Search results for: molecular modeling

Authors: Federico Cabitza, Marco P. Locatelli, Marcello Sarini, Carla Simone

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The paper shows how the CASMAS modeling language, and its associated pervasive computing architecture, can be used to facilitate continuity of care by providing members of patientcentered communities of care with a support to cooperation and knowledge sharing through the usage of electronic documents and digital devices. We consider a scenario of clearly fragmented care to show how proper mechanisms can be defined to facilitate a better integration of practices and information across heterogeneous care networks. The scenario is declined in terms of architectural components and cooperation-oriented mechanisms that make the support reactive to the evolution of the context where these communities operate.

Keywords: Pervasive Computing, Communities of Care, HeterogeneousCare Networks, Multi-Agent System.

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Authors: Lenka Ševelová, Aleš Florian

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Appropriate and progressive tool for analyzing behavior of low volume roads are probabilistic models used in reliability analyses. The necessary part of the probabilistic model is the deterministic model of structural behavior. The FE model of low volume roads is created in the ANSYS software. It is able to determine the state of stress and deformation in any point of the structure and thus generate data required for the reliability analysis. The paper compares two material constitutive models used for modeling of unbound non-homogenous materials used in low volume roads. The first model is linear elastic model according to Hook theory (H model), the second one is nonlinear elastic-plastic Drucker-Prager model (D-P model).

Keywords: FEA, FEM, geotechnical materials, low volume roads, material constitutive models, pavement.

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Authors: Tokuei Sako, Paul-Antoine Hervieux

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The energy-level structure of a pair of electron and positron confined in a quasi-one-dimensional nano-scale potential well has been investigated focusing on its trend in the small limit of confinement strength ω, namely, the Wigner molecular regime. An anisotropic Gaussian-type basis functions supplemented by high angular momentum functions as large as l = 19 has been used to obtain reliable full configuration interaction (FCI) wave functions. The resultant energy spectrum shows a band structure characterized by ω for the large ω regime whereas for the small ω regime it shows an energy-level pattern dominated by excitation into the in-phase motion of the two particles. The observed trend has been rationalized on the basis of the nodal patterns of the FCI wave functions. 

Keywords: Confined systems, positron, wave function, Wigner molecule, quantum dots.

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Authors: J. Fernandez de Canete, S. Fernandez-Calvo, I. García-Moral

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This paper presents and discusses the application of the object-oriented modelling software SIMSCAPE to hydraulic systems, with particular reference to multivariable proportional-integral-derivative (PID) control. As a result, a particular modelling approach of a double cylinder-piston coupled system is proposed and motivated, and the SIMULINK based PID tuning tool has also been used to select the proper controller parameters. The paper demonstrates the usefulness of the object-oriented approach when both physical modelling and control are tackled.

Keywords: Object-oriented modeling, multivariable hydraulic system, multivariable PID control, computer simulation.

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Authors: Santosh Kr. Choudhary

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In this article, LQR based PID controller design for 3DOF helicopter system is investigated. The 3-DOF helicopter system is a benchmark laboratory model having strongly nonlinear characteristics and unstable dynamics which make the control of such system a challenging task. This article first presents the mathematical model of the 3DOF helicopter system and then illustrates the basic idea and technical formulation for controller design. The paper explains the simple approach for the approximation of PID design parameters from the LQR controller gain matrix. The simulation results show that the investigated controller has both static and dynamic performance, therefore the stability and the quick control effect can be obtained simultaneously for the 3DOF helicopter system.

Keywords: 3DOF helicopter system, PID controller, LQR controller, modeling, simulation.

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Authors: Le Thuy Mai, Vu Nguyen Thanh

Abstract:

β-Glucosidase is an important enzyme for production of ethanol from lignocellulose. With hydrolytic activity on cellooligosaccharides, especially cellobiose, β-glucosidase removes product inhibitory effect on cellulases and forms fermentable sugars. In this study, β-glucosidase encoding gene (BGL1) from traditional starter yeast Saccharomycosis fibuligera BMQ908 was cloned and expressed in Pichia pastoris. BGL1 of S. fibuligera BMQ 908 shared 98% nucleotide homology with the closest GenBank sequence (M22475) but identity in amino-acid sequences of catalytic domains. Recombinant plasmid pPICZαA/BGL1 containing the sequence encoding BGL1 mature protein and α-factor secretion signal was constructed and transformed into methylotrophic yeast P. pastoris by electroporation. The recombinant strain produced single extracellular protein with molecular weight of 120 kDa and cellobiase activity of 60 IU/ml. The optimum pH of the recombinant β-glucosidase was 5.0 and the optimum temperature was 50°C.

