Search results for: molecular modeling

Authors: Syed Islam, Yiyun Huang, Sebastian Magierowski, Ebrahim Ghafar-Zadeh

Abstract:

This paper presents system level CMOS solid-state nanopore techniques enhancement for speedup next generation molecular recording and high throughput channels. This discussion also considers optimum number of base-pair (bp) measurements through channel as an important role to enhance potential read accuracy. Effective power consumption estimation offered suitable range of multi-channel configuration. Nanopore bp extraction model in statistical method could contribute higher read accuracy with longer read-length (200 < read-length). Nanopore ionic current switching with Time Multiplexing (TM) based multichannel readout system contributed hardware savings.

Keywords: DNA, Nanopore, Amplifier, ADC, Multichannel.

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

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Authors: E. Asadzadeh, M. Alam

Abstract:

This study offers a comprehensive review of the research papers published in the field of cooling towers and gives an insight into the latest developments of the natural draught cooling towers. Different modeling, analysis and design techniques are summarized and the challenges are discussed. The 118 references included in this paper are mostly concentrated on the review of the published papers after 2005. The present paper represents a complete collection of the studies done for cooling towers and would give an updated material for the researchers and design engineers in the field of hyperbolic cooling towers.

Keywords: Hyperbolic cooling towers, earthquakes, wind, nonlinear behavior, buckling, collapse, interference.

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Authors: Abhishek Soni, Bhagat Singh

Abstract:

In the present work, reverse engineering (RE) approach has been used to create a 3D model of a fractured femur bone using the computed tomography (CT) scan data. Thereafter, counter fit fixation plates of Titanium alloy (Ti6Al4V) have been designed and analyzed considering physiological static loading conditions. From the analysis, it has been inferred that the stresses and deformation developed are quite low. It implies that these designed customized fixation plates are able to provide stable fixation resulting in improved fracture union.

Keywords: Biomechanical evaluations, customized implant, reverse engineering, titanium alloy.

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Authors: Mario Gianni, Manuel A. Ruiz Garcia, Fiora Pirri

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In this work, we present a Bayesian non-parametric approach to model the motion control of ATVs. The motion control model is based on a Dirichlet Process-Gaussian Process (DP-GP) mixture model. The DP-GP mixture model provides a flexible representation of patterns of control manoeuvres along trajectories of different lengths and discretizations. The model also estimates the number of patterns, sufficient for modeling the dynamics of the ATV.

Keywords: Dirichlet processes, Gaussian processes, robot control learning, tracked vehicles.

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Authors: J. Maděra, M. Jerman, R. Černý

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Temperature, relative humidity and overhygroscopic moisture fields in a sandstone wall provided with interior thermal insulation were calculated in order to assess the hygric performance of the retrofitted wall. Computational simulations showed that during the time period of 10 years which was subject of investigation no overhygroscopic moisture appeared in the analyzed building envelope so that it performed in a satisfactory way from the hygric point of view.

Keywords: Sandstone wall, interior thermal insulation, moisture, computational modeling.

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Authors: Jaroslav Krutil, František Pochylý, Simona Fialová

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The article presents two mathematical models of the interaction between a rotating shaft and an incompressible fluid. The mathematical model includes both the journal bearings and the axially traversed hydrodynamic sealing gaps of hydraulic machines. A method is shown for the identification of additional effects of the fluid acting on the rotor of the machine, both for a linear and a nonlinear model. The interaction is expressed by matrices of mass, stiffness and damping.

Keywords: CFD modeling, hydrodynamic gap, matrices of mass, stiffness and damping, nonlinear mathematical model.

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Authors: Olga A. Berillo, Assel S. Issabekova, Anatoly T. Ivashchenko

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MiRNAs participate in gene regulation of translation. Some studies have investigated the interactions between genes and intragenic miRNAs. It is important to study the miRNA binding sites of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid programmes were used to compute the hybridization free energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%, and 39.7% of miRNA binding sites were present in the 5'UTRs, CDSs, and 3'UTRs, respectively. The density of the binding sites for miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to 8.0 times greater than in the CDS and 3'UTR, respectively. Three types of miRNA interactions with mRNAs have been revealed: 5'- dominant canonical, 3'-compensatory, and complementary binding sites. MiRNAs regulate gene expression, and information on the interactions between miRNAs and mRNAs could be useful in molecular medicine. We recommend that newly described sites undergo validation by experimental investigation.

