Search results for: chromosome dynamics

Authors: T. J. Jamaleddine

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Purge columns or degasser vessels are widely used in the polyolefin process for removing trapped hydrocarbons and in-excess catalyst residues from the polymer particles. A uniform distribution of purged gases coupled with a plug-flow characteristic inside the column system is desirable to obtain optimum desorption characteristics of trapped hydrocarbon and catalyst residues. Computational Fluid Dynamics (CFD) approach is a promising tool for design optimization of these vessels. The success of this approach is profoundly dependent on the solution strategy and the choice of geometrical layout at the vessel outlet. Filling the column with solids and initially solving for the solids flow minimized numerical diffusion substantially. Adopting a cylindrical configuration at the vessel outlet resulted in less numerical instability and resembled the hydrodynamics flow of solids in the hopper segment reasonably well.

Keywords: CFD, degasser vessel, gas-solids flow, gas purging, purge column, species transport

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Authors: Divya Pande

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The dynamics of culture expresses itself in language. Even after India got independence in 1947 English subtly crept in the language of the masses with a silent and powerful flow towards the vernacular. The culture contact resulted in learning and emergence of a new language across the Hindi speaking belt of Northern and Central India. The hybrid words thus formed displaced the original word and got contextualized and absorbed in the language of the common masses. The research paper explores the interesting new vocabulary used extensively in the urban and rural districts of the state of Uttar- Pradesh which is the most populous state of India. The paper adopts a two way classification- formal and contextual for the analysis of the hybrid vocabulary of the linguistic items where one element is necessarily from the English language and the other from the Hindi. The new vocabulary represents languages of the wider world cutting across the geographical and the cultural barriers. The paper also broadly points out to the Hinglish commonly used in the state.

Keywords: assimilation, culture contact, Hinglish, hybrid words

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Authors: Mitchell J. Baum, Badin Gibbes, Greg Collecutt

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This study details a three-dimensional field-scale numerical investigation conducted for the Gold Coast Desalination Plant (GCDP) offshore multiport brine diffuser. Quantitative assessment of diffuser performance with regard to trajectory, dilution and mapping of seafloor concentration distributions was conducted for 100% plant operation. The quasi-steady Computational Fluid Dynamics (CFD) simulations were performed using the Reynolds averaged Navier-Stokes equations with a k-ω shear stress transport turbulence closure scheme. The study compliments a field investigation, which measured brine plume characteristics under similar conditions. CFD models used an iterative mesh in a domain with dimensions 400 m long, 200 m wide and an average depth of 24.2 m. Acoustic Doppler current profiler measurements conducted in the companion field study exhibited considerable variability over the water column. The effect of this vertical variability on simulated discharge outcomes was examined. Seafloor slope was also accommodated into the model. Ambient currents varied predominantly in the longshore direction – perpendicular to the diffuser structure. Under these conditions, the alternating port orientation of the GCDP diffuser resulted in simultaneous subjection to co-propagating and counter-propagating ambient regimes. Results from quiescent ambient simulations suggest broad agreement with empirical scaling arguments traditionally employed in design and regulatory assessments. Simulated dynamic ambient regimes showed the influence of ambient crossflow upon jet trajectory, dilution and seafloor concentration is significant. The effect of ambient flow structure and the subsequent influence on jet dynamics is discussed, along with the implications for using these different simulation approaches to inform regulatory decisions.

Keywords: computational fluid dynamics, desalination, field-scale simulation, multiport brine diffuser, negatively buoyant jet

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Authors: Saeed Khandan Siar, Stefan Tenbohlen, Christian Breuer, Raphael Lebreton

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The goal of this article is to investigate the detailed temperature distribution and the fluid flow of an oil cooled winding of a power transformer by means of computational fluid dynamics (CFD). The experimental setup consists of three passes of a zig-zag cooled disc type winding, in which losses are modeled by heating cartridges in each winding segment. A precise temperature sensor measures the temperature of each turn. The laboratory setup allows the exact control of the boundary conditions, e.g. the oil flow rate and the inlet temperature. Furthermore, a simulation model is solved using the open source computational fluid dynamics solver OpenFOAM and validated with the experimental results. The model utilizes the laminar and turbulent flow for the different mass flow rate of the oil. The good agreement of the simulation results with experimental measurements validates the model.