Keywords: β-Glucosidase, Pichia pastoris, Saccharomycopsisfibuligera, recombinant enzyme.

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Authors: Akshata S. Malani, Anagha D. Chaudhari, Rajeshkumar U. Sambhe

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Nanotechnology in pristine sense refers to building of structures at atomic and molecular scale. Meticulously nanotechnology encompasses the nanomaterials with at least one dimension size ranging from 1 to 100 nanometres. Unlike the literal meaning of its name, nanotechnology is a massive concept beyond imagination. This paper predominantly deals with relevance of nanotechnology in automotive industries. New generation of automotives looks at nanotechnology as an emerging trend of manufacturing revolution. Intricate shapes can be made out of fairly inexpensive raw materials instead of conventional fabrication process. Though the current era have enough technology to face competition, nanotechnology can give futuristic implications to pick up the modern pace. Nanotechnology intends to bridge the gap between automotives with superior technical performance and their cost fluctuation. Preliminarily, it is an area of great scientific interest and a major shaper of many new technologies. Nanotechnology can be an ideal building block for automotive industries, under constant evolution offering a very wide scope of activity. It possesses huge potential and is still in the embryonic form of research and development.

Keywords: Nanotechnology, nanomaterials, manufacturing, automotive industry.

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Authors: Dipankar Dhabak, Soumya Pandit

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This paper presents an adaptive technique for generation of data required for construction of artificial neural network-based performance model of nano-scale CMOS inverter circuit. The training data are generated from the samples through SPICE simulation. The proposed algorithm has been compared to standard progressive sampling algorithms like arithmetic sampling and geometric sampling. The advantages of the present approach over the others have been demonstrated. The ANN predicted results have been compared with actual SPICE results. A very good accuracy has been obtained.

Keywords: CMOS Inverter, Nano-scale, Adaptive Sampling, ArtificialNeural Network

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Authors: Radoslav Židek, Veronika Šidlová, Radovan Kasarda, Birgit Fuerst-Waltl

Abstract:

Machine learning represents a set of topics dealing with the creation and evaluation of algorithms that facilitate pattern recognition, classification, and prediction, based on models derived from existing data. The data can present identification patterns which are used to classify into groups. The result of the analysis is the pattern which can be used for identification of data set without the need to obtain input data used for creation of this pattern. An important requirement in this process is careful data preparation validation of model used and its suitable interpretation. For breeders, it is important to know the origin of animals from the point of the genetic diversity. In case of missing pedigree information, other methods can be used for traceability of animal´s origin. Genetic diversity written in genetic data is holding relatively useful information to identify animals originated from individual countries. We can conclude that the application of data mining for molecular genetic data using supervised learning is an appropriate tool for hypothesis testing and identifying an individual.

Keywords: Genetic data, Pinzgau cattle, supervised learning.

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Authors: B. Bakır, İ. Batmaz, F. A. Güntürkün, İ. A. İpekçi, G. Köksal, N. E. Özdemirel

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The main aim of this study is to identify the most influential variables that cause defects on the items produced by a casting company located in Turkey. To this end, one of the items produced by the company with high defective percentage rates is selected. Two approaches-the regression analysis and decision treesare used to model the relationship between process parameters and defect types. Although logistic regression models failed, decision tree model gives meaningful results. Based on these results, it can be claimed that the decision tree approach is a promising technique for determining the most important process variables.

Keywords: Casting industry, decision tree algorithm C5.0, logistic regression, quality improvement.

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Authors: J.Zouhair, D.Ellison

Abstract:

This paper includes a review of three physics simulation packages that can be used to provide researchers with a virtual ground for modeling, implementing and simulating complex models, as well as testing their control methods with less cost and time of development. The inverted pendulum model was used as a test bed for comparing ODE, DANCE and Webots, while Linear State Feedback was used to control its behavior. The packages were compared with respect to model creation, solving systems of differential equation, data storage, setting system variables, control the experiment and ease of use. The purpose of this paper is to give an overview about our experience with these environments and to demonstrate some of the benefits and drawbacks involved in practice for each package.

