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Computer Games That Help Explain Nature
August 28, 2015   
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What is the simplest way to teach difficult aspects of physics and biology to young people? Nuclear physicist Krzysztof Wo¼niak and synthetic biologist Anna Olchowik have found a way: creating special computer games for this purpose.

Wo¼niak, from the Polish Academy of Sciences’ Institute of Nuclear Physics in Cracow, is investigating heavy nuclei collisions as part of the European Organization for Nuclear Research’s (CERN) Atlas particle physics experiment under way in Geneva, Switzerland.

Olchowik, from the University of Warsaw, coordinated the participation of a university team in a high-profile synthetic biology competition held by the Massachusetts Institute of Technology in the United States.

What’s the matter with matter?

More than 3,000 scientists from Poland, including researchers from the Institute of Nuclear Physics, are taking part in the Atlas experiment. The project, which got under way in 1992, involves the use of a special detector called Atlas to study head-on collisions of protons with extraordinarily high energies. The researchers want to learn more about the basic forces that have shaped the universe since the beginning of time and will determine its fate. They are probing riddles such as the origin of mass, extra dimensions of space, microscopic black holes, and evidence for dark matter in the universe.

CERN physicists collide heavy ions to free quarks, recreating the conditions that existed in the universe just after the Big Bang. Wo¼niak works with a system for collecting data obtained during such collisions. Collisions of heavy nuclei release energy that can generate what is known as quark-gluon plasma, a highly energized form of matter that contains unbound quarks and gluons believed to have been present ten millionths of a second after the Big Bang.

In that millisecond, the universe was filled with an astonishingly hot, dense soup made of all kinds of particles moving at nearly the speed of light. This mixture was dominated by quarks—fundamental bits of matter—and by gluons, carriers of the strong force that normally “glues” quarks together into familiar protons and neutrons and other miniparticles. In those first fleeting moments of extreme temperature, however, quarks and gluons were bound only weakly, free to move on their own in what is called a quark-gluon plasma.

To find out about the properties of quark-gluon plasma, the scientists are using impressive testing equipment located underground at CERN facilities. The apparatus is 45 meters in length and 25 meters in height.

Wo¼niak organizes workshops for young people to help them learn more about CERN projects and in general about the work of a physicist. The workshops are called “Become a Particle Physicist for a Day” and encourage school and university students to learn about matter, the laws governing quarks, data used by physicists, and ways of obtaining this information. The workshops are taking place in Cracow, Bielsko-Bia³a, Tarnów and Nowy S±cz. Wo¼niak is conducting these workshops together with doctoral students and young employees from the Institute of Nuclear Physics. About 130

For his efforts to popularize science, Wo¼niak was awarded a zl.33,000 grant from the Foundation for Polish Science. He says the money will enable him to organize meetings with young people, and to build a special model to show how particles are accelerated and how collisions come about. The model will be built at the Institute of Nuclear Physics.

Wo¼niak is creating a special computer game to explain the mechanism of quarks merging into hadrons. “Quarks do not exist in nature on their own,” says Wo¼niak. “They need to either combine into quark-antiquark pairs, or groups of three quarks. The computer game is designed to show how this type of mechanism works in nature.”

The secrets of synthetic biology

Meanwhile, Olchowik deals with synthetic biology, which involves designing and creating simplified organisms. It is an interdisciplinary branch of biology that combines disciplines such as biotechnology, evolutionary biology, molecular biology, systems biology, biophysics and computer engineering. It’s like building organisms from elements resembling Lego blocks, Olchowik says. Synthetic biology combines the achievements of molecular biology and genetic engineering and also uses mathematical modeling techniques. Olchowik has developed a computer game to bring the secrets of synthetic biology closer to young people.

Olchowik was a member of the University of Warsaw team during the iGEM competition, an international contest for students run by the International Genetically Engineered Machine (iGEM) Foundation, an independent, nonprofit organization dedicated to the advancement of synthetic biology. In the competition, teams create projects in a laboratory and then present them at the Massachusetts Institute of Technology. In 2010, students from the University of Warsaw’s Faculty of Biology returned with a gold medal from Boston after presenting a system based on genetically modified Escherichia coli bacteria that are capable of penetrating eukaryotic cells. Biologists have shown that proteins secreted by these bacteria may cause natural death in cancer cells.

A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. There is a fundamental distinction between prokaryotes and eukaryotes in cellular biology that is considered to be the most important distinction among groups of organisms. Eukaryotic cells contain membrane-bound organelles, such as the nucleus, while prokaryotic cells do not. Prokaryotes were the only form of life on Earth for millions of years until more complicated eukaryotic cells came into being through the process of evolution.

In 2014, the Warsaw team presented its FluoSafe project during the European finals of the iGEM competition in Lyon, France. As part of the project, the researchers have obtained a bacterium that, thanks to a modified green fluorescent protein (GFP), glows in the presence of carcinogenic acrylamide, which is found in foods such as French fries and fried meat. Green fluorescent protein is a versatile biological marker for monitoring various physiological processes and visualizing protein localization. The protein is naturally found in the North American jellyfish Aequorea victoria, and works by absorbing energy from blue light in the environment and emitting a green glow in response. Now scientists use the protein to track how cancer cells spread and how infections progress.

“Synthetic biology makes it possible to create or modify organisms in a simple way—it’s a bit like building with Lego blocks,” Olchowik says. “Standard pieces of DNA can be easily combined to build organisms that have new functions—and thus obtain bacteria that perform useful functions. One example is arsenic biosensors, fluorescent bacteria that can be used to build lamps.”

Olchowik is working on a computer game for children about a bacterium that can perform specific functions. The game is intended for middle and high school students and will be available without charge via the internet, through mobile devices using the Android operating system.

“The game will be dynamic, interesting graphically, and adapted to mobile devices,” says Olchowik. “A player will be expected to obtain a new piece of DNA with a specific function. It’s about experimenting and matching pieces of DNA with different functions to see how bacteria adapt to the environment.”

The game is part of a larger popular science project that Olchowik has prepared using a zl.40,000 grant from the Foundation for Polish Science. The core of the project is basic programming workshops for researchers in life sciences such as biology, geography, physics and chemistry. The training is intended for high school leavers and university students.

“We want to offer four workshops focusing on simple programming language and show how it can be used in bioinformatics,” Olchowik says. “This may be based, for example, on a search for sequence motifs [recurring patterns in DNA with a presumed biological function] in a chromosome.”

The team behind the game includes a graphic artist and a software engineer. The project benefits from funds for promotion through blog entries, publications, and placing the game in a play store.

The Foundation for Polish Science supports projects designed to improve the scientific community’s relations with the public. Its Engage competition is financed by the European Social Fund and the Human Capital Operational Programme. Adam Zieliński, a director at the Foundation for Polish Science, says science is becoming increasingly complicated and it is essential that scientists learn about how talk with non-experts, in an understandable way, about how they work.

“We didn’t really want to copy existing educational initiatives such as science festivals and campaigns by the Copernicus Science Center in Warsaw or the Experyment Science Center in Gdynia,” says Zieliński. “With the Engage program, we are primarily concerned about financing civic education projects. It’s about the involvement of non-scientists in the research process—not so much in presentations, demonstrations, watching explosions, but in actual research work. In such projects, students take part in the process of planning scientific experiments and help collect and analyze data.”
Karolina Olszewska
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