Keywords: CFD, conjugated heat transfer, power transformers, temperature distribution

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Authors: Yong Eun Yoon, Eric N. Johnson, Liling Ren

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Multirotor is one of the most popular types of small unmanned aircraft systems and has already been used in many areas including transport, military, surveillance, and leisure. Together with its popularity, the needs for proper flight control is growing because in most applications it is required to conduct its missions autonomously, which is in many aspects based on autonomous flight control. There have been many studies about the flight control for multirotor, but there is still room for enhancements in terms of performance and efficiency. This paper presents an autonomous flight control method for multirotor based on alternative input output linearization coupled with nested saturations. With alternative choice of the output of the multirotor flight control system, we can reduce computational cost regarding Lie algebra, and the linearized system can be stabilized with the introduction of nested saturations with real poles of our own design. Stabilization of internal dynamics is also based on the nested saturations and accompanies the determination of part of desired states. In particular, outer control loops involving state variables which originally are not included in the output of the flight control system is naturally rendered through this internal dynamics stabilization. We can also observe that desired tilting angles are determined by error dynamics from outer loops. Simulation results show that in any tracking situations multirotor stabilizes itself with small time constants, preceded by tuning process for control parameters with relatively low degree of complexity. Future study includes control of piecewise linear behavior of multirotor with actuator saturations, and the optimal determination of desired states while tracking multiple waypoints.

Keywords: automatic flight control, input output linearization, multirotor, nested saturations

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Authors: Arash Sadeghi, Taimaz Larimian

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This study explores the intricate interplay between community-based social capital (CBSC) and neighbourhood dynamics in enhancing resilience of Iranian SMEs, particularly under the strain of international sanctions. Utilising fuzzy-set Qualitative Comparative Analysis (fsQCA), we examine how different dimensions of CBSC—structural, relational, and cognitive—interact with neighbourhood socio-economic and built-environment characteristics to influence SME resilience. Findings reveal four configurations that contribute to the presence of resistance and five configurations associated with the adaptation outcome. Each configuration demonstrates a distinct combination of social capital elements, which vary according to the specific socio-economic and built-environmental characteristics of the neighbourhoods. The first configuration highlights the importance of structural social capital in deprived areas for building resistance, while the second emphasises the role of relational social capital in low-density, minimally deprived areas. Overall, cognitive social capital seems to be less effective in driving economic resilience compared to structural and relational types. This research contributes to the literature by providing a nuanced understanding of the synergistic effects of CBSC dimensions and neighbourhood characteristics on SME resilience. By adopting a configurational approach, we move beyond traditional methodologies, offering a comprehensive view of the complex dynamics of CBSC and neighbourhood characteristics and their impact on SME resilience in varying neighbourhoods.

Keywords: community-based social capital, fuzzy-set qualitative comparative analysis (fsQCA), place-based resilience, resistance

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Authors: Takele Bekele Bayu

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Though Ethiopia is an ancient country with ethnocultural and linguistic diversity, modern Ethiopia came into being in the second half of the 19th century under the military expansion of King Menelik II. Since then, the subsequent political system in the country failed to recognize and accommodate the country’s ethnolinguistic diversity. However, in 1991 the new government led by the Ethiopian People's Revolutionary Democratic Front (EPRDF) adopted federal-state structuring whereby constitutionally recognized and institutionally accommodated the country’s diversity. This investigation aimed to analyze drivers of ethnic conflict and its dynamism along the Eastern shared border of the Somali and Oromia regional administrations within the federal framework. The paper employed a comparative research design, adopted mixed research methods, and used survey questionnaires and focus group discussions (FGDs) for data collection. The study found that the Somali-Oromo conflict is complex and the dynamics and the sources of conflict in the study areas are similar.

Keywords: Ethiopia, Oromo, Somali, ethnic conflict, federalism

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Authors: Etsuo Morishita

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In this paper, we show shallow water in a tin box as an analogous simulation tool for high-speed aerodynamics education and research. It is customary that we use a water tank to create shallow water flow. While a flow in a water tank is not necessarily uniform and is sometimes wavy, we can visualize a clear supercritical flow even when we move a body manually in stationary water in a simple shallow tin box. We can visualize a blunt shock wave around a moving circular cylinder together with a shock pattern around a diamond airfoil. Another interesting analogous experiment is a hydrodynamic shock tube with water and tea. We observe the contact surface clearly due to color difference of the two liquids those are invisible in the real gas dynamics experiment. We first revisit the similarities between high-speed aerodynamics and shallow water hydraulics. Several educational and research experiments are then introduced for engineering students. Shallow water experiments in a tin box simulate properly the high-speed flows.

