermolecular cancer therapy. Naturally, more additional experimental and clinical procedures are needed in this survey.

Keywords: myeloma cells, acute myeloid leukemia, bioinformatics analysis, bortezomib

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Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

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This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

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Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua

Abstract:

Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.

Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune

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Authors: Dena Alhaloul

Abstract:

The Middle East and North Africa (MENA) region is characterized by diverse cultures, economies, and social structures. Fertility rates in MENA have seen significant changes over time, with variations among countries and subregions. Understanding fertility patterns in this region is essential due to its impact on demographic dynamics, healthcare, labor markets, and social policies. Rising or declining fertility rates have far-reaching consequences for the region's socioeconomic development. The main thrust of this study is to comprehensively examine fertility rates in the Middle East and North Africa (MENA) region. It aims to understand the distribution, determinants, and temporal trends of fertility rates in MENA countries. The study seeks to provide insights into the factors influencing fertility decisions, assess how fertility rates have evolved over time, and potentially develop statistical models to characterize these trends. As for the methodology of the study, the study uses descriptive statistics to summarize and visualize fertility rate data. It also uses regression analyses to identify determinants of fertility rates as well as statistical modeling to characterize temporal trends in fertility rates. The conclusion of this study The research will contribute to a deeper understanding of fertility dynamics in the MENA region, shedding light on the distribution of fertility rates, their determinants, and historical trends.

Keywords: fertility, distribution, modeling, regression

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Authors: Mudassar Iqbal, Riaz Hussain, Khalid Mehmood, Farah Ali, Fazal Mahmood, Abdul Ghaffar

Abstract:

Corynebacterium pseudotuberculosis is an important cause of caseous lymphadenitis (CL), a complex, chronic devastating and destructive disease of small ruminants. In present study, postmortem examination of Chinkara deer (n=25) was conducted in year 2014. Pus samples suggestive of CL were collected from the superficial lymph nodes, liver, spleen and lungs during necropsy and subjected to standard microbiological procedures for isolation and molecular analysis of bacterial pathogens. Pus samples collected from carcasses (25) presenting clinical lesions of C. pseudotuberculosis infection was identified in 19 (76%) carcasses on the basis of culture characteristics. The frequency of C. pseudotuberculosis bacterium was higher in older animals as compared to young animals. Grossly, multiple tubercles of variable size having caseous material were observed in liver, lungs, spleen and lymph nodes. Histopathologically, tissue sections from all the visceral organs were extensively plugged with abscess. In present study specific prolineiminopeptidase (PIP) gene of the C. pseudotuberculosis was amplified by the Polymerase chain reaction technique (PCR) in 17(25) cases. The efficient and reliable molecular analysis along with necropsy findings in present study can be used as valuable approach for diagnosis of caseous lymphadenitis in small ruminants.

Keywords: Chinkara deer, Corynebacterium pseudotuberculosis, Caseous lymphadenitis, PCR

Procedia PDF Downloads 475

Authors: Ritesh K. Shukla

Abstract:

Degradation of biological samples in terms of macromolecules (DNA, RNA, and protein) are the major challenges in the forensic investigation which misleads the result interpretation. Currently, there are no precise methods available to circumvent this problem. Therefore, at the preliminary level, some methods are urgently needed to solve this issue. In this order, Comet assay is one of the most versatile, rapid and sensitive molecular biology technique to assess the DNA degradation. This technique helps to assess DNA degradation even at very low amount of sample. Moreover, the expedient part of this method does not require any additional process of DNA extraction and isolation during DNA degradation assessment. Samples directly embedded on agarose pre-coated microscopic slide and electrophoresis perform on the same slide after lysis step. After electrophoresis microscopic slide stained by DNA binding dye and observed under fluorescent microscope equipped with Komet software. With the help of this technique extent of DNA degradation can be assessed which can help to screen the sample before DNA fingerprinting, whether it is appropriate for DNA analysis or not. This technique not only helps to assess degradation of DNA but many other challenges in forensic investigation such as time since deposition estimation of biological fluids, repair of genetic material from degraded biological sample and early time since death estimation could also be resolved. With the help of this study, an attempt was made to explore the application of well-known molecular biology technique that is Comet assay in the field of forensic science. This assay will open avenue in the field of forensic research and development.

Keywords: comet assay, DNA degradation, forensic, molecular biology

Procedia PDF Downloads 149

Authors: Christopher Deekia Nwimae, Nigel Simms, Liyun Lao

Abstract:

Erosion in pipe bends caused by particles is a major obstacle in the oil and gas fields and might cause the breakdown of production equipment. This work studied the effects imposed by flow velocity and impact of solid particles diameter in an elbow; erosion rate was verified with experimental data using the computational fluid dynamics (CFD) approach. Two-way coupled Euler-Lagrange and discrete phase model was employed to calculate the air/solid particle flow in an elbow. One erosion model and three-particle rebound models were used to predict the erosion rate on the 90° elbows. The generic erosion model was used in the CFD-based erosion model, and after comparing it with experimental data, results showed agreement with the CFD-based predictions as observed.

Keywords: erosion, prediction, elbow, computational fluid dynamics

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Authors: K. Jagannath, Akhilesh Kotian, S. S. Sharma, Achutha Kini U., P. R. Prabhu

Abstract:

Boiling process is characterized by the rapid formation of vapour bubbles at the solid–liquid interface (nucleate boiling) with pre-existing vapour or gas pockets. Computational fluid dynamics (CFD) is an important tool to study bubble dynamics. In the present study, CFD simulation has been carried out to determine the bubble detachment diameter and its terminal velocity. Volume of fluid method is used to model the bubble and the surrounding by solving single set of momentum equations and tracking the volume fraction of each of the fluids throughout the domain. In the simulation, bubble is generated by allowing water-vapour to enter a cylinder filled with liquid water through an inlet at the bottom. After the bubble is fully formed, the bubble detaches from the surface and rises up during which the bubble accelerates due to the net balance between buoyancy force and viscous drag. Finally when these forces exactly balance each other, it attains a constant terminal velocity. The bubble detachment diameter and the terminal velocity of the bubble are captured by the monitor function provided in FLUENT. The detachment diameter and the terminal velocity obtained is compared with the established results based on the shape of the bubble. A good agreement is obtained between the results obtained from simulation and the equations in comparison with the established results.

Keywords: bubble growth, computational fluid dynamics, detachment diameter, terminal velocity

Procedia PDF Downloads 379