Keywords: Exon, intron, miRNA, oncogene.

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Authors: Tamara Grujic, Mirjana Bonkovic

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Measurements and quantitative analysis of kinematic parameters of human hand movements have an important role in different areas such as hand function rehabilitation, modeling of multi-digits robotic hands, and the development of machine-man interfaces. In this paper the assessment and evaluation of the reachto- grasp movement by using computerized and robot-assisted method is described. Experiment involved the measurements of hand positions of seven healthy subjects during grasping three objects of different shapes and sizes. Results showed that three dominant phases of reach-to-grasp movements could be clearly identified.

Keywords: Human hand, kinematics, reach-to-grasp movement.

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Authors: A. Brahma

Abstract:

Drying is a phenomenon that accompanies the hardening of hydraulic materials. This study is concerned the modelling of drying shrinkage of the hydraulic materials and the prediction of the rate of spontaneous deformations of hydraulic materials during hardening. The model developed takes consideration of the main factors affecting drying shrinkage. There was agreement between drying shrinkage predicted by the developed model and experimental results. In last we show that developed model describe the evolution of the drying shrinkage of high performances concretes correctly.

Keywords: Drying, hydraulic concretes, shrinkage, modeling, prediction.

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Authors: Shuib Rambat, Ruzsyahriman Jenal, John Elgy

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This paper presented the potential of smart phone to provide support on mapping the indoor asset. The advantage of using the smart phone to generate the indoor map is that it has the ability to capture, store and reproduces still or video images; indeed most of us do have this powerful gadget. The captured images usually used by maintenance team to save a record for future reference. Here, these images are used to generate 3D models of an object precisely and accurately for efficient and effective solution in data gathering. Thus, it could be a resource for an informative database in asset management.

Keywords: 3D modeling, Asset Management, Object Extraction, Smart Device

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Authors: S. Mahalakshmi, B. Senthil Arasu

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As per the recent changes happening in the global policies, climate related changes and the impact it causes across every sector are viewed as green swan events – in essence, climate related changes can happen often and lead to risk and lot of uncertainty, but need to be mitigated instead of considering them as black swan events. This brings about a question on how this risk can be computed, so that the financial institutions can plan to mitigate it. Climate related changes impact all risk types – credit risk, market risk, operational risk, liquidity risk, reputational risk and others. And the models required to compute this have to consider the different industrial needs of the counterparty, as well as the factors that are contributing to this – be it in the form of different risk drivers, or the different transmission channels or the different approaches and the granular form of data availability. This brings out to the suggestion that the climate related changes, though it affects Pillar I risks, will be a Pillar II risk. This has to be modeled specifically based on the financial institution’s actual exposure to different industries, instead of generalizing the risk charge. And this will have to be considered as the additional capital to be met by the financial institution in addition to their Pillar I risks, as well as the existing Pillar II risks. In this paper, we present a risk assessment framework to model and assess climate change risks - for both credit and market risks. This framework helps in assessing the different scenarios, and how the different transition risks affect the risk associated with the different parties. This research paper delves on the topic of increase in concentration of greenhouse gases, that in turn causing global warming. It then considers the various scenarios of having the different risk drivers impacting credit and market risk of an institution, by understanding the transmission channels, and also considering the transition risk. The paper then focuses on the industry that’s fast seeing a disruption: automobile industry. The paper uses the framework to show how the climate changes and the change to the relevant policies have impacted the entire financial institution. Appropriate statistical models for forecasting, anomaly detection and scenario modeling are built to demonstrate how the framework can be used by the relevant agencies to understand their financial risks. The paper also focuses on the climate risk calculation for the Pillar II capital calculations, and how it will make sense for the bank to maintain this in addition to their regular Pillar I and Pillar II capital.

Keywords: Capital calculation, climate risk, credit risk, pillar II risk, scenario modeling.

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Authors: Marc Landry, Azeddine Kaddouri, Yassine Bouslimani, Mohsen Ghribi

Abstract:

In this paper, a new alignment method based on the particle swarm optimization (PSO) technique is presented. The PSO algorithm is used for locating the optimal coupling position with the highest optical power with three-degrees of freedom alignment. This algorithm gives an interesting results without a need to go thru the complex mathematical modeling of the alignment system. The proposed algorithm is validated considering practical tests considering the alignment of two Single Mode Fibers (SMF) and the alignment of SMF and PCF fibers.