Keywords: aerodynamics compressible flow, gas dynamics, hydraulics, shock wave

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Authors: Vasileios Floros

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This article delves into the intricate interplay between leadership styles and teacher satisfaction within the Greek educational framework, underscoring the pivotal role of school leadership in shaping educational success and fostering a conducive school culture. Through a comprehensive analysis, the study explores various leadership theories, the psychological contract between teachers and leaders, and the impact of leadership on teacher job satisfaction and group dynamics within educational institutions. It highlights how leadership efficacy can significantly influence the organizational climate, teacher motivation, and, ultimately, educational outcomes. The findings suggest that effective leadership, characterized by a deep understanding of teacher psychology, thoughtful engagement with the school culture, and strategic application of leadership styles, can lead to heightened teacher satisfaction and enhanced educational performance. This research offers valuable insights for educational policymakers, school leaders, and the broader academic community interested in optimizing leadership practices to foster an enriching educational environment in Greece.

Keywords: educational leadership, teacher satisfaction, school culture, leadership styles, Greek education

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Authors: Rosario Rivera Rubite, Ching-I Peng, Che-Wei Lin, Mark Hughes, Yoshiko Kono, Kuo-Fang Chung

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The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.

Keywords: conservation, endemic , herbarium , limestone, phylogenetics, taxonomy

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Authors: Alexander Blokhin, Ekaterina Kruglova, Boris Semisalov

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Mathematical model based on the mesoscopic theory of polymer dynamics is developed for numerical simulation of the flows of polymeric liquid between two coaxial cylinders. This model is a system of nonlinear partial differential equations written in the cylindrical coordinate system and coupled with the heat conduction equation including a specific dissipation term. The stationary flows similar to classical Poiseuille ones are considered, and the resolving equations for the velocity of flow and for the temperature are obtained. For solving them, a fast pseudospectral method is designed based on Chebyshev approximations, that enables one to simulate the flows through the channels with extremely small relative values of the radius of inner cylinder. The numerical analysis of the dependance of flow on this radius and on the values of dissipation constant is done.

Keywords: dynamics of polymeric liquid, heat dissipation, singularly perturbed problem, pseudospectral method, Chebyshev polynomials, stabilization technique

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Authors: Weikang Gong, Chunhua Li

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Dynamics plays an essential role in function exertion of proteins. Elastic network model (ENM), a harmonic potential-based and cost-effective computational method, is a valuable and efficient tool for characterizing the intrinsic dynamical properties encoded in biomacromolecule structures and has been widely used to detect the large-amplitude collective motions of proteins. Gaussian network model (GNM) and anisotropic network model (ANM) are the two often-used ENM models. In recent years, many ENM variants have been proposed. Here, we propose a small but effective modification (denoted as modified mENM) to the multiscale ENM (mENM) where fitting weights of Kirchhoff/Hessian matrixes with the least square method (LSM) is modified since it neglects the details of pairwise interactions. Then we perform its comparisons with the original mENM, traditional ENM, and parameter-free ENM (pfENM) on reproducing dynamical properties for the six representative proteins whose molecular dynamics (MD) trajectories are available in http://mmb.pcb.ub.es/MoDEL/. In the results, for B-factor prediction, mENM achieves the best performance among the four ENM models. Additionally, it is noted that with the weights of the multiscale Kirchhoff/Hessian matrixes modified, interestingly, the modified mGNM/mANM still has a much better performance than the corresponding traditional ENM and pfENM models. As to dynamical cross-correlation map (DCCM) calculation, taking the data obtained from MD trajectories as the standard, mENM performs the worst while the results produced by the modified mENM and pfENM models are close to those from MD trajectories with the latter a little better than the former. Generally, ANMs perform better than the corresponding GNMs except for the mENM. Thus, pfANM and the modified mANM, especially the former, have an excellent performance in dynamical cross-correlation calculation. Compared with GNMs (except for mGNM), the corresponding ANMs can capture quite a number of positive correlations for the residue pairs nearly largest distances apart, which is maybe due to the anisotropy consideration in ANMs. Furtherly, encouragingly the modified mANM displays the best performance in capturing the functional motional modes, followed by pfANM and traditional ANM models, while mANM fails in all the cases. This suggests that the consideration of long-range interactions is critical for ANM models to produce protein functional motions. Based on the analyses, the modified mENM is a promising method in capturing multiple dynamical characteristics encoded in protein structures. This work is helpful for strengthening the understanding of the elastic network model and provides a valuable guide for researchers to utilize the model to explore protein dynamics.

