Search results for: structural equation modeling.

Authors: Chun-Ta Chen, Te-Tan Liao, Hoang-Vuong Pham

Abstract:

In this paper motion analysis on a winding stair-climbing is investigated using our proposed rotational arm type of robotic wheelchair. For now, the robotic wheelchair is operated in an open mode to climb winding stairs by a dynamic turning, therefore, the dynamics model is required to ensure a passenger-s safety. Equations of motion based on the skid-steering analysis are developed for the trajectory planning and motion analysis on climbing winding stairs. Since the robotic wheelchair must climb a winding staircase stably, the winding trajectory becomes a constraint equation to be followed, and the Baumgarte-s method is used to solve for the constrained dynamics equations. Experimental results validate the behavior of the prototype as it climbs a winding stair.

Keywords: Climb, robotic wheelchair, skid-steering, windingstair .

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Authors: Xu Guoliang, Tan Qingping

Abstract:

Color printing proceeds with multiple halftone separations overlay. Because of separation overlay misalignment in printing, the percentage of different primary color combination may vary and it will result in color shift. In traditional printing procedure with AM halftone, every separation has different screening angle to make the superposition pattern in a random style, which will reduce the color shift. To evaluate the color shift of printing with hybrid halftoning, we simulate printing procedure with halftone images overlay and calculate the color difference between expected color and color in different overlay misalignment configurations. The color difference for hybrid halftone and AM halftone is very close. So the color shift for hybrid halftone is acceptable with current color printing procedure.

Keywords: color printing, AM halftone, Hybrid halftone, misalignment, color shift, Neugebauer Color Equation

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Authors: S.A.M. Yatim, Z.B. Ibrahim, K.I. Othman, F. Ismail

Abstract:

The implicit block methods based on the backward differentiation formulae (BDF) for the solution of stiff initial value problems (IVPs) using variable step size is derived. We construct a variable step size block methods which will store all the coefficients of the method with a simplified strategy in controlling the step size with the intention of optimizing the performance in terms of precision and computation time. The strategy involves constant, halving or increasing the step size by 1.9 times the previous step size. Decision of changing the step size is determined by the local truncation error (LTE). Numerical results are provided to support the enhancement of method applied.

Keywords: Backward differentiation formulae, block backwarddifferentiation formulae, stiff ordinary differential equation, variablestep size.

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Authors: Smarajit Ghosh , Karma Sonam Sherpa

Abstract:

This paper reports a new and accurate method for load-flow solution of radial distribution networks with minimum data preparation. The node and branch numbering need not to be sequential like other available methods. The proposed method does not need sending-node, receiving-node and branch numbers if these are sequential. The proposed method uses the simple equation to compute the voltage magnitude and has the capability to handle composite load modelling. The proposed method uses the set of nodes of feeder, lateral(s) and sub lateral(s). The effectiveness of the proposed method is compared with other methods using two examples. The detailed load-flow results for different kind of load-modellings are also presented.

Keywords: Load−flow, Feeder, Lateral, Power, Voltage, Composite, Exponential

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Authors: A. A. Akande, B. P. Dhonge, B. W. Mwakikunga, A. G. J. Machatine

Abstract:

This article presents gate-voltage controlled humidity sensing performance of vanadium dioxide nanoparticles prepared from NH₄VO₃ precursor using microwave irradiation technique. The X-ray diffraction, transmission electron diffraction, and Raman analyses reveal the formation of VO₂ (B) with V₂O₅ and an amorphous phase. The BET surface area is found to be 67.67 m²/g. The humidity sensing measurements using the patented lateral-gate MOSFET configuration was carried out. The results show the optimum response at 5 V up to 8 V of gate voltages for 10 to 80% of relative humidity. The dose-response equation reveals the enhanced resilience of the gated VO₂ sensor which may saturate above 272% humidity. The response and recovery times are remarkably much faster (about 60 s) than in non-gated VO₂ sensors which normally show response and recovery times of the order of 5 minutes (300 s).

Keywords: VO2, VO2 (B), V2O5, MOSFET, gate voltage, humidity sensor.

