S3++ 2016

Požega, July 30th - August 9th

Projects Workshops Lectures


Levitation by Electromagnetic Force

Levitation concerns pushing an object with a force, (normally) to counteract the effects of the gravitational pull on the object. Different forces can be used to produce it but the underlying principle is always the same. Various areas such as biology, civil engineering and space exploration in their research use levitation techniques. As an example, in biology optical tweezers can be used for studying microscopic cells and their constituents and in civil engineering magnetic levitating trains are being used in transportation.

This project will consist of levitating an object of small mass inside a (vacuum) chamber using various means and techniques. Students will develop a prototype of the aforementioned levitating structure and acquire theoretical background of the phenomenon, with focus on the development of an experimental prototype.

Davor Zaluški
University of Zagreb, Croatia

Davor Zaluški, Ph.D. graduated from University of Zagreb, Faculty of Electrical Engineering and Computing. His research areas are electromagnetics and metamaterials. His hobbies include playing chess, and going to the gym.

Boris Okorn
University of Zagreb and Ruđer Bošković Institute, Croatia

Boris Okorn is a PhD student on the University of Zagreb, Faculty of electrical engineering and computing, and a research assistant on the Ruđer Bošković Institute. His area of research is nano-electromagnetics. Outside of work his interest include, but are not limited to: rowing, cycling, lindy hop, music and looking for a place to grow tomatoes. Or tomatoes... Either, neither.

Talk to a flower to become a part of the Internet

The Internet is growing everyday and new "Smart" Objects are now capable of interacting with it. We can blindly trust them or understand them and personalize them to suit our needs. We use the Internet for many of our everyday tasks without knowing how it works. Opening this black box and adapting it for new purposes is the job of computer networks researchers.

This project will be about communicating with flowers: how flowers can produce data and communicate with the Internet. We will plug some cables together, connect various sensors and make them communicate with each other. More generally, we will see how to produce data and numerical content and how all that can be integrated with the Internet. There will be discussions about Internet, privacy, open-source, and many more! We will build a prototype with easy to find products and personalize it, step-by-step, to suit our needs.

Keoma Brun
Inria-Paris, France

Keoma is 1st year PhD student at Inria-Paris. He works in developing the computer networks for sensors that communicate wirelessly. He currently studies environmental monitoring applications and would be happy to continue doing that. Aside from that, he likes to do rock-climbing, play some percussions and perpetuate the NSA conspiracy about privacy.

DNA and genetic engineering – Bioluminescent bacteria?

Have you ever seen the sea glowing? Or wondered why the fireflies glow? The answer is in the bioluminescence, which is the production and emission of light by a living organism. In order to talk about bioluminescence we have to start from the beginning, and it starts with a molecule of life – DNA. DNA molecule is built out of nucleotides and the important information arises from their sequence. The majority of information stored in human DNA consists of genes that code for proteins. Some organisms such as bacteria can be easily modified and therefore produce the proteins of interest. What will happen, if we want to make a bacteria produce a protein, the kind of protein which is involved in light emitting reaction but isn’t coded in its sequence? Is it possible that it’ll start to glow? That’s exactly what we will try to do! Observing bacterial transformation will demonstrate the power of genetic engineering. This is important because it will help us to answer many important questions using a simple example.

Our observations will demonstrate the relationship between the genetic constitution of an organism and its physical attributes and also change in phenotype. The experimental task is to create a luminescent population of bacteria by introducing a plasmid into bacteria. We will modify the bacteria to produce luciferase (the enzyme that catalyzes the light-emitting reaction) and enzymes that produce the luciferins (the substrates for the light-emitting reaction). Also we will learn about the PCR, various sterile techniques when working with bacteria, and if there is time left maybe do some side experiments!

Maja Jokić
University of Belgrade, Serbia

Maja is a third year student of Biochemistry at Faculty of Chemistry in Belgrade. She participated in Summer School of Science 2015 (S3 camp) as a swapshop leader. She is currently doing her first research project at Institute of molecular genetics and genetic engineering. In her free time, Maja enjoys reading, drawing, and playing darts with friends.

We are our choices – How do cells make decisions?

The cells in our body constantly have to adjust to us: Are you doing orts? Are you eating? Do you have a little wound? Every time something changes, cells have to adapt or protect themselves to the new situation. To be able to deal with their surroundings, cells have to make decisions constantly. And when cells do not respond correctly (when they are too fast, too slow or not responding at all) this might lead to diseases. Therefore, it is important that we understand how cells make decisions upon a changing environment.