Keywords: Particle-swarm optimization, optical fiber, automatic alignment.

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Authors: Mehmet Savsar

Abstract:

This paper presents a model for an unreliable production line, which is operated according to demand with constant work-in-process (CONWIP). A simulation model is developed based on the discrete model and several case problems are analyzed using the model. The model is utilized to optimize storage space capacities at intermediate stages and the number of kanbans at the last stage, which is used to trigger the production at the first stage. Furthermore, effects of several line parameters on production rate are analyzed using design of experiments.

Keywords: Production line simulator, Push-pull system, JIT system, Constant WIP, Machine failures.

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Authors: Paratibha Aggarwal, Yogesh Aggarwal

Abstract:

The paper presents the potential of fuzzy logic (FL-I) and neural network techniques (ANN-I) for predicting the compressive strength, for SCC mixtures. Six input parameters that is contents of cement, sand, coarse aggregate, fly ash, superplasticizer percentage and water-to-binder ratio and an output parameter i.e. 28- day compressive strength for ANN-I and FL-I are used for modeling. The fuzzy logic model showed better performance than neural network model.

Keywords: Self compacting concrete, compressive strength, prediction, neural network, Fuzzy logic.

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Authors: Asim Cengiz, Dede Basturk, Hakan Ozalp

Abstract:

Practicing recurring resistance workout such as may cause changes in human muscle. These changes may be because combination if several factors determining physical fitness. Thus, it is important to identify these changes. Several studies were reviewed to investigate these changes. As a result, the changes included positive modifications in amplified citrate synthase (CS) maximal activity, increased capacity for pyruvate oxidation, improvement on molecular signaling on human performance, amplified resting muscle glycogen and whole GLUT4 protein content, better health outcomes such as enhancement in cardiorespiratory fitness. Sprint training also have numerous long long-term changes inhuman body such as better enzyme action, changes in muscle fiber and oxidative ability. This is important because SV is the critical factor influencing maximal cardiac output and therefore oxygen delivery and maximal aerobic power.

Keywords: Sprint, training, performance, exercise.

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Authors: Zita Šereš, Dragana Šoronja Simović, Ljubica Dokić, Lidietta Giorno, Biljana Pajin, Cecilia Hodur, Nikola Maravić

Abstract:

Membrane technology is convenient for separation of suspended solids, colloids and high molecular weight materials that are present. The idea is that the waste stream from edible oil industry, after the separation of oil by using skimmers is subjected to microfiltration and the obtained permeate can be used again in the production process. The wastewater from edible oil industry was used for the microfiltration. For the microfiltration of this effluent a tubular membrane was used with a pore size of 200 nm at transmembrane pressure in range up to 3 bar and in range of flow rate up to 300 L/h. Box–Behnken design was selected for the experimental work and the responses considered were permeate flux and chemical oxygen demand (COD) reduction. The reduction of the permeate COD was in the range 40-60% according to the feed. The highest permeate flux achieved during the process of microfiltration was 160 L/m²h.

Keywords: Ceramic membrane, edible oil, microfiltration, wastewater.

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Authors: Gabriel Quintero

Abstract:

This paper presents the result of the implementation of a series of algorithms intended to be used for representing in most of the 3D geographic software, even Google Earth, the subsurface formations properties combining 2D charts or 3D plots over a 3D background, allowing everyone to use them, no matter the economic size of the company for which they work. Besides the existence of complex and expensive specialized software for modeling subsurface formations based on the same information provided to this one, the use of this open source development shows a higher and easier usability and good results, limiting the rendered properties and polygons to a basic set of charts and tubes.

Keywords: Chart, earth, formations, subsurface, visualization.

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Authors: S. W. Hong, Y. S. Choi, T. H. Chung, J. H. Song, H. S. Kim

Abstract:

Bio-electrical responses obtained from freshwater sediments by employing microbial fuel cell (MFC) technology were investigated in this experimental study. During the electricity generation, organic matter in the sediment was microbially oxidized under anaerobic conditions with an electrode serving as a terminal electron acceptor. It was found that the sediment organic matter (SOM) associated with electrochemically-active electrodes became more humified, aromatic, and polydispersed, and had a higher average molecular weight, together with the decrease in the quantity of SOM. The alteration of characteristics of the SOM was analogous to that commonly observed in the early stage of SOM diagenetic process (i.e., humification). These findings including an elevation of the sediment redox potential present a possibility of the MFC technology as a new soil/sediment remediation technique based on its potential benefits: non-destructive electricity generation and bioremediation.