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Authors: Buntheng Chhorn, WooYoung Jung

Abstract:

Large-scale swing has been used in entertainment and performance, especially in circus, for a very long time. To increase the safety of this type of structure, a thorough analysis for displacement and bearing stress was performed for an extreme condition where a full cycle swing occurs. Different masses, ranging from 40 kg to 220 kg, and velocities were applied on the swing. Then, based on the solution of differential dynamics equation, swing velocity response to harmonic force was obtained. Moreover, the resistance capacity was estimated based on ACI steel structure design guide. Subsequently, numerical analysis was performed in ABAQUS to obtain the stress on each frame of the swing. Finally, the analysis shows that the expansion of swing structure frame section was required for mass bigger than 150kg.

Keywords: Swing structure, displacement, bearing stress, dynamic loads response, finite element analysis.

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Authors: C. Patrascioiu, V. Matei, N. Nicolae

Abstract:

The paper describes the experiments and the kinetic parameters calculus of the gasoil hydrofining. They are presented experimental results of gasoil hidrofining using Mo and promoted with Ni on aluminum support catalyst. The authors have adapted a kinetic model gasoil hydrofining. Using this proposed kinetic model and the experimental data they have calculated the parameters of the model. The numerical calculus is based on minimizing the difference between the experimental sulf concentration and kinetic model estimation.

Keywords: Hydrofining, kinetic, modeling, optimization.

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Authors: Pan Cheng, Jin Huang, Guang Zeng

Abstract:

Elastic boundary eigensolution problems are converted into boundary integral equations by potential theory. The kernels of the boundary integral equations have both the logarithmic and Hilbert singularity simultaneously. We present the mechanical quadrature methods for solving eigensolutions of the boundary integral equations by dealing with two kinds of singularities at the same time. The methods possess high accuracy O(h3) and low computing complexity. The convergence and stability are proved based on Anselone-s collective compact theory. Bases on the asymptotic error expansion with odd powers, we can greatly improve the accuracy of the approximation, and also derive a posteriori error estimate which can be used for constructing self-adaptive algorithms. The efficiency of the algorithms are illustrated by numerical examples.

Keywords: boundary integral equation, extrapolation algorithm, aposteriori error estimate, elasticity.

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Authors: Aqsa Jamil, Hiroshi Tamura, Hiroshi Katsuchi, Jiaqi Wang

Abstract:

Yield point represents the upper limit of forces which can be applied on a specimen without causing any permanent deformation. After yielding, the behavior of specimen suddenly changes including the possibility of cracking or buckling. So, the accumulation of damage or type of fracture changes depending on this condition. As it is difficult to accurately detect yield points of the several stress concentration points in structural steel specimens, an effort has been made in this research work to develop a convenient technique using thermography (temperature-based detection) during tensile tests for the precise detection of yield point initiation. To verify the applicability of thermography camera, tests were conducted under different loading conditions and measuring the deformation by installing various strain gauges and monitoring the surface temperature with the help of thermography camera. The yield point of specimens was estimated by the help of temperature dip which occurs due to the thermoelastic effect during the plastic deformation. The scattering of the data has been checked by performing repeatability analysis. The effect of temperature imperfection and light source has been checked by carrying out the tests at daytime as well as midnight and by calculating the signal to noise ratio (SNR) of the noised data from the infrared thermography camera, it can be concluded that the camera is independent of testing time and the presence of a visible light source. Furthermore, a fully coupled thermal-stress analysis has been performed by using Abaqus/Standard exact implementation technique to validate the temperature profiles obtained from the thermography camera and to check the feasibility of numerical simulation for the prediction of results extracted with the help of thermographic technique.

Keywords: Signal to noise ratio, thermoelastic effect, thermography, yield point.

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Authors: H. D. Ibrahim, H. C. Chinwenyi, T. Danjuma

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An option is defined as a financial contract that provides the holder the right but not the obligation to buy or sell a specified quantity of an underlying asset in the future at a fixed price (called a strike price) on or before the expiration date of the option. This paper examined two approaches for derivation of Partial Differential Equation (PDE) options price valuation formula for the Heston stochastic volatility model. We obtained various PDE option price valuation formulas using the riskless portfolio method and the application of Feynman-Kac theorem respectively. From the results obtained, we see that the two derived PDEs for Heston model are distinct and non-unique. This establishes the fact of incompleteness in the model for option price valuation.

Keywords: Option price valuation, Partial Differential Equations, Black-Scholes PDEs, Ito process.

