S3 2023

Požega, July 23rd - August 2nd

Projects Workshops Lectures


Microfactories: How To Reprogram Bacteria

From biologically derived drugs to laundry detergent, more and more of the products we encounter in our day-to-day lives contain protein components. Have you ever thought about how these proteins are made on a great scale? Usually, this is done through the transformation of microorganisms like bacteria or yeast. Bacterial transformation is the process in which bacterial cells take up foreign genetic material (e.g. DNA) from their environment and incorporate it into their own genome. This allows proteins, which are encoded by DNA, to be produced in great amounts. This process is an important tool in genetic engineering, because it allows scientists to study protein function, structure and interactions. Importantly, proteins produced by bacterial transformation can also be used in therapeutic and industrial applications, including vaccine production and the development of insect-resistant crops.

In this project, we will use molecular biology techniques to reprogram the bacteria Escherichia coli and have it produce green fluorescent protein (GFP). We will purify the produced protein and take advantage of its fluorescence to observe how different experimental conditions affect protein production in our bacterial factories. By doing so, we will develop a better understanding of good laboratory practice and a range of important skills like media preparation, working under sterile conditions, gel electrophoresis and purifying proteins with chromatography. In the end, we will use GFP as a case study in online bioinformatics databases to get a greater appreciation of how gene sequence, protein structure and biological function affect one another.

Irma Komljenovic
University of Aberdeen; School of Medicine, Medical Sciences and Nutrition

Irma is a third-year molecular biology undergraduate student at the University of Aberdeen. She developed her love of science in high school by attending different summer schools (including S3!). She is most interested in the ability to modify and optimise assays to give answers to specific hypotheses and accommodate new discoveries in the field. In her free time, Irma enjoys jigsaw puzzles, embroidery, going on hikes and thrifting.

Tinca Radzichevici
University of Aberdeen; School of Medicine, Medical Sciences and Nutrition

Tinca is a third-year biotechnology student at the University of Aberdeen, originally from Moldova. Her love for biology began in high school, where she participated in projects similar to S3, both at home and in Romania. After spending her last summer at the Helmholtz Zentrum in Munich, she discovered her interest in bioinformatics and its essential role in capturing and understanding biological data. In her free time, you can find her (re)reading books, immersed in DIY projects, and preparing to run her first marathon. She also loves being in nature and exploring new places.

Elephant on the road – how do deep models handle the unexpected?

Deep models are computing systems designed to imitate the function of a human brain. They are usually trained on large amounts of data to perform different types of statistical analysis. They have shown tremendous potential for application in many different fields such as image analysis, text analysis, or medicine. Still, the good performance of deep models in controlled environments might not necessarily translate to their success in real-world settings. Take, for example, deep models intended for autonomous driving. They will most likely be trained to recognize the most common elements of driving scenes, such as cars, people, road tracks, etc. So, what happens if an elephant suddenly appears in front of the car? Our models can only classify it into one of the known classes. We could modify our training data to include elephants, but ultimately it is impossible to foresee every possible scenario. The next best thing is to equip deep models with the ability to say they do not know the correct answer. This ability of deep models to recognize potential failure is critical for their safe deployment in real-world applications.

In this project, we will train simple image classification models, test their performance on expected inputs, and see how they respond to unexpected data. We will discuss potential methods for detecting model failure and see how we can compare different models with respect to their ability to detect anomalies. We will look at possible modifications to the model and training procedure that increase robustness to unusual input. Finally, we will combine the acquired insights to produce better classification models.

Petra Bevandic
University of Zagreb, Faculty of Electrical Engineering and Computing

Petra is a last-year PhD student and teaching assistant at the Faculty of Electrical Engineering and Computing at the University of Zagreb. Her research is in the field of image analysis, primarily of road driving images. She focuses on improving model robustness for real-world applications. Currently, she is trying to figure out how to automatically connect visual concepts across multiple datasets to train general-purpose models. Outside of work, she enjoys painting, classic movies, books, yoga, and pub quizzes.

Biology crash course: All of biology in 10 days

Biology is the science of life – from free RNA, which acts like a simple computer code, to complex ecosystems that have minds of their own, it teaches us about ourselves, our environment and role in universe. The insight that biology provides allows us to create medicine, grow food, cure diseases, and develop as a species. Have you ever stopped to think about the different plants in your garden or the many sorts of critters living in the soil? Or exactly genes are and how they work? Where we come from and what we will look like in the future?

In this project, we will explore the field of biology in a very simple and creative, yet efficient manner. We will explore every subfield of biology in various ways, following the evolutionary tree of life as a guide. We will perform lab and field work – drying and determining plant species, dissecting animals and growing bacteria in a gel. Throughout the process, we will construct a mind map to better understand our samples and the intersecting subfields they represent. We will build as full as picture as possible of biology as a whole and learn how to draw scientifically, collect live samples, dissect, determine species and do sterile lab work.