Keywords: elastic network model, ENM, multiscale ENM, molecular dynamics, parameter-free ENM, protein structure

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Authors: Said Belaaouad

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This study aimed to explore the quantitative structure-activity relationship (QSAR) of 1,2,4-Triazine-3(2H)-one derivative as a potential anticancer agent against breast cancer. The electronic descriptors were obtained using the Density Functional Theory (DFT) method, and a multiple linear regression techniques was employed to construct the QSAR model. The model exhibited favorable statistical parameters, including R2=0.849, R2adj=0.656, MSE=0.056, R2test=0.710, and Q2cv=0.542, indicating its reliability. Among the descriptors analyzed, absolute electronegativity (χ), total energy (TE), number of hydrogen bond donors (NHD), water solubility (LogS), and shape coefficient (I) were identified as influential factors. Furthermore, leveraging the validated QSAR model, new derivatives of 1,2,4-Triazine-3(2H)-one were designed, and their activity and pharmacokinetic properties were estimated. Subsequently, molecular docking (MD) and molecular dynamics (MD) simulations were employed to assess the binding affinity of the designed molecules. The Tubulin colchicine binding site, which plays a crucial role in cancer treatment, was chosen as the target protein. Through the simulation trajectory spanning 100 ns, the binding affinity was calculated using the MMPBSA script. As a result, fourteen novel Tubulin-colchicine inhibitors with promising pharmacokinetic characteristics were identified. Overall, this study provides valuable insights into the QSAR of 1,2,4-Triazine-3(2H)-one derivative as potential anticancer agent, along with the design of new compounds and their assessment through molecular docking and dynamics simulations targeting the Tubulin-colchicine binding site.

Keywords: QSAR, molecular docking, ADMET, 1, 2, 4-triazin-3(2H)-ones, breast cancer, anticancer, molecular dynamic simulations, MMPBSA calculation

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Authors: Phanindra Prasad Thummala, Umran Tezcan Un

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In this study, hydrodynamics analysis of two batch type electrocoagulation stirred tank reactors, used for the electrocoagulation treatment of Cr(VI) wastewater, was carried using computational fluid dynamics (CFD). The aim of the study was to evaluate the impact of mixing characteristics on overall performance of electrocoagulation reactor. The CFD simulations were performed using ANSYS FLUENT 14.4 software. The mixing performance of each reactor was evaluated by numerically modelling tracer dispersion in each reactor configuration. The uniformity in tracer dispersion was assumed when 90% of the ratio of the maximum to minimum concentration of the tracer was realized. In parallel, experimental evaluation of both the electrocoagulation reactors for removal of Cr(VI) from wastewater was also carried out. The results of CFD and experimental analysis clearly show that the reactor which can give higher uniformity in lesser time, will perform better as an electrocoagulation reactor for removal of Cr(VI) from wastewater.

Keywords: CFD, stirred tank reactors, electrocoagulation, Cr(VI) wastewater

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Authors: Hosein Falahaty, Hitoshi Gotoh, Abbas Khayyer

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Performance of a Hamiltonian based particle method in simulation of nonlinear structural dynamics is subjected to investigation in terms of stability and accuracy. The governing equation of motion is derived based on Hamilton's principle of least action, while the deformation gradient is obtained according to Weighted Least Square method. The hyper-elasticity models of Saint Venant-Kirchhoff and a compressible version similar to Mooney- Rivlin are engaged for the calculation of second Piola-Kirchhoff stress tensor, respectively. Stability along with accuracy of numerical model is verified by reproducing critical stress fields in static and dynamic responses. As the results, although performance of Hamiltonian based model is evaluated as being acceptable in dealing with intense extensional stress fields, however kinds of instabilities reveal in the case of violent collision which can be most likely attributed to zero energy singular modes.

Keywords: Hamilton's principle of least action, particle-based method, hyper-elasticity, analysis of stability

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Authors: Jatin Gupta, Bishakh Bhattacharya