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Authors: A. Kargar, A. Kianifar, H. Mohammadiun

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Two-dimensional heat conduction within a composed solid material with a constant internal heat generation has been investigated numerically in a sector of the rotor a generator. The heat transfer between two adjacent materials is assumed to be purely conduction. Boundary conditions are assumed to be forced convection on the fluid side and adiabatic on symmetry lines. The control volume method is applied for the diffusion energy equation. Physical coordinates are transformed to the general curvilinear coordinates. Then by using a line-by-line method, the temperature distribution in a sector of the rotor has been determined. Finally, the results are normalized and the effect of cooling fluid on the maximum temperature of insulation is investigated.

Keywords: general curvilinear coordinates , jacobian, controlvolume.

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Authors: Tarunjit S. Butalia, William E. Wolfe

Abstract:

This study demonstrates the use of Class F fly ash in combination with lime or lime kiln dust in the full depth reclamation (FDR) of asphalt pavements. FDR, in the context of this paper, is a process of pulverizing a predetermined amount of flexible pavement that is structurally deficient, blending it with chemical additives and water, and compacting it in place to construct a new stabilized base course. Test sections of two structurally deficient asphalt pavements were reclaimed using Class F fly ash in combination with lime and lime kiln dust. In addition, control sections were constructed using cement, cement and emulsion, lime kiln dust and emulsion, and mill and fill. The service performance and structural behavior of the FDR pavement test sections were monitored to determine how the fly ash sections compared to other more traditional pavement rehabilitation techniques. Service performance and structural behavior were determined with the use of sensors embedded in the road and Falling Weight Deflectometer (FWD) tests. Monitoring results of the FWD tests conducted up to 2 years after reclamation show that the cement, fly ash+LKD, and fly ash+lime sections exhibited two year resilient modulus values comparable to open graded cement stabilized aggregates (more than 750 ksi). The cement treatment resulted in a significant increase in resilient modulus within 3 weeks of construction and beyond this curing time, the stiffness increase was slow. On the other hand, the fly ash+LKD and fly ash+lime test sections indicated slower shorter-term increase in stiffness. The fly ash+LKD and fly ash+lime section average resilient modulus values at two years after construction were in excess of 800 ksi. Additional longer-term testing data will be available from ongoing pavement performance and environmental condition data collection at the two pavement sites.

Keywords: Coal fly ash, full depth reclamation, FWD, pavement rehabilitation

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Authors: M. H. Kargarnovin, K. Momeni

Abstract:

The study of the stress distribution on a hollow cylindrical fiber placed in a composite material is considered in this work and an analytical solution for this stress distribution has been constructed. Finally some parameters such as fiber-s thickness and fiber-s length are considered and their effects on the distribution of stress have been investigated. For finding the governing relations, continuity equations for the axisymmetric problem in cylindrical coordinate (r,o,z) are considered. Then by assuming some conditions and solving the governing equations and applying the boundary conditions, an equation relates the stress applied to the representative volume element with the stress distribution on the fiber has been found.

Keywords: Axial Loading, Composite, Hollow CylindricalFiber, Stress Distribution.

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Authors: P. Tueku, P. Supnithi, R. Wongsathan

Abstract:

Heat-Assisted Magnetic Recording (HAMR) is one of the leading technologies identified to enable areal density beyond 1 Tb/in² of magnetic recording systems. A key challenge to HAMR designing is accuracy of positioning, timing of the firing laser, power of the laser, thermo-magnetic head, head-disk interface and cooling system. We study the effect of HAMR parameters on transition center and transition width. The HAMR is model using Thermal Williams-Comstock (TWC) and microtrack model. The target and equalizer are designed by the minimum mean square error (MMSE). The result shows that the unit energy constraint outperforms other constraints.

Keywords: Heat-Assisted Magnetic Recording, Thermal Williams-Comstock equation, Microtrack model, Equalizer.

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Authors: C. A. Gilkeson, C. J. Noakes, P. A. Sleigh, M. A. I. Khan, M. A. Camargo-Valero

Abstract:

Understanding how airborne pathogens are transported through hospital wards is essential for determining the infection risk to patients and healthcare workers. This study utilizes Computational Fluid Dynamics (CFD) simulations to explore possible pathogen transport within a six-bed partitioned Nightingalestyle hospital ward. Grid independence of a ward model was addressed using the Grid Convergence Index (GCI) from solutions obtained using three fullystructured grids. Pathogens were simulated using source terms in conjunction with a scalar transport equation and a RANS turbulence model. Errors were found to be less than 4% in the calculation of air velocities but an average of 13% was seen in the scalar field. A parametric study of variations in the pathogen release point illustrated that its distribution is strongly influenced by the local velocity field and the degree of air mixing present.

