Grid Computing in Physics and Life Sciences

Certain sciences such as physics, chemistry or biology, have a strong computational aspect and use computing infrastructures to advance their scientific goals. Often, high performance and/or high throughput computing infrastructures such as clusters and computational Grids are applied to satisfy computational needs. In addition, these sciences are sometimes characterised by scientific collaborations requiring resource sharing which is typically provided by Grid approaches. In this article, I discuss Grid computing approaches in High Energy Physics as well as in bioinformatics and highlight some of my experience in both scientific domains.

Traffic Signal Design and Simulation for Vulnerable Road Users Safety and Bus Preemption

Mostly, pedestrian-car accidents occurred at a signalized interaction is because pedestrians cannot across the intersection safely within the green light. From the viewpoint of pedestrian, there might have two reasons. The first one is pedestrians cannot speed up to across the intersection, such as the elders. The other reason is pedestrians do not sense that the signal phase is going to change and their right-of-way is going to lose. Developing signal logic to protect pedestrian, who is crossing an intersection is the first purpose of this study. Another purpose of this study is improving the reliability and reduce delay of public transportation service. Therefore, bus preemption is also considered in the designed signal logic. In this study, the traffic data of the intersection of Chong-Qing North Road and Min-Zu West Road, Taipei, Taiwan, is employed to calibrate and validate the signal logic by simulation. VISSIM 5.20, which is a microscopic traffic simulation software, is employed to simulate the signal logic. From the simulated results, the signal logic presented in this study can protect pedestrians crossing the intersection successfully. The design of bus preemption can reduce the average delay. However, the pedestrian safety and bus preemptive signal will influence the average delay of cars largely. Thus, whether applying the pedestrian safety and bus preemption signal logic to an isolated intersection or not should be evaluated carefully.

Minimum Fluidization Velocities of Binary-Solid Mixtures: Model Comparison

An accurate prediction of the minimum fluidization velocity is a crucial hydrodynamic aspect of the design of fluidized bed reactors. Common approaches for the prediction of the minimum fluidization velocities of binary-solid fluidized beds are first discussed here. The data of our own careful experimental investigation involving a binary-solid pair fluidized with water is presented. The effect of the relative composition of the two solid species comprising the fluidized bed on the bed void fraction at the incipient fluidization condition is reported and its influence on the minimum fluidization velocity is discussed. In this connection, the capability of packing models to predict the bed void fraction is also examined.

Heterogeneous Artifacts Construction for Software Evolution Control

The software evolution control requires a deep understanding of the changes and their impact on different system heterogeneous artifacts. And an understanding of descriptive knowledge of the developed software artifacts is a prerequisite condition for the success of the evolutionary process. The implementation of an evolutionary process is to make changes more or less important to many heterogeneous software artifacts such as source code, analysis and design models, unit testing, XML deployment descriptors, user guides, and others. These changes can be a source of degradation in functional, qualitative or behavioral terms of modified software. Hence the need for a unified approach for extraction and representation of different heterogeneous artifacts in order to ensure a unified and detailed description of heterogeneous software artifacts, exploitable by several software tools and allowing to responsible for the evolution of carry out the reasoning change concerned.

A Hidden Dimension in Site Planning: Exploring Affective Experience as Part of Sense of Place on the Farm Kromdraai, Vredefort Dome World Heritage Site, South Africa

Uniqueness and distinctiveness of localities (referred to as genius loci or sense of place) are important to ensure people-s identification with their locality. Existing frameworks reveals that the affective dimension of environments is rarely mentioned or explored and limited public participation was used in constructing the frameworks. This research argues that the complexity of sense of place would be recognised and appropriate planning guidelines formulated by exploring and integrating the affective dimension of a site. Aims of the research therefore are to (i) explore relational dimensions between people and a natural rural landscape, (ii) to implement a participatory approach to obtain insight into different relational dimensions, and (ii) to concretise socio-affective relational dimensions into site planning guidelines. A qualitative, interdisciplinary research approach was followed and conducted on the farm Kromdraai, Vredefort Dome World Heritage Site. In essence the first phase of the study reveals various affective responses and projections of personal meanings. The findings in phase 1 informed the second phase, to involve people from various disciplines and different involvement with the area to make visual presentations of appropriate planning and design of the site in order to capture meanings of the interactions between people and their environment. Final site planning and design guidelines were formulated, based on these. This research contributed to provide planners with new possibilities of exploring the dimensions between people and places as well as to develop appropriate methods for participation to obtain insight into the underlying meanings of sites.

