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“World of Biophysics” Booklet

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“World of Biophysics” Booklet THE WORLD OF PHYSICS THE VOICE OF PHYSICS IN SOUTH AFRICA THE WORLD OF INDEX EDITORS NOTE Welcome to the 2nd 'World of Biophysics' page 1 booklet! What is Biophysics? For this edition we have collected a completely page 2 new set of articles, all written by active South Electromagnetic Radiation African physicists. This booklet doesn't only introduce you to some of the basic concepts and page 3 powerful experimental techniques used in Protein Structure & Biotechnology biophysics, but you will also get a glimpse of frontier research of international quality. Read the page 4 personal stories of two students to know what X-Ray Crystallography motivated them to study biophysics Electron Microscopy If you're fascinated by life and intrigued by the fact page 5 that all biological processes are actually based on Plant Power physics, then this booklet is for you. Biophysics is an extremely promising research field with mind- page 6 boggling technological applications Quantum Biology: Quantum Effects in Photosynthesis Enjoy your journey through just a tiny part of the World of Biophysics! page 7 Quantum Biology: Tjaart Krüger The Avian Magnetic Compass Chair of the SAIP Biophysics Initiative page 8 Quantum Biology: Quantum Neural Networks page 9 Surface Enhanced Raman Spectroscopy page 10 Optical Microscopy page 11 Student Profile: Alexander Paradzah page 12 Student Profile: SAIP BIOPHYSICS INITIATIVE Joshua Botha EDITORIAL INFO This publication was sponsored by the Department of Science and Technology and the SAIP. CONTACT INFO Editor & Content Assembly: Tjaart Krüger ([email protected]) Website: http://biophysics.saip.org.za/newsite/ with input from Raymond Sparrow Graphic Design & Layout: E-mail: [email protected] SO Productions ([email protected]) what is what do BIOPHYSICS? BIOPHYSICISTS study? Biophysics is the branch of physics that applies the methods and Biophysicists study life at every level, from the molecular scale to theories of physics to study biological systems. In short, cells, whole organisms and even ecosystems. This involves biophysicists study the physics of living systems. developing new experimental and computational tools to understand at a fundamental level the structure, interactions, Studying the patterns in life using state-of-the-art physics dynamics, and ultimately the function of biological systems. experimental techniques and complex computational models is The biological questions of interest to biophysics are as diverse as the most powerful way to find out how life works at the the organisms of biology and the properties of all their fundamental level. This is not an easy task, though. Living systems components, for example: are exceedingly rich in variety and complexity, while the laws of physics are often best studied in simple, well-controlled How does the brain process and store information? circumstances. How does the heart pump blood? How do viruses invade cells? The challenge of biophysics lies exactly here: to bridge the How do plants harness sunlight to make food? complexity of life and the simplicity of the mathematical laws of How are genes switched on and off? nature. Biophysics combines the complex beauty of biology with How do nature's nano-machines (like motor proteins the rigour of physics. and enzymes) move to do their work? Biophysics discovers how to modify micro-organisms for producing biofuel (replacing gasoline and diesel fuel) and bio- electricity (replacing petroleum products and coal for producing what tools are used by electricity). It discovers the biological cycles of heat, light, water, carbon, nitrogen, oxygen and the organisms involved throughout BIOPHYSICISTS? our planet. Biophysics harnesses micro-organisms to clean our water and to produce lifesaving drugs. Many interesting biological phenomena occur on the scales ranging from micrometres to nanometres. These phenomena can be probed and visualised using, for example, electromagnetic how can radiation to obtain information about the structure, function, and dynamics of the biological systems on all levels of complexity. BIOPHYSICS be used? The interesting properties that determine behaviour include Biophysics is a wellspring of innovation and instrumentation for conductivity and binding energy, which can only be measured and any high-tech economy. The previous century has evidenced described using physical methods. Much of the discipline of great progress in treating diseases. Biophysics helped to create experimental biophysics is devoted to overcoming the problems powerful vaccines against infectious diseases. It described and of obtaining reliable measurements of the exquisite and delicate controlled diseases of metabolism, such as