Keywords: Natural, Ventilation, Pathogen, Transport

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Authors: Jeon Chi-Ho, Lee Jae-Bin, Shim Chang-Su

Abstract:

National bridge inventory in Korea shows that the number of old prestressed concrete (PSC) bridgeover 30 years of service life is rapidly increasing. Recently tendon corrosion is one of the most critical issues in the maintenance of PSC bridges. In this paper, mechanical properties of corroded strands, which were removed from old bridges, were evaluated using tensile test. In the result, the equations to express the mechanical behavior of corroded strand were derived and compared to existing equation. For the decision of tendon replacement, it is necessary to evaluate the effect of corrosion level on strength and ductility of the structure. Considerations on analysis of PSC girders were introduced, and decision making on tendon replacement was also proposed.

Keywords: Prestressed concrete bridge, prestressing steel, corrosion, strength, ductility.

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Authors: M.Imanova, G.Mehdiyeva, V.Ibrahimov

Abstract:

Solution of some practical problems is reduced to the solution of the integro-differential equations. But for the numerical solution of such equations basically quadrature methods or its combination with multistep or one-step methods are used. The quadrature methods basically is applied to calculation of the integral participating in right hand side of integro-differential equations. As this integral is of Volterra type, it is obvious that at replacement with its integrated sum the upper limit of the sum depends on a current point in which values of the integral are defined. Thus we receive the integrated sum with variable boundary, to work with is hardly. Therefore multistep method with the constant coefficients, which is free from noted lack and gives the way for finding it-s coefficients is present.

Keywords: Volterra integro-differential equations, multistepmethods, finite-difference methods, initial value problem

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Authors: Hai Huu Le, Paul Junor, Moshi Geso, Graeme O’Keefe

Abstract:

In this paper, the authors propose a personal wearable directionally-sensitive radiation dosimeter using multiple semiconductor CdZnTe detectors. The proposed dosimeter not only measures the real-time dose rate but also provide the direction of the radioactive source. A linear relationship between radioactive source direction and the radiation intensity measured by each detectors is established and an equation to determine the source direction is derived by the authors. The efficiency and accuracy of the proposed dosimeter is verified by simulation using Geant4 package. Results have indicated that in a measurement duration of about 7 seconds, the proposed dosimeter was able to estimate the direction of a 10μCi 137/55Cs radioactive source to within 2 degrees.

Keywords: Dose rate, Geant4 package, radiation detectors, radioactive source direction.

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Authors: Djarot B. Darmadi, John Norrish, Anh Kiet Tieu

Abstract:

Solutions for the temperature profile around a moving heat source are obtained using both analytic and finite element (FEM) methods. Analytic and FEM solutions are applied to study the temperature profile in welding. A moving heat source is represented using both point heat source and uniform distributed disc heat source models. Analytic solutions are obtained by solving the partial differential equation for energy conservation in a solid, and FEM results are provided by simulating welding using the ANSYS software. Comparison is made for quasi steady state conditions. The results provided by the analytic solutions are in good agreement with results obtained by FEM.

Keywords: Analytic solution, FEM, Temperature profile, HeatSource Model

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Authors: Yunquan Ke, Chunfang Miao

Abstract:

In this paper, the exponential stability of periodic solutions in inertial neural networks with unbounded delay are investigated. First, using variable substitution the system is transformed to first order differential equation. Second, by the fixed-point theorem and constructing suitable Lyapunov function, some sufficient conditions guaranteeing the existence and exponential stability of periodic solutions of the system are obtained. Finally, two examples are given to illustrate the effectiveness of the results.

Keywords: Inertial neural networks, unbounded delay, fixed-point theorem, Lyapunov function, periodic solutions, exponential stability.