Davor Merkas
University of Zagreb, Faculty of Science

Davor is a graduate student of biology, currently attending his first year of an experimental biology master’s at the Universitiy of Zagreb. His love for nature, and later biology, started at a young age, when he would spend most of his free time playing in his garden with plants and insects of all kinds. Now he spends most of his days doing research, planning projects and motivating his colleagues to chase their ideas. He considers biology a part of his identity and considers it more than just a job. So, as you can imagine, his other hobbies – like gardening, keeping house plants and insects, sci-fi movies and shows – all contain a healthy level of biology :)

Observing and modelling galaxies far-far away

It's a great time to be an astrophysicist with many telescopes producing observations that improve our knowledge of the Universe. These telescopes are giving us not only beautiful images of the sky but also probe the darkest corners of the Universe in pursuit of distant astronomical objects. As we search for more distant astrophysical objects, we are looking back in time to see the birth of galaxies. But the farther we look, more blurry observations become, and a life of an astrophysicist becomes harder. Therefore, a larger effort must be put in interpreting what we see. Additionally, far-away objects become increasingly different from our surrounding making them tough to model. Consequently, new observations can challenge our theories of how galaxies came to be and can help learn the nature of many unknowns we have, such as dark matter and dark energy and help us tell the story of our Universe.

Using observations of modern telescopes (Hubble Space Telescope or ALMA) we will look at the data and see what real galaxies look like. We will target interesting candidates that could potentially help us solve some of the astrophysical problems. Using these objects, we will use a set of standard astrophysical tools with which we can create a story about the galaxy, describing it in physical terms. Then we can put these observations in perspective with current theories and other observations. Who knows, maybe a new theory will emerge out of this project?!

Ivan Nikolic
Scuola Normale Superiore, Pisa, Italy

Ivan is a third year PhD Student at Scuola Normale Superiore in Pisa, Italy. His main research interests are interpretation of early universe observations and modelling of young galaxies. He loves to talk about astrophysics, but he‘s not very good in naming constellations. In his free time, he likes outdoor activities, running, climbing and other sports. He also likes reading, watching football and being lazy.

Have you ever seen temperature?

We are all used to acoustics in our daily lives. It is present whenever we sing, or listen to songs on the radio, or on our earphones. When you go to a concert, for example, probably you have even felt the sound waves if you stood close to the sound boxes. Since these are pressure waves, it is physically possible to see them, and it's one of the most interesting aspects of acoustics. Acoustics is one of the oldest fields in Physics, and still today new applications and new phenomena are found. In an ultrasound exam, high frequency waves (ultrasonic waves) are emitted towards specific parts of the body. By analyzing the reflected waves, cancer, clots, and other abnormalities can be diagnosed. Now, imagine you light a candle. When you put your hands hands close to it, it is possible to also feel the heat coming out of it. This heat propagates and oscillates air particles around, and this is what you feel. Now, is it possible to see temperature as well?

In this project, you will learn everything about different oscillating systems such as a simple harmonic oscillator, an oscillating membrane that produces patterns of Lissajous figures, and, finally, be able to construct a system to see temperature variations. This is the goal of this workshop. To get to this point, you will learn how to build and troubleshoot simple and complex physics experiments (experiment design), how to make image processing, video analysis, and make experimental variations to test different hypotheses.

Matheus Azevedo Silva Pessôa
Physics Department, McGill University, Canada

Matheus is a physics PhD student from McGill University studying the physics of DNA molecules for genomics applications. For his MSc, he studied radioastronomy and Cosmology. During undergrad, participating in the International Physicists’ Tournament (IPT) guaranteed experience in multiple fields of physics at a time, always with an experimentally driven approach. Building a setup for sonoluminescence is one of his personal dreams.


From Boring to Soaring: Level Up Your Science Presentations

In today's fast-paced world, it is not enough to simply have great research results – you also need to be able to present them with impact. Whether you are presenting at a conference, pitching a new project, or communicating with policy makers, your presentation skills are crucial for success. This interactive workshop is designed to help you level up your science presentations and captivate your audience, no matter where in the world you are.

Alongside tips and tricks, we will learn how to overcome stage fright, structure your presentation and engage your audience through storytelling and other techniques. You will gain the confidence and skills you need to shine on the stage and make a lasting impression on your audience. Don't miss out on this opportunity to take your presentation skills to the next level!

Eva Bernadett Benyei
Department of Biochemistry, University of Cambridge

Eva Bernadett Benyei is a qualified medical doctor and current PhD Student at the Department of Biochemistry, University of Cambridge. Her focus is on better understanding polymicrobial communication and how these inter-species interactions are remodelled following antibiotic challenge. Eva has had enthusiasm for science since her high school years, when she first got involved with research. She also gained experience in science communication and management as leader of various organizations supporting young scientists. Her long-term goal is to bridge the spheres of research, medicine and business to support the development of applicable innovations.

Research swapshops

Molecular gastronomy – chemistry in the kitchen

Gastronomy is the art and knowledge involved in preparing and eating good food. Molecular gastronomy looks on it with a more scientific approach and uses new techniques for its preparation, transformation and artistic presentation. During this project we will try to be more aware of chemistry and physics involved in everyday cooking and demonstate one of the unusual ways of serving liquid.