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With the aging process, many people start suffering from the problem of weak limbs resulting in mobility disorders and loss of sensory and motor function of limbs. Wearable robotic devices are viable solutions to help people suffering from these issues by augmenting their strength. These robotic devices, popularly known as exoskeletons aides user by providing external power and controlling the dynamics so as to achieve desired motion. Present work studies a simplified dynamic model of the human gait. A four link open chain kinematic model is developed to describe the dynamics of Single Support Phase (SSP) of the human gait cycle. The dynamic model is developed integrating mathematical models of the motion of inverted and triple pendulums. Stance leg is modeled as inverted pendulum having single degree of freedom and swing leg as triple pendulum having three degrees of freedom viz. thigh, knee, and ankle joints. The kinematic model is formulated using forward kinematics approach. Lagrangian approach is used to formulate governing dynamic equation of the model. For a system of nonlinear differential equations, numerical method is employed to obtain system response. Reference trajectory is generated using human body simulator, LifeMOD. For optimal mechanical design and controller design of exoskeleton system, it is imperative to study parameter sensitivity of the system. Six different parameters viz. thigh, shank, and foot masses and lengths are varied from 85% to 115% of the original value for the present work. It is observed that hip joint of swing leg is the most sensitive and ankle joint of swing leg is the least sensitive one. Changing link lengths causes more deviation in system response than link masses. Also, shank length and thigh mass are most sensitive parameters. Finally, the present study gives an insight on different factors that should be considered while designing a lower extremity exoskeleton.

Keywords: lower limb exoskeleton, multibody dynamics, energy based formulation, optimal design

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Authors: Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi

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In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. In this paper, we aim to apply a particle-based method, Smoothed Dissipative Particle Dynamics (SDPD), to simulate the motion and deformation of RBCs in complex micro-tubes. We first present the theoretical models, including SDPD model, RBC-fluid interaction model, RBC deformation model, RBC aggregation model, and boundary treatment model. After that, we show the verification and validation of these models, by comparing our numerical results with the theoretical, experimental and previously-published numerical results. Finally, we provide some simulation cases, such as the motion and deformation of RBCs in rectangular, cylinder, curved, bifurcated, and constricted micro-tubes, respectively.

Keywords: aggregation, deformation, red blood cell, smoothed dissipative particle dynamics

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Authors: Patel Kailash P, Patel Parimal M

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The effect of coal fly ash treatment on the chromosomes of Raphanus sativus L. was investigated. The seeds of Raphanus sativusL. were placed in petri dishes in three replicates and allowed to germinate for five days in different concentration of coal fly ash solution. The root was treated with the diluted, semidiluted, and concentrated solution of fly ash while the control group had distilled water.The total aberration were examined. The mitotic index was calculated and the results were statically evaluated by the analysis of variance 5% significant level. The mitotic index decreased as the concentration increased. The highest mitotic index value was diluted fly ash solution while the least was concentrated fly ash treatment. The results show the most frequent chromosomal abnormalities observed included: chromatid bridge, c-mitosis, and stickiness. Concentrated fly ash solution is much more genotoxic than semidiluted fly ash solution, as it induced more aberrations having percentage abnormalities for the highest concentration tested. Increased fly ash pollution can lead to some irreversible cytogenetic effect in plants. The study is an attempt to corroborate the toxic effect of coal fly ash of thermal power plant on the chromosome of plants. These results will be useful in environmental monitoring of the cytotoxicity of coal fly ash.

Keywords: coal fly-ash, genotoxic, cytogenetic, mitotic index, Raphanus sativus L.

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Authors: Yosra Mefteh Rekik

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A computational agent-based model of financial markets stresses interactions and dynamics among a very diverse set of traders. The growing body of research in this area relies heavily on computational tools which by-pass the restrictions of an analytical method. The main goal of this research is to understand how the stock market operates and behaves how to invest in the stock market and to study traders’ behavior within the context of the artificial stock markets populated by heterogeneous agents. All agents are characterized by adaptive learning behavior represented by the Artificial Neuron Networks. By using agent-based simulations on artificial market, we show that the existence of heterogeneous agents can explain the price dynamics in the financial market. We investigate the relation between market diversity and market efficiency. Our empirical findings demonstrate that greater market heterogeneity play key roles in market efficiency.

Keywords: agent-based modeling, artificial stock market, heterogeneous expectations, financial stylized facts, computational finance

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Authors: Alexandros Lioulemes, Michail Theofanidis, Varun Kanal, Konstantinos Tsiakas, Maher Abujelala, Chris Collander, William B. Townsend, Angie Boisselle, Fillia Makedon

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This paper presents a home-based robot-rehabilitation instrument, called ”MAGNI Dynamics”, that utilized a vision-based kinematic/dynamic module and an adaptive haptic feedback controller. The system is expected to provide personalized rehabilitation by adjusting its resistive and supportive behavior according to a fuzzy intelligence controller that acts as an inference system, which correlates the user’s performance to different stiffness factors. The vision module uses the Kinect’s skeletal tracking to monitor the user’s effort in an unobtrusive and safe way, by estimating the torque that affects the user’s arm. The system’s torque estimations are justified by capturing electromyographic data from primitive hand motions (Shoulder Abduction and Shoulder Forward Flexion). Moreover, we present and analyze how the Barrett WAM generates a force-field with a haptic controller to support or challenge the users. Experiments show that by shifting the proportional value, that corresponds to different stiffness factors of the haptic path, can potentially help the user to improve his/her motor skills. Finally, potential areas for future research are discussed, that address how a rehabilitation robotic framework may include multisensing data, to improve the user’s recovery process.