Keywords: DANCE, Inverted Pendulum, ODE, Simulation Packages, Webots.

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Authors: Noor Muzamil Mohamad, Abdul Manaf Ali, Hamzah Mohd Salleh

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Phytases (myo-inositol hexakisphosphate phosphohydrolases; EC 3.1.3.8) catalyze the hydrolysis of phytic acid (myoinositol hexakisphosphate) to the mono-, di-, tri-, tetra-, and pentaphosphates of myo-inositol and inorganic phosphate. Therrmophilic bacteria isolated from water sampled from hot spring. About 120 isolates of bacteria were successfully isolated form hot spring water sample and tested for extracellular phytase producing. After 5 passages of the screening on the PSM media, 4 isolates were found stable in producing phytase enzyme. The 16s RDNA sequencing for identification of bacteria using molecular technique revealed that all isolates those positive in phytase producing are belong to Geobacillus spp. And Anoxybacillus spp. Anoxybacillus rupiensis UniSZA-7 were identified for their carbon source utilization using Phenotype Microarray Plate of Biolog and found they utilize several kind of carbon source provided.

Keywords: Phytase, Phytic Acid, Thermophilic Bacteria, PSM Media and Phytase Assay

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Authors: A. Thabet, M. Boutayeb, M. N. Abdelkrim

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This paper investigates a method for the state estimation of nonlinear systems described by a class of differential-algebraic equation (DAE) models using the extended Kalman filter. The method involves the use of a transformation from a DAE to ordinary differential equation (ODE). A relevant dynamic power system model using decoupled techniques will be proposed. The estimation technique consists of a state estimator based on the EKF technique as well as the local stability analysis. High performances are illustrated through a simulation study applied on IEEE 13 buses test system.

Keywords: Power system, Dynamic decoupled model, Extended Kalman Filter, Convergence analysis, Time computing.

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Authors: A. Meftah, D. Zarga, M. Yahiaoui

Abstract:

In this paper, we have used an analytical method to analyze the vibratory behavior of plates in materials with gradient of properties, simply supported, proposing a refined non polynomial theory. The number of unknown functions involved in this theory is only four, as compared to five in the case of other higher shear deformation theories. The transverse shearing effects are studied according to the thickness of the plate. The motion equations for the FGM plates are obtained by the Hamilton principle application, the solutions are obtained using the Navier method, and then the fundamental frequencies are found, solving an eigenvalue equation system, the results of this analysis are presented and compared to those available in the literature.

Keywords: FGM plates, Navier method, vibratory behavior.

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

Abstract:

In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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Authors: Elnaz Afshari, Siamak Najarian

Abstract:

Having considered tactile sensing and palpation of a surgeon in order to detect kidney stone during open surgery; we present the 2D model of nephrolithiasis (two dimensional model of kidney containing a simulated stone). The effects of stone existence that appear on the surface of kidney (because of exerting mechanical load) are determined. Using Finite element method, it is illustrated that the created stress patterns on the surface of kidney and stress graphs not only show existence of stone inside kidney, but also show its exact location.

Keywords: Nephrolithiasis, Minimally Invasive Surgery, Artificial Tactile Sensing, Finite Element Method.

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Authors: H. Bouadi, M. Bouchoucha, M. Tadjine

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In this paper; we are interested principally in dynamic modelling of quadrotor while taking into account the high-order nonholonomic constraints in order to develop a new control scheme as well as the various physical phenomena, which can influence the dynamics of a flying structure. These permit us to introduce a new state-space representation. After, the use of Backstepping approach for the synthesis of tracking errors and Lyapunov functions, a sliding mode controller is developed in order to ensure Lyapunov stability, the handling of all system nonlinearities and desired tracking trajectories. Finally simulation results are also provided in order to illustrate the performances of the proposed controller.

Keywords: Dynamic modeling, nonholonomic constraints, Backstepping, sliding mode.