To get an idea what am I talking about, let me ask you couple of questions... Have you ever thought about why do apples turn brown after some time? Can we stop it? How do cookies „grow“? How to achieve cracked surface on cookies? How can we get the best version (polymorph) of chocolate after melting it? What prevents meringue from falling from container? Is there some sort of glue for meat/fish? Is salt more than a spice? How can we encapsulate liquid? There are soooo many questions that could come to your mind, so rest easy. We will cover some of them during this swapshop through yummy experiments.

We will focus on making juice spheres and making chocolate cracked cookies. (Of course after hard work there comes sweet degustation!)

Swapshop leader: Helena Krizan, University of Zagreb, Faculty of Science

Exploring the Wonders of Conducting Polymers: Unveiling the Secrets of PEDOT, Organic Electronics, and Electrochromism

Are you curious about the cutting-edge field of organic electronics and want to explore the incredible properties of conductive polymer PEDOT:PSS and the mind-blowing concept of electrochromism?

In this workshop you will embark on a journey through the realm of conducting polymers, learning how they conduct electricity and behave in ways that traditional materials cannot. From their unique chemical structures to their remarkable optical and electrical properties, we will uncover the secrets behind these futuristic materials.

Through hands-on experiments and interactive demonstrations, you will have the opportunity to interact with PEDOT:PSS, witnessing firsthand how it can transform from a transparent conductor to a vibrant color-changer with just a small electrical charge. Discover how these materials are revolutionizing fields like flexible electronics, solar cells, and smart windows, and gain insights into the forefront of scientific research.

We aim to guide you in understanding the underlying principles of organic electronics, providing you with the knowledge and skills to explore this exciting field further.

Swapshop leader: Aleksandar Opančar, University of Zagreb, Faculty of Science

Tracking patient's vital signs - hardware and software

If you ever watched any medical TV series or an action flick, you have for sure seen a boxy device that tracks human’s vital signs. That is what we call an ECG monitor. In this workshop, we will explore together the vital signs that we can track in a patient using an ECG monitor.

But what does ECG stand for? ECG is shortened form for electrocardiograph, which is a tool that medical doctors and biomedical engineers use in their everyday work to record heart’s electrical activity and see how our heart works in real time.

Since an ECG signal has a unique shape, we can use the characteristics of an ECG signal to find out the orientation of human heart inside of body without any imaging devices. We will also explore the other vital signs that can tell us more about a patient’s well-being such as blood pressure and blood oxygen levels and how they can be measured without using invasive setups.

Lastly, by coding a Pan-Tompkins algorithm, we will explore how software helps us track the vital signs inside human body and how can we calculate the heart rate from a messy signal.

Swapshop leader: Matija Roglić, University of Zagreb, Faculty of Electrical Engineering and Computing

More coming soon...


Lecture schedule

July 24th, 2023
Lana Ceraj (Ruđer Bošković Institute, Croatia): New Generation of Telescopes: Unveiling Unexplored Horizons of Our Universe

July 31st, 2023
Vaibhav Pai (Tufts University, USA): Endogenous Bioelectric Control of Shape (Morphogenesis) and Regeneration

August 1st, 2023
Tom Crawford (Oxford University, UK): How to Use Maths to Clean the Ocean

More coming soon...

About the lecturers

Lana Ceraj
Ruđer Bošković Institute, Croatia

Lana Ceraj, PhD is an astrophysicist from Zagreb. After completing her doctorate at the Faculty of Science in Zagreb, she has been working as a postdoctoral researcher at the Ruđer Bošković Institute since 2020. In her professional work, she focuses on research in the field of astronomy, utilizing data obtained from observations with the VLA and LOFAR radio telescopes, as well as the Gaia space telescope. Using data from these telescopes, she studies active galactic nuclei, as well as the interstellar medium, and binary star systems of the Milky Way. In addition to her work at the Ruđer Bošković Institute, she has been a long-term collaborator at the Department of Physics, Faculty of Science. In her free time, she engages in science outreach through her Facebook, Instagram, and TikTok profiles, "U lovu na kozmičke zvijeri" where she brings astronomical topics closer to the Croatian general public of all ages.

Vaibhav Pai
Tufts University, USA

Vaibhav Pai, PhD is a Research Scientist at the Allen Discovery Center at Tufts University. His main research interest is in understanding biophysical control of morphogenesis (shape formation in nature). You can find out more on his website or on Google Scholar.

Tom Crawford
Oxford University, UK

Dr Tom Crawford is a maths tutor at the University of Oxford with a mission to share his love of maths with the world through his award-winning website tomrocksmaths.com. Whether he's performing live as the 'Naked Mathematician' with Equations Stripped, telling you about his favourite equations on Numberphile, or getting another maths tattoo (12 and counting), it's safe to say Tom is always finding new ways to misbehave with numbers.