In this project, we will use bacteria as model organisms to study cellular decision-making. We will have to use all our scientific skills to answer some of the urging questions in modern biology. For example, what will bacteria do when they are stressed? Or what will they do when they have the choice between different nutrients? Along the way and with the help of a variety of techniques from biochemistry and molecular biology, we will discover different mechanisms cells can use to adapt to their environment.

Marieke Francisca Buffing
ETH Zürich, Switzerland

Marieke studied biotechnology at Wageningen University (the Netherlands), where she also did her masters in process engineering and molecular biotechnology. During her masters she got more and more interested in the mechanisms that cells use to adapt to their environment. Now, during her PhD at ETH Zurich (Switzerland), she is trying to find out how bacterial species use different protein-metabolite interactions to make fast decisions when their environment changes. When she is not in the lab, Marieke can be mostly found in museums or running around in the forest near the campus.

Electric and magnetic guides and applications

The study of atomic and molecular ions is a major part of the field of atomic and molecular physics. Their internal quantized energy structure is applied in the area of quantum computing. Such applications rely heavily on controlling the motion of ions in laboratory conditions. The control is achieved using electric and magnetic fields, as they can easily be generated and very finely tuned to enable precise control. One such controlling device is a guide - a system of electrodes and magnets that guides an ionic cloud with a given initial velocity along a linear or curved trajectory. Though their internal nature is quantum-mechanical, their motion through the guide is well described “classically” and can be simulated according to Newton's equations, as one would do with macroscopic objects.

During the course of this project, we will build geometry of a guide using electrodes and magnets to manipulate a macroscopic projectile simulating such a process using ions in an actual physics experiment. The design of the setup will be assisted by a computer simulation in Comsol Multiphysics - a finite element simulation tool that will provide us with the necessary input for our setup. After performing the experiment, we will compare its results with the predicted outcomes and subsequently vary the configuration of the experiment. Goals of the project include introducing the concept of guiding forces in atomic and molecular physics, learning how to evaluate a physics simulation in Comsol Multiphysics, and using such simulations in designing experiments.

Matija Žeško
ETH Zürich, Switzerland

Matija received his Master’s degree in Physics from the University of Zagreb and is currently doing his PhD at ETH Zürich, developing methods of trapping highly-excited atoms and molecules. His research interests ultra-cold atoms and molecules, quantum information technology, and research of fundamental principles of quantum mechanics. Other than science, Matija is interested in teaching, reading, languages, and international politics. He volunteers for „Room to read“ and is a member of the Model United Nations society at ETH Zürich.

Genomics age: Reading and understanding our genomes

Only two decades ago, genetics, the study of genes, was considered to be amongst the most popular 'jobs of the future'. Today, we study not only genes, but also the whole genomes. We live in a genomics age. Knowing the complete genomic sequence allows novel approaches to long-standing problems. For example, studying gene networks rather than individual genes has provided novel insights into biological pathways underlying diseases. In cancer, such studies improved the diagnostic process and offered new targets for therapy. Genetic testing for rare inherited mutations, such as BRCA1 and BRCA2 mutations, has been successfully incorporated into clinical practice. Since 2005, Next Generation Sequencing technologies have enabled a >100,000-fold reduction in the cost of DNA sequencing, such that many thousands of individual human genome sequences are being generated, enabling accurate interpretation of personal genomes, particularly in the context of medical genetics.

In this project, we aim to trace genomic variations between a healthy and tumor tissue. In the first part, we will familiarize ourselves with sequencing techniques and learn to analyze their outcome: short reads. For this purpose, we will first manually align short sequences to a much longer sequence, to mimic the alignment process of short reads to a reference genome. Then, we will perform a similar task on real mithochondrial genomes coming from tumor and healthy tissues. We will perform basic quality filtering and map these reads to the reference genome. In the second stage of the project, we will identify the genomic differences between the pairs of the genomes. We will use various databases to identify the genes (and their functions) associated to the changes we observed.

Tugce Bilgin Sonay
University of Zurich, Switzerland

Tugce obtained her PhD from the University of Zurich and she still works there as a post-doctoral researcher funded by Forschungskredit, Switzerland. Her research interests focus mainly on genomic elements that underlie human and great ape phenotypic divergence, including DNA tandem repeats, gene regulation and codon evolution. Tugce taught various genomics courses and workshops. Besides science, she enjoys writing both fiction and non-fiction, cooking inspired by world cuisine recipes, modern dance and wine tasting.


Research swapshop

Asteroids affected all life on Earth, and in a way helped humans survive. How much do you know about our Solar System?