A Hybrid Classification Method using Artificial Neural Network Based Decision Tree for Automatic Sleep Scoring

In this paper we propose a new classification method for automatic sleep scoring using an artificial neural network based decision tree. It attempts to treat sleep scoring progress as a series of two-class problems and solves them with a decision tree made up of a group of neural network classifiers, each of which uses a special feature set and is aimed at only one specific sleep stage in order to maximize the classification effect. A single electroencephalogram (EEG) signal is used for our analysis rather than depending on multiple biological signals, which makes greatly simplifies the data acquisition process. Experimental results demonstrate that the average epoch by epoch agreement between the visual and the proposed method in separating 30s wakefulness+S1, REM, S2 and SWS epochs was 88.83%. This study shows that the proposed method performed well in all the four stages, and can effectively limit error propagation at the same time. It could, therefore, be an efficient method for automatic sleep scoring. Additionally, since it requires only a small volume of data it could be suited to pervasive applications.

Action Potential Propagation in Inhomogeneous 2D Mouse Ventricular Tissue Model

Heterogeneous repolarization causes dispersion of the T-wave and has been linked to arrhythmogenesis. Such heterogeneities appear due to differential expression of ionic currents in different regions of the heart, both in healthy and diseased animals and humans. Mice are important animals for the study of heart diseases because of the ability to create transgenic animals. We used our previously reported model of mouse ventricular myocytes to develop 2D mouse ventricular tissue model consisting of 14,000 cells (apical or septal ventricular myocytes) and to study the stability of action potential propagation and Ca2+ dynamics. The 2D tissue model was implemented as a FORTRAN program code for highperformance multiprocessor computers that runs on 36 processors. Our tissue model is able to simulate heterogeneities not only in action potential repolarization, but also heterogeneities in intracellular Ca2+ transients. The multicellular model reproduced experimentally observed velocities of action potential propagation and demonstrated the importance of incorporation of realistic Ca2+ dynamics for action potential propagation. The simulations show that relatively sharp gradients of repolarization are predicted to exist in 2D mouse tissue models, and they are primarily determined by the cellular properties of ventricular myocytes. Abrupt local gradients of channel expression can cause alternans at longer pacing basic cycle lengths than gradual changes, and development of alternans depends on the site of stimulation.

A Fast Block-based Evolutional Algorithm for Combinatorial Problems

The problems with high complexity had been the challenge in combinatorial problems. Due to the none-determined and polynomial characteristics, these problems usually face to unreasonable searching budget. Hence combinatorial optimizations attracted numerous researchers to develop better algorithms. In recent academic researches, most focus on developing to enhance the conventional evolutional algorithms and facilitate the local heuristics, such as VNS, 2-opt and 3-opt. Despite the performances of the introduction of the local strategies are significant, however, these improvement cannot improve the performance for solving the different problems. Therefore, this research proposes a meta-heuristic evolutional algorithm which can be applied to solve several types of problems. The performance validates BBEA has the ability to solve the problems even without the design of local strategies.

Entanglement-based Quantum Computing by Diagrams of States

We explore entanglement in composite quantum systems and how its peculiar properties are exploited in quantum information and communication protocols by means of Diagrams of States, a novel method to graphically represent and analyze how quantum information is elaborated during computations performed by quantum circuits. We present quantum diagrams of states for Bell states generation, measurements and projections, for dense coding and quantum teleportation, for probabilistic quantum machines designed to perform approximate quantum cloning and universal NOT and, finally, for quantum privacy amplification based on entanglement purification. Diagrams of states prove to be a useful approach to analyze quantum computations, by offering an intuitive graphic representation of the processing of quantum information. They also help in conceiving novel quantum computations, from describing the desired information processing to deriving the final implementation by quantum gate arrays.

A Fully Parallel Reverse Converter

The residue number system (RNS) is popular in high performance computation applications because of its carry-free nature. The challenges of RNS systems design lie in the moduli set selection and in the reverse conversion from residue representation to weighted representation. In this paper, we proposed a fully parallel reverse conversion algorithm for the moduli set {rn - 2, rn - 1, rn}, based on simple mathematical relationships. Also an efficient hardware realization of this algorithm is presented. Our proposed converter is very faster and results to hardware savings, compared to the other reverse converters.