Keywords: human-robot interaction, kinect, kinematics, dynamics, haptic control, rehabilitation robotics, artificial intelligence

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Authors: Shaban Aly, Ali Al-Qahtani, Houari B. Khenous

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Synchronization is an important phenomenon commonly observed in nature. A system of periodically forced complex Duffings oscillators was introduced and shown to display chaotic behavior and possess strange attractors. Such complex oscillators appear in many problems of physics and engineering, as, for example, nonlinear optics, deep-water wave theory, plasma physics and bimolecular dynamics. In this paper, we study the remarkable phenomenon of chaotic synchronization on these oscillator systems, using impulsive synchronization techniques. We derive analytical expressions for impulsive control functions and show that the dynamics of error evolution is globally stable, by constructing appropriate Lyapunov functions. This means that, for a relatively large set initial conditions, the differences between the drive and response systems vanish exponentially and synchronization is achieved. Numerical results are obtained to test the validity of the analytical expressions and illustrate the efficiency of these techniques for inducing chaos synchronization in our nonlinear oscillators.

Keywords: complex nonlinear oscillators, impulsive synchronization, chaotic systems, global exponential synchronization

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Authors: Rong Li, Brian D. Wirth, Bing Liu

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Graphite is the matrix, and structural material in the high temperature gas-cooled reactor exhibits an irradiation response. It is of significant importance to analyze the defect production and evaluate the role of graphite under irradiation. A vast experimental literature exists for graphite on the dimensional change, mechanical properties, and thermal behavior. However, simulations have not been applied to the atomistic perspective. Remarkably few molecular dynamics simulations have been performed to study the irradiation response in graphite. In this paper, irradiation-induced damage cascades in graphite were investigated with molecular dynamics simulation. Statistical results of the graphite defects were obtained by sampling a wide energy range (1–30 KeV) and 10 different runs for every cascade simulation with different random number generator seeds to the velocity scaling thermostat function. The chemical bonding in carbon was described using the adaptive intermolecular reactive empirical bond-order potential (AIREBO) potential coupled with the standard Ziegler–Biersack–Littmack (ZBL) potential to describe close-range pair interactions. This study focused on analyzing the number of defects, the final cascade morphology and the distribution of defect clusters in space, the length-scale cascade properties such as the cascade length and the range of primary knock-on atom (PKA), and graphite mechanical properties’ variation. It can be concluded that the number of surviving Frenkel pairs increased remarkably with the increasing initial PKA energy but did not exhibit a thermal spike at slightly lower energies in this paper. The PKA range and cascade length approximately linearly with energy which indicated that increasing the PKA initial energy will come at expensive computation cost such as 30KeV in this study. The cascade morphology and the distribution of defect clusters in space mainly related to the PKA energy meanwhile the temperature effect was relatively negligible. The simulations are in agreement with known experimental results and the Kinchin-Pease model, which can help to understand the graphite damage cascades and lifetime span under irradiation and provide a direction to the designs of these kinds of structural materials in the future reactors.

Keywords: graphite damage cascade, molecular dynamics, cascade morphology, cascade distribution

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Authors: Olukunle C. Olawole, Dilip K. De, Moses Emetere, Omoje Maxwell

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Graphene can stand very high temperature up to 4500 K in vacuum and has potential for application in thermionic energy converter. In this paper, we discuss the application of energy dynamics principles and the modified Richardson-Dushman Equation, to estimate the efficiency of solar power conversion to electrical power by a solar thermionic energy converter (STEC) containing emitter made of graphene. We present detailed simulation of power output for different solar insolation, diameter of parabolic concentrator, area of the graphene emitter (same as that of the collector), temperature of the collector, physical dimensions of the emitter-collector etc. After discussing possible methods of reduction or elimination of space charge problem using magnetic field and gate, we finally discuss relative advantages of using emitters made of graphene, carbon nanotube and metals respectively in a STEC.

