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.

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.

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.

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.

Feasibility Study on Vanillin Production from Jatropha curcas Stem Using Steam Explosion as a Pretreatment

Jatropha curcas stem was analyzed for chemical compositions: 19.11% pentosan, 42.99% alphacellulose and 24.11% lignin based on dry weight of 100-g raw material. The condition to fractionate cellulose, hemicellulose and lignin in J. curcas stem using steam explosion was optimized. The procedure started from cutting J. curcas stem into small pieces and soaked in water for overnight. After that, they were steam exploded at 214 °C and 21 kg/cm2 for 5 min. The obtained hydrolysate contained 1.55 g/L ferulic acid which after that was used as substrate for vanillin production by Aspergillus niger and Pycnoporus cinnabarinus in one-step process. The maximum 0.65 g/L of vanillin were obtained with the conversion rate of 45.2% based on the initial ferulic acid.

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.

Value–based Group Decision on Support Bridge Selection

Value-based group decision is very complicated since many parties involved. There are different concern caused by differing preferences, experiences, and background. Therefore, a support system is required to enable each stakeholder to evaluate and rank the solution alternatives before engaging into negotiation with the other stakeholders. The support system is based on combination between value-based analysis, multi criteria group decision making based on satisfying options, and negotiation process based on coalition formation. This paper presents the group decision and negotiation on the selection of suitable material for a support bridge structure involving three decision makers, who are an estate manager, a project manager, and an engineer. There are three alternative solutions for the material of the support bridge structure, which are (a1) steel structure, (a2) reinforced concrete structure and (a3) wooden structure.

Children and Advertising: Issues in Consumer Socialization Process

Today advertising is actively penetrating into many spheres of our lives. We cannot imagine the existence of a lot of economic activities without advertising. That mostly concerns trade and services. Everyone of us should look better into the everyday communication and carefully consider the amount and the quality of the information we receive as well as its influence on our behaviour. Special attention should be paid to the young generation. Theoretical and practical research has proved the ever growing influence of information (especially the one contained in advertising) on a society; on its economics, culture, religion, politics and even people-s private lives and behaviour. Children have plenty of free time and, therefore, see a lot of different advertising. Though education of children is in the hands of parents and schools, advertising makers and customers should think with responsibility about the selection of time and transmission channels of child targeted advertising. The purpose of the present paper is to investigate the influence of advertising upon consumer views and behaviour of children in different age groups. The present investigation has clarified the influence of advertising as a means of information on a certain group of society, which in the modern information society is the most vulnerable – children. In this paper we assess children-s perception and their understanding of advertising.

Academic Mobbing in Turkey

People at workplace always face with stress and feel it in their lives. There are many factors that create stress and mobbing is one of them. Mobbing is a psychological terror, conducted systematically toward an individual by others at the same workplace. Mobbing started to become a famous subject last years in U.S and Europe. In Turkey, it is a new concept not because it does not occur, because of human nature that does not allow confessing it. Mobbing is being ignored by people, organizations and also government in our country. The focus of this study will be mobbing in Turkey by examining the workplace mobbing among Turkish academicians. There are other studies about mobbing in Turkey but none of them studied academy. Because mobbing methods change according to sectors and occupations, it is important to analyze each sector to understand the methods used in mobbing and the reactions of victims to these actions. The concept is analyzed in detail before focusing on mobbing at universities. This paper will be unique because there is no information about this specific subject in Turkish literature. In this paper, both qualitative and quantitative methods will be used to describe the mobbing at Turkish academic environment.

Context Modeling and Context-Aware Service Adaptation for Pervasive Computing Systems

Devices in a pervasive computing system (PCS) are characterized by their context-awareness. It permits them to provide proactively adapted services to the user and applications. To do so, context must be well understood and modeled in an appropriate form which enhance its sharing between devices and provide a high level of abstraction. The most interesting methods for modeling context are those based on ontology however the majority of the proposed methods fail in proposing a generic ontology for context which limit their usability and keep them specific to a particular domain. The adaptation task must be done automatically and without an explicit intervention of the user. Devices of a PCS must acquire some intelligence which permits them to sense the current context and trigger the appropriate service or provide a service in a better suitable form. In this paper we will propose a generic service ontology for context modeling and a context-aware service adaptation based on a service oriented definition of context.

Efficiency in Urban Governance towards Sustainability and Competitiveness of City : A Case Study of Kuala Lumpur

Malaysia has successfully applied economic planning to guide the development of the country from an economy of agriculture and mining to a largely industrialised one. Now, with its sights set on attaining the economic level of a fully developed nation by 2020, the planning system must be made even more efficient and focused. It must ensure that every investment made in the country, contribute towards creating the desirable objective of a strong, modern, internationally competitive, technologically advanced, post-industrial economy. Cities in Malaysia must also be fully aware of the enormous competition it faces in a region with rapidly expanding and modernising economies, all contending for the same pool of potential international investments. Efficiency of urban governance is also fundamental issue in development characterized by sustainability, subsidiarity, equity, transparency and accountability, civic engagement and citizenship, and security. As described above, city competitiveness is harnessed through 'city marketing and city management'. High technology and high skilled industries, together with finance, transportation, tourism, business, information and professional services shopping and other commercial activities, are the principal components of the nation-s economy, which must be developed to a level well beyond where it is now. In this respect, Kuala Lumpur being the premier city must play the leading role.

The effects of Garlic Oil (Allium sativa), Turmeric Powder (Curcuma longa Linn) and Monensin on Total Apparent Digestibility of Nutrients in Baloochi Lambs

The objective of this study was to determine the effects of garlic oil (Allium sativa), turmeric powder (Curcuma longa Linn) and Monensin on Total apparent digestibility of nutrients in Baloochi lambs. The experiment was designed as a 4 x 4 Latin square using 4 ruminally baloochi lambs with 4 treatments in four 28-d periods. Treatments were control (no additive), garlic oil (0. 4 g/d), monensin (0. 2 g/d) and turmeric powder (20 g/d). Total apparent digestibility's (% of intake) of organic matter (OM), dry matter (DM), crud protein (CP), ether extract(EE), non fiber carbohydrate (NFC), acid detergent fiber (ADF) and neutral detergent fiber (NDF) in the total tract were not influenced by addition of either additives.