S3++ 2009

Višnjan, July 19th - July 29th

Projects Workshops Lectures


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 Štafa

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.

Bacterial batteries or how to get electricity from mud

If someone would told you to mix a fistful of mud, a pint of wastewater and put some graphite sticks in it, the first thought might be that someone is giving you the recipe for the world's best mud soup. Witchcraft is not at work here, but instead an eco-battery that can power small electronic devices by converting waste to electricity. The magic machines able to perform this intriguing transformation are single-cell organisms living everywhere around us – Their Majesties Bacteria. Bacteria convert a substrate such as glucose, acetate but also waste water into CO2, protons and electrons. These electrons can be transferred to an insoluble acceptor (electrode) and based on this ability bacterial batteries or microbial fuel cells (MFC) have been developed. Microorganisms with direct electron transfer to the anodes of microbial fuel cells, called electricigens, proved to be the most efficient in electricity production. Electricigens are usually naturally metal-reducing bacteria – „rust breathers“.

During the workshop, construction of several MFCs is planned and investigation of productivity under different conditions (varying electrodes, bacteria strains, food, inhibitors). For comparison, in making MFCs should be used both familiar bacterial sorts and those obtained from sediment samples collected by attendants in local creek . Some other features of electricigens will also be investigate, like the ability of reducing metals, using methods of analytical chemistry. Main goal is to achieve understanding bio- and electrochemical principals of MFC, as well to find optimal conditions for maximum power output in given circumstances.

Karmen Čondić - Jurkić

Karmen works as PhD student at Ruđer Bošković Institute in Zagreb, after finishing her undergraduate studies in chemistry. Her research interests lie in the field of computational chemistry, in particular, modeling of enzyme reactions and processes.

Studying cosmic muons using scintillation detectors

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 Đurđević

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 Matanović

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 Panov

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.


Research swapshop

Miracle of Aspirin

Aspirin or acetylsalicylic acid is probably most important drug ever discovered. In this swapshop we will try to synthesize our own aspirin.

Swapshop leader: Dejan Radanović, Faculty of pharmacy and biochemistry, University of Zagreb

Hard Rock Water

Hardness in water is defined as the presence of multivalent cations. Our task will be to determine them and to calculate their exact quantities in various samples of water.

Swapshop leader: Marko Viskić, Faculty of chemical engineering and technology, University of Zagreb

Chocolate Chemistry - Theobromine

Theobromine is often considered as an important biological active substance in chocolate. Our mission is to estimate how much theobromine chocolate samples contain and of course, we'll taste them a little.

Swapshop leader: Željka Majić, Faculty of science, University of Zagreb

Introduction to Computer Science

Computer science offers powerful tools for solving problems natural sciences and mathematics. We will look at the basic concepts of computation and reasoning, and later dive into programming in Python

Swapshop leader: Tibor Pakozdi, Jacobs University Bremen

World of DNA in a homemade lab

We have all heard about DNA, a molecule so exciting to scientists because of its role as the hereditary material in living organisms. In order to learn the basics about its structure and properties, we will make our own homemade lab for isolation and gel electrophoresis of DNA.

Swapshop leaders: Matilda Maleš and Petra Krznar, Faculty of Science, University of Zagreb


Robotics workshop

We will construct a computer-controlled robotized PCR machine. PCR is a method used to 'photocopy' genetic material and is often applied in forensics and in the life sciences. Every student will get to participate in this workshop that will involve robot assembly and interfacing with the computer via simple programs written in Basic.

Leaders: Damjan Pelc (Faculty of Science, University of Zagreb) and Marin Lukas (Faculty of Mechanical Engineering and Naval Arhitecture, University of Zagreb)

Communications workshop

Every performer has to face stage fright or performance anxiety of some degree. How to handle this fear and how to become a good performer are the major points adressed in this workshop. Knowing how to behave during public presentation in a hall or on TV/radio are valuable skills that you’ll need in your scientific career. Learn today, use tomorrow…

Leader: Marko Košiček (Rudjer Boskovic Institute, Zagreb)


Kristina Majsec (University of Zagreb, Croatia): Cytoskeleton - a highway to cancer treatment

Fran Supek (Rudjer Boskovic Institute, Croatia): Presentation of scientific results

Miljen Martic (Novartis, Switzerland): PET:Interactive case study

Jakov Ivkovic (Univeristy of Zagreb, Croatia): The small cute electrocute

Nives Skunca (Rudjer Boskovic Institute, Croatia): Molecular gastronomy: the science behing your lunch

Jarah Evslin (SISSA, Italy): Black holes and the big bang

Jelena Repar (Rudjer Boskovic Institute, Croatia): Matter of life and death: How Deinococcus radiodurans survives extreme irradiation

Physical Department, University of Rijeka: The MAGIC telescopes - Eyes for the extreme universe