Keywords: graphene, high temperature, modified Richardson-Dushman equation, solar thermionic energy converter

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Authors: S. M. Azad, H. Ghodsi Pour, F. Roshannafasa

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In recent years ‘technology management and policymaking’ is one of the most important problems in management science. In this field, different generations of innovation and technology management are presented which the earliest one is Innovation System (IS) approach. In a general classification, innovation systems are divided in to 4 approaches: Technical, sectoral, regional, and national. There are many researches in relation to each of these approaches in different academic fields. Every approach has some benefits. If two or more approaches hybrid, their benefits would be combined. In addition, according to the sectoral structure of the governance model in Iran, in many sectors such as information technology, the combination of three other approaches with sectoral approach is essential. Hence, in this paper, combining two IS approaches (technical and sectoral) and using system dynamics, a generic model is presented for a sample of software industry. As a complimentary point, this article is introducing a new hybrid approach called Techno-Sectoral Innovation System. This TSIS model is accomplished by Changing concepts of the ‘functions’ which came from Technological IS literature and using them into sectoral system as measurable indicators.

Keywords: innovation system, technology, techno-sectoral system, functional indicators, system dynamics

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Authors: Y. Ruchi, A. Prerna, S. Deepshikha

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Amyotrophic lateral sclerosis (ALS), also known as “Lou Gehrig’s disease”. It is a neurodegenerative disease associated with degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord characterized by distal muscle weakness, atrophy, normal sensation, pyramidal signs and progressive muscular paralysis reflecting. ALS2 is a juvenile autosomal recessive disorder, slowly progressive, that maps to chromosome 2q33 and is associated with mutations in the alsin gene, a putative GTPase regulator. In this paper we have done homology modeling of alsin2 protein using multiple templates (3KCI_A, 4LIM_A, 402W_A, 4D9S_A, and 4DNV_A) designed using the Prime program in Schrödinger software. Further modeled structure is used to identify effective binding sites on the basis of structural and physical properties using sitemap program in Schrödinger software, structural and function analysis is done by using Prosite and ExPASy server that gives insight into conserved domains and motifs that can be used for protein classification. This paper summarizes the structural, functional and binding site property of alsin2 protein. These binding sites can be potential drug target sites and can be used for docking studies.

Keywords: ALS, binding site, homology modeling, neuronal degeneration

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Authors: Nermin Gozukirmizi, Buket Cakmak, Sevgi Marakli

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Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant and has been studied as a model plant regarding its short annual life cycle and seven chromosome pairs. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE1 retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0-64% among embryos, roots and leaves. Polymorphism rates were detected to be 0-27% among embryos, 8-60% among roots, and 11-50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23-64%). The internal domains of SIRE1 (gag, env and rt) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for gag, however, different band patterns were observed among samples for rt and env. The sequencing of SIRE1 gag, env and rt domains revealed 79% similarity for gag, 95% for env and 84% for rt to Ty1-copia retrotransposons. SIRE1 retrotransposon was identified in the soybean genome and has been studied on other plants (maize, rice, tomatoe etc.). This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.

Keywords: barley, polymorphism, retrotransposon, SIRE1 virus

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Authors: Habib Onsori, Somayeh Akrami, Mohammad Rahmati

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Deafness is the most common sensory disorder with the frequency of 1/1000 in many populations. Mutations in the GJB2 (CX26) gene at the DFNB1 locus on chromosome 13q12 are associated with congenital hearing loss. Approximately 80% of congenital hearing loss cases are recessively inherited and 15% dominantly inherited. Mutations of the GJB2 gene, encoding gap junction protein Connexin 26 (Cx26), are the most common cause of hereditary congenital hearing loss in many countries. This report presents two cases of different mutations from Iranian patients with bilateral hearing loss. DNA studies were performed for the GJB2 gene by PCR and sequencing methods. In one of them, direct sequencing of the gene showed a heterozygous T→C transition at nucleotide 604 resulting in a cysteine to arginine amino acid substitution at codon 202 (C202R) in the fourth extracellular domain (TM4) of the protein. The analyses indicate that the C202R mutation appeared de novo in the proband with a possible dominant effect (GenBank: KF 638275). In the other one, DNA sequencing revealed a compound heterozygous mutation (35delG, 363delC) in the Cx26 gene that is strongly associated with congenital non-syndromic hearing loss (NSHL). So screening the mutations for hearing loss individuals referring to genetics counseling centers before marriage and or pregnancy is recommended.