Do you know that along with the Sun and planets, our Solar system is full of asteroids, which are chunks of rock left over from the early days of its formation, or from collisions between larger objects like planets? Each day, more than 100 tons of material from asteroids and comets falls toward Earth. Agencies like NASA track asteroids, not only because they could be a threat to humanity by colliding with Earth, but because they can provide us with information about the history of our solar system, and even come handy for mining raw materials in space! In this swapshop, you will get a chance to explore some of the vast amount of data NASA has accumulated about asteroids, and use data analysis to see which new interesting facts can we learn about solar system.

Swapshop leader: Dunja Vučenović, Imperial College London, UK

Demistyfication of GMO

Genetically modified organism, a term that we often come across with, is any organism whose genetic material has been altered using various genetic engineering techniques.However, how much of the data we know about this phenomenon is actually correct ? What are the GMO products that surround us on a daily basis ? What is the story behind the Nobel rewarded concept of „Golden rice“? Which are the most commonly used methods of modification and how scientists tend to solve problems of introducing such modified organisms into the environment? If you are curious to find answers to these or any questions regarding genetically modified organisms this swapshop it just what you need! Also you will be presented with diverse GMO speciments, some of which you never considered to be genetically modified in your wildest dreams,so prepare to be amazed.

Swapshop leader: Iris Grgurina, University of Zagreb, Croatia


Ferrofluids are essentially colloidal solutions which become magnetized when exposed to a magnetic field. With a wide range of application possibilities and many more being explored they have proven to be quite the useful material in science, as well as medicine and engineering. In our workshop, we will explore the theoretical concepts behind ferrofluids and their applicability. Afterwards, students will prepare a ferrofluid and test its properties.

Swapshop leaders: Đesika Kolarić, University of Zagreb, Croatia
Lucija Bujanić, University of Zagreb, Croatia

Determination of water quality

Have you ever wondered what types of water exist? Or what differenciates one type of water from the other? You can have two cups of water that look exactly the same but one may not be for drinking. In our experiment, we will be determining what are the diferences between different water samples and what is the potential of water in global development. It will be our goal to determine how the water quality changes based on the conditions in which the water is situated in, and is it possible to repurpose waters that exclude drinking purposes. Experimental determination of water quality will be conducted using portable „on-site“ kits that give us fast and relative data of water parameters ( nitrates, chlorides, nitrites...) that determine it`s quality. Based on the parameters, quality of the water will be determined, and future potential and repurposing will be suggested. Using microscopic and spectroscopical methods, we can more thorougly describe the water`s micropopulation and concentration of ions that give input on water`s state. Theoretical knowledge will be based of preferable water components and different types, sampling and determination of measured parameters. Several measurements are to be taken to maximize the precision of results, and different water types can be analysed based on the present samples.

Swapshop leader: Pegi Pavletić, University of Rijeka, Croatia

Would you bet on it? How can probability and statistics help you!

Have you ever wondered what the probability of winning the lottery is or how many samples you should take to be certain in your results? Now you have a chance to find out. Probability and statistics are the fields of applied mathematics and are used in almost any other scientific discipline. They won’t tell you the future, but you will certainly know what to expect and what to bet on. You will be surprised how many things closely follow Normal (or Gauss) Distribution, from heights of people, blood pressure, errors in measurement to marks on a test. In the end you can’t escape from statistics or win the war against probability, but once you learn it you can turn the odds in your favour.

Swapshop leader: Petra Bucić, University of Zagreb, Croatia

Chloroplast Isolation

These days every major biology study needs its backup molecular research. One of the many methods in molecular biology is the isolation of chloroplasts by differential centrifugation. The protocol of chloroplasts isolation might seem too complticated since the isolation protocol consists of many long named chemicals. Yet, the application of biochemistry allows us to understand the different mechanisms of processes happening on everyday bases in a plant cell.

Swapshop leader: Dora Grbavac, University of Zagreb, Croatia
Snježana Kodba, University of Zagreb, Croatia


Lecture schedule

July 31st 2016
Toni Milun (College for Applied Computer Engineering Algebra in Zagreb,Croatia): Where maths is fun

August 1st, 2016
Matko Milin (University in Zagreb, Croatia): Space ovens: the beginning and the end of elements

August 2nd, 2016
Bas Dutilh (Utrecht University, The Netherlands): Metagenomic ventures into outer sequence space

August 5th, 2016
Matthias Klinger (AMGEN Research (Munich) GmbH, Germany): Harnessing T cells with BiTE® antibody constructs to fight cancer

August 7th, 2016
Claire Limoge Schraen (Ecole Centrale de Nantes, France): How to provide a large-scale seismic assessment to highly vulnerable masonry structures? Baroque heritage in the French Alps.