Keywords: Anaerobic oxidation, microbial fuel cell, remediation, sediment.

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Authors: S. Heydarzadeh, A. Kadivarian, P. Torkzadeh

Abstract:

Implemented 5-bit 125-MS/s successive approximation register (SAR) analog to digital converter (ADC) on FPGA is presented in this paper.The design and modeling of a high performance SAR analog to digital converter are based on monotonic capacitor switching procedure algorithm .Spartan 3 FPGA is chosen for implementing SAR analog to digital converter algorithm. SAR VHDL program writes in Xilinx and modelsim uses for showing results.

Keywords: Analog to digital converter, Successive approximation, Capacitor switching algorithm, FPGA

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Authors: Mousaab Alrhmoun, Magali Casellas, Michel Baudu, Christophe Dagot

Abstract:

The aim of the study is to improve removal of trace organic contaminants dissolved in activated sludge by the process of filtration with membrane bioreactor combined with modified activated carbon, for a maximum removal of organic compounds characterized by low molecular weight. Special treatment was conducted in laboratory on activated carbon. Tow reaction parameters: the pH of aqueous middle and the type of granular activated carbon were very important to improve the removal and to motivate the electrostatic Interactions of organic compounds with modified activated carbon in addition to physical adsorption, ligand exchange or complexation on the surface activated carbon. The results indicate that modified activated carbon has a strong impact in removal 21 of organic contaminants and in percentage of 100% of the process.

Keywords: Activated carbon, organic contaminants, Membrane bioreactor.

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Authors: C. N. Okafor, M. Maaza, T. A. E. Mokrani

Abstract:

A proton exchange membrane has been developed for direct methanol fuel cell (DMFC). The nanofiber network composite membranes were prepared by interconnected network of Nafion (perfuorosulfonic acid) nanofibers that have been embedded in an uncharged and inert polymer matrix, by electro-spinning. The spinning solution of Nafion with a low concentration (1 wt% compared to Nafion) of high molecular weight poly(ethylene oxide), as a carrier polymer. The interconnected network of Nafion nanofibers with average fiber diameter in the range of 160-700nm, were used to make the membranes, with the nanofiber occupying up to 85% of the membrane volume. The matrix polymer was crosslinked with Norland Optical Adhesive 63 under UV. The resulting membranes showed proton conductivity of 0.10 S/cm at 25°C and 80% RH; and methanol permeability of 3.6 x 10-6 cm2/s.

Keywords: Composite membrane, electrospinning, fuel cell, nanofibers.

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Authors: C. Clements, M. Hasenohr, A. Anvar

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A glider is in essence an unpowered vehicle and in this project we designed and built an oceanic glider, designed to operate underwater. This Glider was designed to collect ocean data such as temperature, pressure and (in future measures physical dimensions of the operating environment) and output this data to an external source. Development of the Oceanic Glider required research into various actuation systems that control buoyancy, pitch and yaw and the dynamics of these systems. It also involved the design and manufacture of the Glider and the design and implementation of a controller that enabled the Glider to navigate and move in an appropriate manner.

Keywords: Ocean Glider, Robot, Automation, Command, Control, Navigation.

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Authors: Amer S. Al-Yahmadi, T.C. Hsia

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This paper seeks to develop simple yet practical and efficient control scheme that enables cooperating arms to handle a flexible beam. Specifically the problem studied herein is that of two arms rigidly grasping a flexible beam and such capable of generating forces/moments in such away as to move a flexible beam along a predefined trajectory. The paper develops a sliding mode control law that provides robustness against model imperfection and uncertainty. It also provides an implicit stability proof. Simulation results for two three joint arms moving a flexible beam, are presented to validate the theoretical results.

Keywords: Sliding mode control, cooperative manipulators.