Keywords: CX26, deafness, GJB2, mutation

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Authors: Tomoaki Hashimoto

Abstract:

Recent technological advance has prompted significant interest in developing the control theory of quantum systems. Following the increasing interest in the control of quantum dynamics, this paper examines the control problem of Schrödinger equation because quantum dynamics is basically governed by Schrödinger equation. From the practical point of view, stochastic disturbances cannot be avoided in the implementation of control method for quantum systems. Thus, we consider here the robust stabilization problem of Schrödinger equation against stochastic disturbances. In this paper, we adopt model predictive control method in which control performance over a finite future is optimized with a performance index that has a moving initial and terminal time. The objective of this study is to derive the stability criterion for model predictive control of Schrödinger equation under stochastic disturbances.

Keywords: optimal control, stochastic systems, quantum systems, stabilization

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Authors: Wael M. Elawady, Mohamed F. Asar, Amany M. Sarhan

Abstract:

This paper adopts a continuous sliding mode control scheme for trajectory tracking control of robot manipulators with structured and unstructured uncertain dynamics and external disturbances. In this algorithm, the equivalent control in the conventional sliding mode control is replaced by a PID control action. Moreover, the discontinuous switching control signal is replaced by a continuous proportional-integral (PI) control term such that the implementation of the proposed control algorithm does not require the prior knowledge of the bounds of unknown uncertainties and external disturbances and completely eliminates the chattering phenomenon of the conventional sliding mode control approach. The closed-loop system with the adopted control algorithm has been proved to be globally stable by using Lyapunov stability theory. Numerical simulations using the dynamical model of robot manipulators with modeling uncertainties demonstrate the superiority and effectiveness of the proposed approach in high speed trajectory tracking problems.

Keywords: PID, robot, sliding mode control, uncertainties

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Authors: Turky Al-Qahtani, Roustem Miftahof

Abstract:

Introduction: Under common assumptions of excitabi-lity, morphological (cellular) homogeneity, and spatial structural anomalies added as required, it has been shown that biological systems are able to display travelling wave dynamics. Being not self-sustainable, existence depends on the electrophysiological state of transmembrane ion channels and it requires an extrinsic/intrinsic periodic source. However, organs in the body are highly multicellular, heterogeneous, and their functionality is the outcome of electro-mechanical conjugation, rather than excitability only. Thus, peristalsis in the gut relies on spatiotemporal myoelectrical pattern formations between the mechanical, represented by smooth muscle cells (SM), and the control, comprised of a chain of primary sensory and motor neurones, components. Synaptically linked through the afferent and efferent pathways, they form a functional unit (FU) of the gut. Aims: These are: i) to study numerically the complex dynamics, and ii) to investigate the possibility of self-sustained myoelectrical activity in the FU. Methods: The FU recreates the following sequence of physiological events: deformation of mechanoreceptors of located in SM; generation and propagation of electrical waves of depolarisation - spikes - along the axon to the soma of the primary neurone; discharge of the primary neurone and spike propagation towards the motor neurone; burst of the motor neurone and transduction of spikes to SM, subsequently producing forces of contraction. These are governed by a system of nonlinear partial and ordinary differential equations being a modified version of the Hodgkin-Huxley model and SM fibre mechanics. In numerical experiments; the source of excitation is mechanical stretches of SM at a fixed amplitude and variable frequencies. Results: Low frequency (0.5 < v < 2 Hz) stimuli cause the propagation of spikes in the neuronal chain and, finally, the generation of active forces by SM. However, induced contractions are not sufficient to initiate travelling wave dynamics in the control system. At frequencies, 2 < v < 4 Hz, multiple low amplitude and short-lasting contractions are observed in SM after the termination of stretching. For frequencies (0.5 < v < 4 Hz), primary and sensory neurones demonstrate strong connectivity and coherent electrical activity. Significant qualitative and quantitative changes in dynamics of myoelectical patterns with a transition to a self-organised mode are recorded with the high degree of stretches at v = 4.5 Hz. Increased rates of deformation lead to the production of high amplitude signals at the mechanoreceptors with subsequent self-sustained excitation within the neuronal chain. Remarkably, the connection between neurones weakens resulting in incoherent firing. Further increase in a frequency of stimulation (v > 4.5 Hz) has a detrimental effect on the system. The mechanical and control systems become disconnected and exhibit uncoordinated electromechanical activity. Conclusion: To our knowledge, the existence of periodic activity in a multicellular, functionally heterogeneous biological system with mechano-electrical dynamics, such as the FU, has been demonstrated for the first time. These findings support the notion of possible peristalsis in the gut even in the absence of intrinsic sources - pacemaker cells. Results could be implicated in the pathogenesis of intestinal dysrythmia, a medical condition associated with motor dysfunction.

Keywords: complex dynamics, functional unit, the gut, dysrythmia

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