Search result: Catalogue data in Autumn Semester 2020
Computational Biology and Bioinformatics Master  More informations at: https://www.cbb.ethz.ch/ | ||||||
 Core CoursesPlease note that the list of core courses is a closed list. Other courses cannot be added to the core course category in the study plan. Also the assignments of courses to core subcategories cannot be changed. Students need to pass at least one course in each core subcategory. A total of 40 ECTS needs to be acquired in the core course category. | ||||||
| Biophysics | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 636-0104-00L | Biophysical Methods Attention: This course was offered in previous semesters with the number: 626-0010-00L "Nanomachines of the Cell (Part I): Principles". Students that already passed course 626-0010-00 cannot receive credits for course 636-0104-00. | W | 4 credits | 3G | D. J. Müller | |
| Abstract | Students will be imparted knowledge in basic and advanced biophysical methods applied to problems in molecular biotechnology. The course is fundamental to applying the methods in their daily and advanced research routines. The students will learn the physical basis of the methods as well as their limitations and possibilities to address existing and future topics in molecular biotechnology. | |||||
| Learning objective | Gain of interdisciplinary competence in experimental and theoretical research, which qualifies for academic scientific work (master's or doctoral thesis) as well as for research in a biotechnology or a pharmaceutical company. The module is of general use in courses focused on modern biomolecular technologies, systems biology and systems engineering. | |||||
| Content | The students will learn basic and advanced knowledge in applying biophysical methods to address problems and overcome challenges in biotechnology, cell biology and life sciences in general. The biological and physical possibilities and limitations of the methods will be discussed and critically evaluated. By the end of the course the students will have assimilated knowledge on a portfolio of biophysical tools widening their research capabilities and aptitude. The biophysical methods to be taught will include: • Light microscopy: Resolution limit of light microscopy, fluorescence, GFP, fluorescence microscopy, DIC, phase contrast, difference between wide-field and confocal microscopy • Super resolution optical microscopy: STED, PALM, STORM, other variations • Electron microscopy: Scanning electron microscopy, transmission electron microscopy, electron tomography, cryo-electron microscopy, single particle analysis and averaging, tomography, sectioning, negative stain • X-ray, electron and neutron diffraction • MRI Imaging • Scanning tunnelling microscopy and atomic force microscopy • Patch clamp technologies: Principles of patch clamp analysis and application. Various patch clamp approaches used in research and industry • Surface plasmon resonance-based biosensors • Molecular pore-based sensors and sequencing devices • Mechanical molecular and cellular assembly devices • Optical and magnetic tweezers • CD spectroscopy • Optogenetics • Molecular dynamics simulations | |||||
| Lecture notes | Hand out will be given to students at lecture. | |||||
| Literature | Methods in Molecular Biophysics (5th edition), Serdyuk et al., Cambridge University Press Biochemistry (5th edition), Berg, Tymoczko, Stryer; ISBN 0-7167-4684-0, Freeman Bioanalytics, Lottspeich & Engels, Wiley VCH, ISBN-10: 3527339191 Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania Methods in Modern Biophysics, Nölting, 3rd Edition, Springer, ISBN-10: 3642030211 | |||||
| Prerequisites / Notice | The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students will prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher. | |||||
| 529-0004-01L | Classical Simulation of (Bio)Molecular Systems | W | 6 credits | 4G | P. H. Hünenberger, S. Riniker | |
| Abstract | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | |||||
| Learning objective | Introduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations. | |||||
| Content | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | |||||
| Lecture notes | Script booklet (copies of powerpoint slides) distributed at the first or second lecture. | |||||
| Literature | See: www.csms.ethz.ch/education/CSBMS | |||||
| Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills than those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark). For more information about the lecture: www.csms.ethz.ch/education/CSBMS | |||||
| 262-6106-00L | Current Topics in Biophysics | W | 6 credits | 3G | external organisers | |
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