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Authors: N. Santatriniaina, J. Deseure, T.Q. Nguyen, H. Fontaine, C. Beitia, L. Rakotomanana

Abstract:

Nowadays, with the increasing of the wafer's size and the decreasing of critical size of integrated circuit manufacturing in modern high-tech, microelectronics industry needs a maximum attention to challenge the contamination control. The move to 300 [mm] is accompanied by the use of Front Opening Unified Pods for wafer and his storage. In these pods an airborne cross contamination may occur between wafers and the pods. A predictive approach using modeling and computational methods is very powerful method to understand and qualify the AMCs cross contamination processes. This work investigates the required numerical tools which are employed in order to study the AMCs cross-contamination transfer phenomena between wafers and FOUPs. Numerical optimization and finite element formulation in transient analysis were established. Analytical solution of one dimensional problem was developed and the calibration process of physical constants was performed. The least square distance between the model (analytical 1D solution) and the experimental data are minimized. The behavior of the AMCs intransient analysis was determined. The model framework preserves the classical forms of the diffusion and convection-diffusion equations and yields to consistent form of the Fick's law. The adsorption process and the surface roughness effect were also traduced as a boundary condition using the switch condition Dirichlet to Neumann and the interface condition. The methodology is applied, first using the optimization methods with analytical solution to define physical constants, and second using finite element method including adsorption kinetic and the switch of Dirichlet to Neumann condition.

Keywords: AMCs, FOUP, cross-contamination, adsorption, diffusion, numerical analysis, wafers, Dirichlet to Neumann, finite elements methods, Fick’s law, optimization.

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Authors: Liu Zhiyuan, Sun Zongdi, Liu Zhiyuan, Sun Zongdi

Abstract:

Qingdao is a seaside city. Taking into account the characteristics of Qingdao, this article established a multiple linear regression model to analyze the impact of macroeconomic factors on housing prices. We used stepwise regression method to make multiple linear regression analysis, and made statistical analysis of F test values and T test values. According to the analysis results, the model is continuously optimized. Finally, this article obtained the multiple linear regression equation and the influencing factors, and the reliability of the model was verified by F test and T test.

Keywords: Housing prices, multiple linear regression model, macroeconomic factors, Qingdao City.

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Authors: J. X. Dong, C. J. An, Z. Chen, E. H. Owens, M. C. Boufadel, E. Taylor, K. Lee

Abstract:

Shorelines are vulnerable to significant environmental impacts from oil spills. Stranded oil can cause potential short- to long-term detrimental effects along beaches that include injuries to ecosystem, socio-economic and cultural resources. In this study, a three-dimensional (3D) numerical modeling approach is developed to evaluate the fate and transport of spilled oil for hypothetical oiled shoreline cases under various combinations of beach geomorphology and environmental conditions. The developed model estimates the spatial and temporal distribution of spilled oil for the various test conditions, using the finite volume method and considering the physical transport (dispersion and advection), sinks, and sorption processes. The model includes a user-friendly interface for data input on variables such as beach properties, environmental conditions, and physical-chemical properties of spilled oil. An experimental meso-scale tank design was used to test the developed model for dissolved petroleum hydrocarbon within shorelines. The simulated results for effects of different sediment substrates, oil types, and shoreline features for the transport of spilled oil are comparable to that obtained with a commercially available model. Results show that the properties of substrates and the oil removal by shoreline effects have significant impacts on oil transport in the beach area. Sensitivity analysis, through the application of the one-step-at-a-time method (OAT), for the 3D model identified hydraulic conductivity as the most sensitive parameter. The 3D numerical model allows users to examine the behavior of oil on and within beaches, assess potential environmental impacts, and provide technical support for decisions related to shoreline clean-up operations.

Keywords: dissolved petroleum hydrocarbons, environmental multimedia model, finite volume method, FVM, sensitivity analysis, total petroleum hydrocarbons, TPH

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Authors: Edward J. Kansa, Pavel Holoborodko

Abstract:

Continuously differentiable radial basis functions (RBFs) are meshfree, converge faster as the dimensionality increases, and is theoretically spectrally convergent. When implemented on current single and double precision computers, such RBFs can suffer from ill-conditioning because the systems of equations needed to be solved to find the expansion coefficients are full. However, the Advanpix extended precision software package allows computer mathematics to resemble asymptotically ideal Platonic mathematics. Additionally, full systems with extended precision execute faster graphical processors units and field-programmable gate arrays because no branching is needed. Sparse equation systems are fast for iterative solvers in a very limited number of cases.