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Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

Abstract:

The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

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Authors: Nurhayati Abdullah, Fauziah Sulaiman, Muhamad Azman Miskam, Rahmad Mohd Taib

Abstract:

Banana pseudo-stem and fruit-bunch-stem are agricultural residues that can be used for conversion to bio-char, biooil, and gases by using thermochemical process. The aim of this work is to characterize banana pseudo-stem and banana fruit-bunch-stem through proximate analysis, elemental analysis, chemical analysis, thermo-gravimetric analysis, and heating calorific value. The ash contents of the banana pseudo-stem and banana fruit-bunch-stem are 11.0 mf wt.% and 20.6 mf wt.%; while the carbon content of banana pseudo-stem and fruit-bunch-stem are 37.9 mf wt.% and 35.58 mf wt.% respectively. The molecular formulas for banana stem and banana fruit-bunch-stem are C24H33NO26 and C19H29NO33 respectively. The measured higher heating values of banana pseudostem and banana fruit-bunch-stem are 15.5MJ/kg and 12.7 MJ/kg respectively. By chemical analysis, the lignin, cellulose, and hemicellulose contents in the samples will also be presented. The feasibility of the banana wastes to be a feedstock for thermochemical process in comparison with other biomass will be discussed in this paper.

Keywords: Banana Waste, Biomass, Renewable Energy, Thermo-chemical Characteristics.

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Authors: N. Li, Y. M. Cheng

Abstract:

In this paper, the classical bearing capacity problem is re-considered from discrete element analysis. In the discrete element approach, the bearing capacity problem is considered from the elastic stage to plastic stage to rupture stage (large displacement). The bearing capacity failure mechanism of a strip footing on soil is investigated, and the influence of micro-parameters on the bearing capacity of soil is also observed. It is found that the distinct element method (DEM) gives very good visualized results, and basically coincides well with that derived by the classical methods.

Keywords: Bearing capacity, distinct element method, failure mechanism, large displacement.

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Authors: Theodosia Prodromou

Abstract:

The article investigates how 14- to 15- year-olds build informal conceptions of inferential statistics as they engage in a modelling process and build their own computer simulations with dynamic statistical software. This study proposes four primary phases of informal inferential reasoning for the students in the statistical modeling and simulation process. Findings show shifts in the conceptual structures across the four phases and point to the potential of all of these phases for fostering the development of students- robust knowledge of the logic of inference when using computer based simulations to model and investigate statistical questions.

Keywords: Inferential reasoning, learning, modelling, statistical inference, simulation.

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Authors: Jung–Min Yang

Abstract:

In this paper, fault recovery for parallel interconnected asynchronous sequential machines is studied. An adversarial input can infiltrate into one of two submachines comprising parallel composition of the considered asynchronous sequential machine, causing an unauthorized state transition. The control objective is to elucidate the condition for the existence of a corrective controller that makes the closed-loop system immune against any occurrence of adversarial inputs. In particular, an efficient existence condition is presented that does not need the complete modeling of the interconnected asynchronous sequential machine.

Keywords: Asynchronous sequential machines, parallel composition, corrective control, fault tolerance.

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Authors: Jonah Gamba

Abstract:

In this paper the problem of estimating the time delay between two spatially separated noisy sinusoidal signals by system identification modeling is addressed. The system is assumed to be perturbed by both input and output additive white Gaussian noise. The presence of input noise introduces bias in the time delay estimates. Normally the solution requires a priori knowledge of the input-output noise variance ratio. We utilize the cascade of a self-tuned filter with the time delay estimator, thus making the delay estimates robust to input noise. Simulation results are presented to confirm the superiority of the proposed approach at low input signal-to-noise ratios.

Keywords: LMS algorithm, Self-tuned filter, Systemidentification, Time delay estimation, .

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Authors: Vishal Awasthi, Krishna Raj

Abstract:

In this paper, firstly, we present the mathematical modeling of finite impulse response (FIR) filter and Cascaded Integrator Comb (CIC) filter for sampling rate reduction and then an extension of Canonical signed digit (CSD) based efficient structure is presented in framework using hybrid signed digit (HSD) arithmetic. CSD representation imposed a restriction that two non-zero CSD coefficient bits cannot acquire adjacent bit positions and therefore, represented structure is not economical in terms of speed, area and power consumption. The HSD based structure gives optimum performance in terms of area and speed with 37.02% passband droop compensation.

Keywords: Multirate filtering, compensation theory, CIC filter, compensation filter, signed digit arithmetic, canonical signed digit.