diabetes. Biophysics nanoscale machines in the cells of living organisms, without provided both the tools and the understanding for treating the destroying them. diseases of growth known as cancers. With the help of biophysics we are witnessing in the 21st century a rapid progress in the Biophysics has undergone rapid advances over the past two understanding of diseases at a fundamental level. decades due mainly to the development of new technologies. These technologies enable multiscale imaging ranging from Society is facing physical and biological problems of global cellular to atomic resolution and allow us to record events on proportions. How will we continue to get sufficient energy? How ultrafast (picosecond to femtosecond) timescales. can we feed the world's population? How do we remediate global warming? How do we preserve biological diversity? How do we Biophysics pushes back barriers that once seemed secure clean and plentiful water? These are crises that require insurmountable. scientific insight and innovation. Based on the principles of physics and the mechanisms of biology, biophysics provides valuable insight and technologies for meeting these challenges. THE WORLD OF 1 BIOPHYSICS Inspiration obtained from the Biophysical Society. ELECTROMAGNETIC RADIATION Electromagnetic (or EM) radiation is a quite peculiar form of energy. We can describe it classically as a self-propagating wave consisting of electric and magnetic fields that oscillate exactly in phase. According to the Theory of Quantum Mechanics, EM radiation is composed of photons, i.e., small packets of energy. These photons can have virtually any energy and are classified into different classes according to their energy, as shown by the EM spectrum. According to the wave theory, each value of energy can be converted into a distinct frequency and wavelength of the corresponding EM wave. ELECTROMAGNETIC SPECTRUM EM radiation exhibits numerous remarkable properties. You will encounter a few of them in the other articles in this booklet. For example, the phenomenon of diffraction is explained and applied to X-rays on p. 4 and applied to visible light on p. 10. The quantum nature of EM radiation brings about a number of exotic properties, as highlighted on pp. 6-8. A lot of interesting effects arise when EM radiation interacts with a sample. These effects can be investigated using a set of techniques known as spectroscopy. The two most commonly studied spectroscopic effects are absorption of the EM radiation by the sample, and spontaneous emission, also known as fluorescence, whereby EM radiation with a slightly lower energy is emitted. Raman spectroscopy is a frequently used technique to study molecular vibrations and is introduced on p. 9. This technique is based on the inelastic scattering of EM radiation by a sample whereby the energy of the EM radiation changes due to its interaction with the vibrations of the molecules in the sample. Molecular vibrations normally correspond to energy in the near-infrared region of the EM spectrum. When a molecule's electron cloud responds non-linearly to the electric field of an EM wave, this property can be exploited to bring about interesting non-linear effects, as explained on p. 10. Finally, one can actively modify the waveform of an EM wave; for example, shaping the phase or intensity of the wave front in a predetermined way (see also on p. 10). With all its fascinating features, EM radiation is an extremely powerful and versatile tool to study biological systems. Visible light, which covers only a small fraction of the EM spectrum, is the most commonly used form of EM radiation simply because we can guide and observe it the best. The year 2015 is known as the UNESCO International Year of Light and is therefore an opportune moment to publish this edition of 'The World of Biophysics' brochure. THE WORLD OF BIOPHYSICS 2 PROTEIN STRUCTURE & BIOTECHNOLOGY Trevor Sewell, University of Cape Town Applications of biological molecules have a huge commercial potential, but scientists first have to understand the structures of proteins at the deepest atomic level. Being able to unlock these secrets locally is an important component in the global economic success of South Africa. South Africa has a long history of involvement in biotechnology. The “first-generation” biotechnology used organisms to grow one of the world's largest brewing companies, a globally renowned wine industry, and important programmes in plant and animal breeding. The “second generation” went a step further and introduced useful characteristics into micro-organisms. Now the “third generation” engineers molecules and cells, creating products like industrial enzymes (i.e., the chemical “reactors”), therapeutic agents, pesticides, and vaccines. To tap into this potential one needs to have
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