Keywords: Meshless spectrally convergent, partial differential equations, extended arithmetic precision, no branching.

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Authors: Rinaldo Christian Tanumara, Ming Xie

Abstract:

Color categorization is shared among members in a society. This allows communication of color, especially when using natural language such as English. Hence sociable robot, to live coexist with human in human society, must also have the shared color categorization. To achieve this, many works have been done relying on modeling of human color perception and mathematical complexities. In contrast, in this work, the computer as brain of the robot learns color categorization through interaction with humans without much mathematical complexities.

Keywords: Color categorization, color learning, machinelearning.

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Authors: Nurhakimah Ab. Rahman, Lazim Abdullah

Abstract:

According to fuzzy arithmetic, dual fuzzy polynomials cannot be replaced by fuzzy polynomials. Hence, the concept of ranking method is used to find real roots of dual fuzzy polynomial equations. Therefore, in this study we want to propose an interval type-2 dual fuzzy polynomial equation (IT2 DFPE). Then, the concept of ranking method also is used to find real roots of IT2 DFPE (if exists). We transform IT2 DFPE to system of crisp IT2 DFPE. This transformation performed with ranking method of fuzzy numbers based on three parameters namely value, ambiguity and fuzziness. At the end, we illustrate our approach by two numerical examples.

Keywords: Dual fuzzy polynomial equations, Interval type-2, Ranking method, Value.

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Authors: Megawati, Wahyudi B. Sediawan, Hary Sulistyo, Muslikhin Hidayat

Abstract:

Rice husk is a lignocellulosic source that can be converted to ethanol. Three hundreds grams of rice husk was mixed with 1 L of 0.18 N sulfuric acid solutions then was heated in an autoclave. The reaction was expected to be at constant temperature (isothermal), but before that temperature was achieved, reaction has occurred. The first liquid sample was taken at temperature of 140 0C and repeated every 5 minute interval. So the data obtained are in the regions of non-isothermal and isothermal. It was observed that the degradation has significant effects on the ethanol production. The kinetic constants can be expressed by Arrhenius equation with the frequency factors for hydrolysis and sugar degradation of 1.58 x 105 1/min and 2.29 x 108 L/mole/min, respectively, while the activation energies are 64,350 J/mole and 76,571 J/mole. The highest ethanol concentration from fermentation is 1.13% v/v, attained at 220 0C.

Keywords: degradation, ethanol, hydrolysis, rice husk

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Authors: Megawati, Wahyudi B. Sediawan, Hary Sulistyo, Muslikhin Hidayat

Abstract:

Rice husk is a lignocellulosic source that can be converted to ethanol. Three hundreds grams of rice husk was mixed with 1 L of 0.18 N sulfuric acid solutions then was heated in an autoclave. The reaction was expected to be at constant temperature (isothermal), but before that temperature was achieved, reaction has occurred. The first liquid sample was taken at temperature of 140 0C and repeated every 5 minute interval. So the data obtained are in the regions of non-isothermal and isothermal. It was observed that the degradation has significant effects on the ethanol production. The kinetic constants can be expressed by Arrhenius equation with the frequency factors for hydrolysis and sugar degradation of 1.58 x 105 min-1 and 2.29 x 108 L/mole-min, respectively, while the activation energies are 64,350 J/mole and 76,571 J/mole. The highest ethanol concentration from fermentation is 1.13% v/v, attained at 220 0C.

Keywords: degradation, ethanol, hydrolysis, rice husk.

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Authors: Anton Purnama

Abstract:

Multiport diffusers are the effective engineering devices installed at the modern marine outfalls for the steady discharge of effluent streams from the coastal plants, such as municipal sewage treatment, thermal power generation and seawater desalination. A mathematical model using a two-dimensional advection-diffusion equation based on a flat seabed and incorporating the effect of a coastal tidal current is developed to calculate the compounded concentration following discharges of desalination brine from a sea outfall with multiport diffusers. The analytical solutions are computed graphically to illustrate the merging of multiple brine plumes in shallow coastal waters, and further approximation will be made to the maximum shoreline's concentration to formulate dilution of a multiport diffuser discharge.

Keywords: Desalination brine discharge, mathematical model, multiport diffuser, two sea outfalls.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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