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Authors: Abdelghani Dendouga, Nour-Eddine Bouguechal, Souhil Kouda, Samir Barra

Abstract:

A behavioral model of a second order switchedcapacitor Sigma-Delta modulator is presented. The purpose of this work is the presentation of a behavioral model of a second order switched capacitor ΣΔ modulator considering (Error due to Clock Jitter, Thermal noise Amplifier Noise, Amplifier Slew-Rate, Non linearity of amplifiers, Gain error, Charge Injection, Clock Feedthrough, and Nonlinear on-resistance). A comparison between the use of MOS switches and the use transmission gate switches use is analyzed.

Keywords: Charge injection, clock feed through, Sigma Deltamodulators, Sigma Delta non-idealities, switched capacitor.

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Authors: Hans H. Diel

Abstract:

A computer model of Quantum Theory (QT) has been developed by the author. Major goal of the computer model was support and demonstration of an as large as possible scope of QT. This includes simulations for the major QT (Gedanken-) experiments such as, for example, the famous double-slit experiment. Besides the anticipated difficulties with (1) transforming exacting mathematics into a computer program, two further types of problems showed up, namely (2) areas where QT provides a complete mathematical formalism, but when it comes to concrete applications the equations are not solvable at all, or only with extremely high effort; (3) QT rules which are formulated in natural language and which do not seem to be translatable to precise mathematical expressions, nor to a computer program. The paper lists problems in all three categories and describes also the possible solutions or circumventions developed for the computer model.

Keywords: Computability, Foundation of Quantum Mechanics, Measurement Process, Modeling.

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Authors: D. Almazo, M. Toledo, C. Rodríguez

Abstract:

This work presents a methodology for the design and manufacture of propellers oriented to the experimental verification of theoretical results based on the combined model. The design process begins by using algorithms in Matlab which output data contain the coordinates of the points that define the blade airfoils, in this case the NACA 6512 airfoil was used. The modeling for the propeller blade was made in NX7, through the imported files in Matlab and with the help of surfaces. Later, the hub and the clamps were also modeled. Finally, NX 7 also made possible to create post-processed files to the required machine. It is possible to find the block of numbers with G & M codes about the type of driver on the machine. The file extension is .ptp. These files made possible to manufacture the blade, and the hub of the propeller.

Keywords: Airfoil, CAM, manufacturing, mathematical algorithm, numeric control, propeller design, simulation.

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Authors: Marco Hemmerling

Abstract:

The paper outlines the relevance of computational geometry within the design and production process of architecture. Based on two case studies, the digital chain - from the initial formfinding to the final realization of spatial concepts - is discussed in relation to geometric principles. The association with the fascinating complexity that can be found in nature and its underlying geometry was the starting point for both projects presented in the paper. The translation of abstract geometric principles into a three-dimensional digital design model – realized in Rhinoceros – was followed by a process of transformation and optimization of the initial shape that integrated aesthetic, spatial and structural qualities as well as aspects of material properties and conditions of production.

Keywords: Architecture, Computer Aided Architectural Design, 3D-Modeling, Rapid Prototyping, CAD/CAM.

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Authors: Peter Pfeifer, Julian Pfeifer, Niko Pfeifer

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Information processing is at the focus of brain and cognition research. This work has a different perspective, it starts with behaviors. The detailed analysis of behaviors leads to the discovery that a significant proportion of them are based on only five basic drives. These basic drives are combinable, and the combinations result in the diversity of human behavior and thinking. The key elements are drive memories. They collect memories of drive-related situations and feelings. They contain variations of basic drives in numerous areas of life and build combinations with different meanings depending on the area. Human thinking could be explained with variations on these nested combinations of basic drives.

Keywords: Cognitive modeling, psycholinguistics, psychology, psychophysiology of cognition.

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Authors: Costin Pribeanu, Rytis Vilkonis, Dragoş Daniel Iordache

Abstract:

User interaction components of Augmented Reality (AR) systems have to be tested with users in order to find and fix usability problems as early as possible. In this paper we will report on a user-centered design approach for AR systems following the experience acquired during the design and evaluation of a software prototype for an AR-based educational platform. In this respect we will focus on the re-design of the user task based on the results from a formative usability evaluation. The basic idea of our approach is to describe task scenarios in a tabular format, to develop a task model in a task modeling environment and then to simulate the execution.

Keywords: AR-based educational systems, task-based design, usability evaluation.

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