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Projects

School is organized into projects. For a short description of each project and project leaders' biographies, see below.

• The Ames test - mutations in reverse gear (web-report)
• Studying cosmic muons using scintillation detectors (web-report)
• Will hydrogen be caged in your future fuel tank? (web-report)
• Intelligent Data Analysis – From Data to Knowledge (web-report)
• Remotely Operated Underwater Vehicle (web-report)

The Ames test - mutations in reverse gear

Mutations as hereditary changes in genetic material can occur spontaneously or they can be induced by different physical or chemical agents. Although they are the driving force of the evolution they can also lead to sterility in germ line or to development of cancers. In our everyday life we are exposed to number of different chemicals and drugs that had to be tested for their potential to cause mutations. One of the fastest tests is the Ames mutagenicity assay that uses a set of Salmonella strains that have defined mutations in various genes encoding proteins involved in histidine biosynthesis. While these cells can not grow on a media lacking histidine, cells in which the reversal of the defined mutation occurred can. If an investigated chemical is a mutagen, the number of revertants will increase in a dose related manner. Although this is a bacterial test, it has been shown that most of the chemicals that were mutagenic in Ames assay also exhibit rodent mutagenicity.
In this project students will learn basics of microbiology, molecular genetics and toxicology. Students will make growth curves of Salmonella strains and they will perform genetic analysis to confirm the genotype of strains that will be used for mutagenicity testing. At the end, students will determine toxicity and mutagenicity of different chemicals.

Anamarija is a doctoral student at the Laboratory for Biology and Microbial Genetics at Faculty of Food Technology and Biotechnology in Zagreb, Croatia. Her research interests include molecular genetics, genetic recombination and gene targeting.

Cosmic rays are high energy particles originating from space that strike the earth from all directions. Most of these particles come from sources within our galaxy and the Sun. They are mostly hydrogen and helium nuclei, although electrons and heavier elements are also present. These particles collide with other particles in the Earth's atmosphere, mainly oxygen and nitrogen molecules, and produce a shower of secondary particles, mostly pions and kaons which then decay into muons. It is these muons, along with electrons, positrons and photons, which are also produced by the shower, that we detect with ground based detectors. Cosmic rays have been very important in the development of particle physics before particle accelerators and led to the discovery of subatomic particles including the positron and muon.
The students will construct a scintillation detector to detect cosmic rays and use it to study the properties of cosmic muons such as their speed, lifetime and angular distribution and using their results try to determine why we detect muons on the ground. The necessary concepts of particle physics, data acquisition and data analysis will also be covered.

Branko is an undergraduate physics student at the Faculty of Science, University of Zagreb. He has participated in the S3 since 2004 first as a student, then as a technical assistant and a leader of the 'Research Swapshop', and finally as a school organizer. His interests include particle physics, cosmology and education.

Will hydrogen be caged in your future fuel tank?

The eventual utilization of hydrogen as the fuel of the future depends critically on the development of new materials which can store large amounts of hydrogen safely and reversibly under near-ambient conditions. One such possibility are a new class of solid materials which contain numerous pores, or cavities, in which hydrogen molecules can be effectively bound for application in hydrogen storage. In this project students will use some computational approaches to investigate the ability of different molecular compounds to adsorb and store hydrogen. More specifically, your studies will focus on certain nanostructured carbon materials such as fullerenes or carbon nanotubes as well as clathrate hydrates, where hydrogen molecules are trapped inside polyhedral cages formed by frozen water molecules.
In the course of the project students will learn about the nature of the interactions between hydrogen and the molecules that constitute the host material and describe these in a manner suitable for computational studies. They will subsequently be instructed in the use of the computer codes for perfoming Monte Carlo simulations and explore energetics, locations and populations of hydrogen molecules in the various cages. Students will learn how to interpret the results and draw their own conclusions about the viability of the materials investigated for hydrogen storage.

Ivana is a postdoctoral researcher at Department of Chemistry, New York University.  She obtained her Ph.D. working in a Theoretical Chemistry Group at Ruđer Bošković Institute in Zagreb and Free University Berlin. Her work is mainly motivated by the understanding of quantum dynamics of hydrogen bonded systems.

Intelligent Data Analysis – From Data to Knowledge

Data analysis is a process of gathering, modeling, and transforming data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making. Data analysis has multiple facets, encompassing diverse techniques under a variety of names, in different business, science, and social science domains.
In this project the students will get knowledgeable about the process of intelligent data analysis by using artificial intelligence methods. We will learn the basic approaches and techniques in data analysis working on real life data from different domains, such as marketing (e.g. detect what products are bought together in a supermarket), medicine (e.g. predicting if a patient has some disease or not ) and ecology (e.g. predicting burned areas in forest fires). We will employ several data analysis software toolboxes: WEKA, ORANGE and KNIME. We will then explore inside these highly modular and easy to learn toolboxes, modify existing methods and try to program our own methods by using Java or Python computer languages. After the basics of data analysis are covered, we will deal with more complex data analysis like: analysis of text and analysis of social networks. One text analysis task would include automatic grouping of text documents (e.g. news articles, contents of blogs) into smaller groups according to the contents of the documents, and another task would be to learning to recognize whether a document belongs in one category or another. Social network analysis deals with analysis of the relationships and flows between people, groups, organizations, computers, web sites etc. A task for social network analysis could be for example analysis of person's friendships in Facebook or MySpace. For this purpose we will use software for visualizing large document collections Document Atlas and software for analysis of large networks Pajek .

Panče is a research assistant at Jožef Stefan Institute in Ljubljana, Slovenia, and PhD student at the Jožef Stefan International Postgraduate School. His research interests are in the domain of data mining and knowledge discovery from databases, knowledge representation and ontology engineering.

Remotely Operated Underwater Vehicle

Remotely operated underwater vehicles (usually referred to as ROVs) are small unmanned underwater robots designed for high risk environmental missions in science and technology. They are used for wreck exploration, cable and pipeline surveillance and other purposes. A common classification of ROVs runs according to their size - a micro or mini ROV weighs less than 15 kg and only has a camera on board; workclass ROVs have different manipulators, can reach much greater depths (2000 to 7000 m) and usually perform lighter tasks, while trenching (or burial) ROVs have the strongest propulsion and manipulation systems and are used for cable laying. The importance of ROVs has been continually growing since the first military machines were constructed in the 1950's; they have notably played a crucial role in the exploration of the RMS Titanic and Bismarck wrecks. The aim of this project is to develop, design and construct a remotely operated mini-ROV equipped with a camera - a 'floating eyeball'. In the course of the project participants will learn the basics of Computer Aided Design (CAD), automation and control, electronics and microcontroller programming, as well as the relevant physics - fluid mechanics and material strength. They will construct the ROV to be fully functional and perform a surveillance mission in Porec harbour. .

Marin and Damjan are second and third year students of engineering and physics at the Zagreb University, respectively. They share interests in robotics and experimental physics, and already have participated in the S3 as project leaders last year.