The Effects of Visual Elements and Cognitive Styles on Students Learning in Hypermedia Environment

One of the major features of hypermedia learning is its non-linear structure, allowing learners, the opportunity of flexible navigation to accommodate their own needs. Nevertheless, such flexibility can also cause problems such as insufficient navigation and disorientation for some learners, especially those with Field Dependent cognitive styles. As a result students learning performance can be deteriorated and in turn, they can have negative attitudes with hypermedia learning systems. It was suggested that visual elements can be used to compensate dilemmas. However, it is unclear whether these visual elements improve their learning or whether problems still exist. The aim of this study is to investigate the effect of students cognitive styles and visual elements on students learning performance and attitudes in hypermedia learning environment. Cognitive Style Analysis (CSA), Learning outcome in terms of pre and post-test, practical task, and Attitude Questionnaire (AQ) were administered to a sample of 60 university students. The findings revealed that FD students preformed equally to those of FI. Also, FD students experienced more disorientation in the hypermedia learning system where they depend a lot on the visual elements for navigation and orientation purposes. Furthermore, they had more positive attitudes towards the visual elements which escape them from experiencing navigation and disorientation dilemmas. In contrast, FI students were more comfortable, did not get disturbed or did not need some of the visual elements in the hypermedia learning system.

On the Parameter Optimization of Fuzzy Inference Systems

Nowadays, more engineering systems are using some kind of Artificial Intelligence (AI) for the development of their processes. Some well-known AI techniques include artificial neural nets, fuzzy inference systems, and neuro-fuzzy inference systems among others. Furthermore, many decision-making applications base their intelligent processes on Fuzzy Logic; due to the Fuzzy Inference Systems (FIS) capability to deal with problems that are based on user knowledge and experience. Also, knowing that users have a wide variety of distinctiveness, and generally, provide uncertain data, this information can be used and properly processed by a FIS. To properly consider uncertainty and inexact system input values, FIS normally use Membership Functions (MF) that represent a degree of user satisfaction on certain conditions and/or constraints. In order to define the parameters of the MFs, the knowledge from experts in the field is very important. This knowledge defines the MF shape to process the user inputs and through fuzzy reasoning and inference mechanisms, the FIS can provide an “appropriate" output. However an important issue immediately arises: How can it be assured that the obtained output is the optimum solution? How can it be guaranteed that each MF has an optimum shape? A viable solution to these questions is through the MFs parameter optimization. In this Paper a novel parameter optimization process is presented. The process for FIS parameter optimization consists of the five simple steps that can be easily realized off-line. Here the proposed process of FIS parameter optimization it is demonstrated by its implementation on an Intelligent Interface section dealing with the on-line customization / personalization of internet portals applied to E-commerce.

Assessment of Resistance of Wheat Genotypes (T. aestivum and T. durum) To Boron Toxicity

Research on the boron (B) toxicity problems had recently considerable relation, especially in the dry regions of the world. Development of resistant varieties to B toxicity is a high priority on these regions, where the soils have high levels of B. Thus, this study aimed to assessment the resistance of wheat genotypes to B toxicity using the agronomic and physiologic parameters. For this aim, a pot experiment, based on a completely randomized design with three replications, was conducted using the soil of calcareous usthochrepts. In the study, twenty different wheat genotypes of T. aestivum and T. Durum were used. Boron fertilizer at the levels of 0 (-B), 30 mg B kg-1 (+B) as H3BO3 was applied to the pots. After harvest, plant dry matter yield was recorded, and total B concentrations in tops of wheat plants were determined. The results have revealed the existence of a large genotypic variation among wheat genotypes to their physiologic and agronomic susceptibility to B toxicity.

State-Space PD Feedback Control

A challenged control problem is when the performance is pushed to the limit. The state-derivative feedback control strategy directly uses acceleration information for feedback and state estimation. The derivative part is concerned with the rateof- change of the error with time. If the measured variable approaches the set point rapidly, then the actuator is backed off early to allow it to coast to the required level. Derivative action makes a control system behave much more intelligently. A sensor measures the variable to be controlled and the measured in formation is fed back to the controller to influence the controlled variable. A high gain problem can be also formulated for proportional plus derivative feedback transformation. Using MATLAB Simulink dynamic simulation tool this paper examines a system with a proportional plus derivative feedback and presents an automatic implementation of finding an acceptable controlled system. Using feedback transformations the system is transformed into another system.

Robust Stability in Multivariable Neural Network Control using Harmonic Analysis

Robust stability and performance are the two most basic features of feedback control systems. The harmonic balance analysis technique enables to analyze the stability of limit cycles arising from a neural network control based system operating over nonlinear plants. In this work a robust stability analysis based on the harmonic balance is presented and applied to a neural based control of a non-linear binary distillation column with unstructured uncertainty. We develop ways to describe uncertainty in the form of neglected nonlinear dynamics and high harmonics for the plant and controller respectively. Finally, conclusions about the performance of the neural control system are discussed using the Nyquist stability margin together with the structured singular values of the uncertainty as a robustness measure.