About the lecturers

Toni Milun
College for Applied Computer Engineering Algebra in Zagreb,Croatia

Toni Milun is a mathematics lecturer at the College for Applied Computer Engineering Algebra in Zagreb. In 1999 he graduated from the Faculty of Science in Zagreb and was awarded the title of professor of mathematics and physics. In 2012 he completed postgraduate specialist study of Statistical Methods for Economic Analysis and Forecasting at the Faculty of Economics and Business in Zagreb. He is currently completing a doctoral program in Business Economics at the Faculty of Economics in Rijeka. In April 2011 together with his student Nikola Mujdžić he launched a website www.tonimilun.com with more then 2,000 free video-lectures in mathematics and statistics. The project received Croatian Pride Award. Toni is the author and host of TV show Financijalac, a financial education series aimed at educating broader audiences on everyday financial matters. In his spare time, he enjoys swimming, athletics, yoga, meditation, fitness, reading books from different fields: mathematics, psychology, economics, education, etc.

Matko Milin
University in Zagreb, Croatia

Matko Milin is an experimental physicist in Croatia, and his research is mainly focused on nuclear physics and astrophysics. His scientific career started at Rudjer Boskovic Institute in Zagreb, after which he spent some time at Hahn-Meitner-Institute in Berlin. From 2010 he is assistant professor at Department of Physics of Faculty of Science in Zagreb. His scientific interest are states of light atomic nuclei and emergence of elements (“nucleosynthesis”) in different “universe scenarios”.

Bas Dutilh
Utrecht University, The Netherlands

The most interesting things in the world are ecology and evolution; Bas wants to know how these two processes have created the beautiful living world around us. Ecology and evolution interact with complex feedback loops at many levels, and the details always make fascinating stories to tell, as long as you understand them completely, and can explain them very well. He believes that the best place to study these processes are in microbiomes: the ecosystems of micro-organisms and viruses that we can find everywhere in and around us. Using the computer, Bas analyzes big datasets called metagenomes that contain lots of information about the ecology and evolution of microbiomes. In these datasets, he looks for new micro-organisms, he tries to predict how they interact with each other both ecologically and evolutionarily, and he builds models of these interactions in the computer. Only if he can model a certain process in the computer, then he is satisfied that he completely understands it. Bas studied biology and got his PhD in 2007. He currently has a small group of people working with him on questions like those described above, and he collaborates a lot with scientists from other research fields and from countries around the world.

Matthias Klinger
AMGEN Research (Munich) GmbH, Germany

Matthias Klinger is the Principal Scientist of BiTE® (bispecific T-cell engager) Immunology at Amgen Research (Munich) GmbH, Germany. While gaining his M.S. in biochemistry from the University Regensburg, Germany, Dr. Klinger also completed course work of the Graduate Immunology Program at Washington University in St. Louis, USA. Subsequently, he undertook a Ph.D. at the Interfaculty Institute of Cell Biology at Eberhard Karls University Tübingen, Germany in association with Micromet AG, a biotechnology company based in Munich. Dr. Klinger joined the faculty at Micromet AG after completing his Ph.D., becoming the Associate Director of BiTE® Immunology. He joined Amgen in 2012 and assumed his current position in 2013. Dr. Klinger’s research focuses on the mitigation of clinically important BiTE®-induced adverse drug reactions, on BiTE®-mediated T-cell signaling, and on BiTE® engineering and development.

Claire Limoge Schraen
Ecole Centrale de Nantes, France

Claire Limoge Schraen, a French architect and structural engineer, obtained a PhD in architecture and civil engineering in the LMT-ENS Cachan laboratory, at the Paris-Sclay University. During her PhD thesis, she has developped a large-scale method for the assessment of the seismic vulnerability of masonry architectural heritage, well suited to moderate seismic zones. Her work was focused on the religious baroque heritage in the French Alps, but the method can be applied to any masonry heritage. To this aim she developped tools covering a large spectrum in the earthquake engineering : discret model with rigid particles, continuous damaging macromodel, in-situ vibratory measures, modal updating of complexe models, subrogate simplified models and fragility curves. She received one of the 2014 L'Oréal-Unesco French Doctoral Fellowship for her PhD thesis. Claire is currently working as postdoctoral fellow with Pr. Kotronis in the Research Intitute in Civil Engineering and Mechanics at the Ecole Centrale de Nantes, France. They aim developping subrogate models allowing engineers to use non linear computation and obtain more accurate results even for complexe structures in a limited time.