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Authors: Robert Prucek, Aleš Panáček, Jan Filip, Libor Kvítek, Radek Zbořil

Abstract:

The preparation of Cu nanoparticles (NPs) through the reduction of copper ions by sodium borohydride in the presence of sodium polyacrylate with a molecular weight of 1200 is reported. Cu NPs were synthesized at a concentration of copper salt equal to 2.5, 5, and 10 mM, and at a molar ratio of copper ions and monomeric unit of polyacrylate equal to 1:2. The as-prepared Cu NPs have diameters of about 2.5–3 nm for copper concentrations of 2.5 and 5 mM, and 6 nm for copper concentration of 10 mM. Depending on the copper salt concentration and concentration of additionally added polyacrylate to Cu particle dispersion, primarily formed NPs grow through the process of aggregation and/or coalescence into clusters and/or particles with a diameter between 20–100 nm. The amount of additionally added sodium polyacrylate influences the stability of Cu particles against air oxidation. The catalytic efficiency of the prepared Cu particles for the reduction of 4-nitrophenol is discussed.

Keywords: Copper, nanoparticles, sodium polyacrylate, catalyst, 4-nitrophenol.

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Authors: M. A. Serag-Eldin

Abstract:

The paper presents the results of simple measurements conducted on a model of a wind-driven venturi-type room ventilator. The ventilator design is new and was developed employing mathematical modeling. However, the computational model was not validated experimentally for the particular application considered. The paper presents the performance of the ventilator model under laboratory conditions, for five different wind tunnel speeds. The results are used to both demonstrate the effectiveness of the new design and to validate the computational model employed to develop it.

Keywords: Venturi-flow, ventilation, Wind-energy, Wind flow.

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Authors: Yi-Ping Fang, Yi-Ting Wong

Abstract:

Transcription factor p53 has a powerful tumor suppressing function that is associated with many cancers. However, p53 of the molecular weight was higher make the limitation across to skin or cell membrane. Thymidine dinucleotide (pTT), an oligonucleotide, can activate the p53 transcription factor. pTT is a hydrophilic and negative charge oligonucleotide, which delivery in to cell membrane need an appropriate carrier. The aim of this study was to improve the bioavailability of the nucleotide fragment, thymidine dinucleotide (pTT), using elasic liposome carriers to deliver the drug into the skin. The study demonstrate that dioleoylphosphocholine (DOPC) incorporated with sodium cholate at molar ratio 1:1 can archived the particle size about 220 nm. This elastic liposome could penetration through skin from stratum corneum to whole epidermis by confocal laser scanning microscopy (CLSM). Moreover, we observed the the slight increase in generation of p53 by western blot.

Keywords: Elastic liposome, Tymidine dinucleotide, p53, Topical delivery

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Authors: M. Sasajima, T. Yamaguchi, M. Watanabe, Y. Koike

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This paper discusses the propagation of sound waves in air, specifically in narrow rectangular pathways of an occluded-ear simulator for acoustic measurements. In narrow pathways, both the speed of sound and the phase of the sound waves are affected by the damping of the air viscosity. Herein, we propose a new finite-element method (FEM) that considers the effects of the air viscosity. The method was developed as an extension of existing FEMs for porous, sound-absorbing materials. The results of a numerical calculation for a three-dimensional ear-simulator model using the proposed FEM were validated by comparing with theoretical lumped-parameter modeling analysis and standard values.

Keywords: Ear simulator, FEM, simulation, viscosity.

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Authors: J. Alizadeh K., R. S. Ashofteh, A. Asadi Lari

Abstract:

Railway vehicle wheels are designed to operate in harsh environments and to withstand high hydrostatic contact pressures. This situation may result in critical circumstances, in particular wheel breakage. This paper presents a time history of a series of broken wheels during a time interval [2007-2008] belongs to locomotive fleet on Iranian Railways. Such fractures in locomotive wheels never reported before. Due to the importance of this issue, a research study has been launched to find the potential reasons of this problem. The authors introduce a FEM model to indicate how and where the wheels could have been affected during their operation. Then, the modeling results are presented and discussed in detail.

Keywords: Crack, fatigue, FE analysis, wheel.

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Authors: R. Gunabalan, S. Immanuel Prabakaran, J. Reegan, S. Ganesh

Abstract:

This paper describes a software approach for modeling inverter fed induction motor drive using Laboratory Virtual Instrument Engineering Workbench (LabVIEW). The reason behind the selection of LabVIEW software is because of its strong graphical interface, flexibility of its programming language combined with built-in tools designed specifically for test, measurement and control. LabVIEW is generally used in most of the applications for data acquisition, test and control. In this paper, inverter and induction motor are modeled using LabVIEW toolkits. Simulation results are presented and are validated.

Keywords: Induction motor, LabVIEW, State model.

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