Analysis of the Visual Preference of Patterns in Pedestrian Roads

The purpose of this study is to analyze the visual preference of patterns in pedestrian roads. In this study, animation was applied for the estimation of dynamic streetscape. Six patterns of pedestrian were selected in order to analyze the visual preference. The shapes are straight, s-curve, and zigzag. The ratio of building's height and road's width are 2:1 and 1:1. Twelve adjective pairs used in the field investigation were selected from adjectives which are used usually in the estimation of streetscape. They are interesting-boring, simple-complex, calm-noisy, open-enclosed, active-inactive, lightly-depressing, regular-irregular, unique-usual, rhythmic-not rhythmic, united-not united, stable-unstable, tidy-untidy. Dynamic streetscape must be considered important in pedestrian shopping mall and park because it will be an attraction. So, s-curve pedestrian road, which is the most beautiful as a result of this study, should be designed in this area. Also, the ratio of building's height and road's width along pedestrian road should be reduced.

Structural Sustainability Techniques for RC High Rise Buildings

Over the early years of the 21st century, cities throughout the Middle East, particularly in the Gulf region have expanded more rapidly than ever before. Given the presence of a large volume of high-rise buildings allover the region, the local authority aims to set a new standard for sustainable development; with an integrated approach to maintain a balance between economy, quality, environmental protection and safety of life. In the very near future, as mandatory requirements, sustainability will be the criteria that should be included in all building projects. It is well known in the building sustainability topics that structural design engineers do not have a key role in this matter. In addition, the LEED (Leadership in Energy and Environmental Design) has looked almost exclusively on the environmental components and materials specifications. The objective of this paper is to focus and establish groundwork for sustainability techniques and applications related to the RC high-rise buildings design, from the structural point of view. A set of recommendations related to local conditions, structural modeling and analysis is given, and some helpful suggestions for structural design team work are addressed. This paper attempts to help structural engineers in identifying the building sustainability design, in order to meet local needs and achieve alternative solutions at an early stage of project design.

Study on the Production of Chromite Refractory Brick from Local Chromite Ore

Chromite is one of the principal ore of chromium in which the metal exists as a complex oxide (FeO.Cr2O3).The prepared chromite can be widely used as refractory in high temperature applications. This study describes the use of local chromite ore as refractory material. To study the feasibility of local chromite, chemical analysis and refractoriness are firstly measured. To produce chromite refractory brick, it is pressed under a press of 400 tons, dried and fired at 1580°C for fifty two hours. Then, the standard properties such as cold crushing strength, apparent porosity, apparent specific gravity, bulk density and water absorption that the chromite brick should possess were measured. According to the results obtained, the brick made by local chromite ore was suitable for use as refractory brick.

Relationship between Food Resources and Brooding Site by Asiatic Houbara (Chlamydotis macqueenii ) in Central Steppe of Iran

Knowledge of food resource of the houbara which an endangered species would be a important step toward the preservation of this bird. Adequate study has not been done in this field and therefore the food sources of the houbara during the brooding season was studied in the central steppe of Iran. In order to determine the density of insect in plant communities the pitfall trap was used , positioned in five linear transects divided between plant communities and in two repetitions. The results showed that the among communities there was a significant difference in term of the number beetles and ants ( p= 0.01, F2, 29= 4.66) collectively. Also bush steppe habitat had a higher arthropoda density in comparison with the shrub steppe habitat. Considering that most houbara nests were found in the bush steppe habitat .It seems this habitat provides the most available food supply for the houbara chicks.

Measuring the Structural Similarity of Web-based Documents: A Novel Approach

Most known methods for measuring the structural similarity of document structures are based on, e.g., tag measures, path metrics and tree measures in terms of their DOM-Trees. Other methods measures the similarity in the framework of the well known vector space model. In contrast to these we present a new approach to measuring the structural similarity of web-based documents represented by so called generalized trees which are more general than DOM-Trees which represent only directed rooted trees.We will design a new similarity measure for graphs representing web-based hypertext structures. Our similarity measure is mainly based on a novel representation of a graph as strings of linear integers, whose components represent structural properties of the graph. The similarity of two graphs is then defined as the optimal alignment of the underlying property strings. In this paper we apply the well known technique of sequence alignments to solve a novel and challenging problem: Measuring the structural similarity of generalized trees. More precisely, we first transform our graphs considered as high dimensional objects in linear structures. Then we derive similarity values from the alignments of the property strings in order to measure the structural similarity of generalized trees. Hence, we transform a graph similarity problem to a string similarity problem. We demonstrate that our similarity measure captures important structural information by applying it to two different test sets consisting of graphs representing web-based documents.