Search result: Catalogue data in Autumn Semester 2022
Biomedical Engineering Master  
Track Courses  
Medical Physics  
Track Core Courses During the Master programme, a minimum of 12 CP must be obtained from track core courses.  
Number  Title  Type  ECTS  Hours  Lecturers  

227031100L  Qubits, Electrons, Photons  W  6 credits  3V + 2U  T. Zambelli  
Abstract  Indepth analysis of the quantum mechanics origin of nuclear magnetic resonance (qubits, twolevel systems), of LASER (quantization of the electromagnetic field, photons), and of electron transfer (from electrochemistry to photosynthesis).  
Learning objective  Beside electronics nanodevices, DITET is pushing its research in the fields of NMR (MRI), electrochemistry, bioelectronics, nanooptics, and quantum information, which are all rationalized in terms of quantum mechanics. Starting from the axioms of quantum mechanics, we will derive the fascinating theory describing spin and qubits, electron transitions and transfer, photons and LASER: quantum mechanics is different because it mocks our daily Euclidean intuition! In this way, students will work out a robust quantum mechanics (theoretical!!!) basis which will help them in their advanced studies of the following masters: EEIT (batteries), Biomedical Engineering (NMR, bioelectronics), Quantum Engineering, Micro and Nanosystems. IMPORTANT: "qubits" from the point of view of NMR (and NOT from that of quantum computing!).  
Content  • Lagrangian and Hamiltonian: Symmetries and Poisson Brackets • Postulates of QM: Hilbert Spaces and Operators • Heisenberg’s Matrix Mechanics: Hamiltonian and Time Evolution Operator • Density Operator • Spin: Qubits, Bloch Equations, and NMR • Entanglement • Symmetries and Corresponding Operators • Schrödinger's Wave Mechanics: Electrons in a Periodic Potential and Energy Bands • Harmonic Oscillator: Creation and Annihilation Operators • Identical Particles: Bosons and Fermions • Quantization of the Electromagnetic Field: Photons, Absorption and Emission, LASER • Electron Transfer: Marcus Theory via BornOppenheimer, FranckCondon, LandauZener  
Lecture notes  No lecture notes because the proposed textbooks together with the provided supplementary material are more than exhaustive! !!!!! I am using OneNote. All lectures and exercises will be broadcast via ZOOM and correspondingly recorded (link in Moodle) !!!!!  
Literature  • J.S. Townsend, "A Modern Approach to Quantum Mechanics", Second Edition, 2012, University Science Books • M. Le Bellac, "Quantum Physics", 2011, Cambridge University Press • (Lagrangian and Hamiltonian) L. Susskind, G. Hrabovsky, "Theoretical Minimum: What You Need to Know to Start Doing Physics", 2014, Hachette Book Group USA Supplementary material will be uploaded in Moodle. _ _ _ _ _ _ _ + (as rigorous and profound presentation of the mathematical framework) G. Dell'Antonio, "Lectures on the Mathematics of Quantum Mechanics I", 2015, Springer + (as account of those formidable years) G. Gamow, "Thirty Years that Shook Physics", 1985, Dover Publications Inc.  
Prerequisites / Notice  The course has been intentionally conceived to be selfconsistent with respect to QM for those master students not having encountered it in their track yet. Therefore, a presumably large overlapping has to be expected with a (welcome!) QM introduction course like the DITET "Physics II". A solid base of Analysis I & II as well as of Linear Algebra is really helpful.  
Competencies 
 
227038510L  Biomedical Imaging  W  6 credits  5G  S. Kozerke, K. P. Prüssmann  
Abstract  Introduction to diagnostic medical imaging based on electromagnetic and acoustic fields including Xray planar and tomographic imaging, radiotracer based nuclear imaging techniques, magnetic resonance imaging and ultrasoundbased procedures.  
Learning objective  Upon completion of the course students are able to: • Explain the physical and mathematical foundations of diagnostic medical imaging systems • Characterize system performance based on signaltonoise ratio, contrasttonoise ratio and transfer function • Design a basic diagnostic imaging system chain including data acquisition and data reconstruction • Identify advantages and limitations of different imaging methods in relation to medical diagnostic applications  
Content  • Introduction (intro, overview, history) • Signal theory and processing (foundations, transforms, filtering, signaltonoise ratio) • Xrays (production, tissue interaction, contrast, modular transfer function) • Xrays (resolution, detection, digital subtraction angiography, Radon transform) • Xrays (filtered backprojection, spiral computed tomography, image quality, dose) • Nuclear imaging (radioactive tracer, collimation, point spread function, SPECT/PET) • Nuclear imaging (detection principles, image reconstruction, kinetic modelling) • Magnetic Resonance (magnetic moment, spin transitions, excitation, relaxation, detection) • Magnetic Resonance (plane wave encoding, Fourier reconstruction, pulse sequences) • Magnetic Resonance (contrast mechanisms, gradient and spinecho, applications) • Ultrasound (mechanical wave generation, propagation in tissue, reflection, transmission) • Ultrasound (spatial and temporal resolution, phased arrays) • Ultrasound (Doppler shift, implementations, applications) • Summary, example exam questions  
Lecture notes  Lecture notes and handouts  
Literature  Webb A, Smith N.B. Introduction to Medical Imaging: Physics, Engineering and Clinical Applications; Cambridge University Press 2011  
Prerequisites / Notice  Analysis, Linear algebra, Physics, Basics of signal theory, Basic skills in Matlab/Python programming  
Competencies 
 
227094300L  Radiobiology  W  2 credits  2V  M. Pruschy  
Abstract  The purpose of this course is to impart basic knowledge in radiobiology in order to handle ionizing radiation and to provide a basis for predicting the radiation risk.  
Learning objective  By the end of this course the participants will be able to: a) interpret the 5 Rs of radiation oncology in the context of the hallmarks of cancer b) understand factors which underpin the differing radiosensitivities of different tumors c) follow rational strategies for combined treatment modalities of ionizing radiation with targeted agents d) understand differences in the radiation response of normal tissue versus tumor tissue e) understand different treatment responses of the tumor and the normal tissue to differential clinicalrelated parameters of radiotherapy (dose rate, LET etc.).  
Content  Einführung in die Strahlenbiologie ionisierender Strahlen: Allgemeine Grundlagen und Begriffsbestimmungen; Mechanismen der biologischen Strahlenwirkung; Strahlenwirkung auf Zellen, Gewebe und Organe; Modifikation der biologischen Strahlenwirkung; Strahlenzytogenetik: Chromosomenveränderungen, DNADefekte, Reparaturprozesse; Molekulare Strahlenbiologie: Bedeutung inter und intrazellulärer Signalübermittlungsprozesse, Apoptose, ZellzyklusCheckpoints; Strahlenrisiko: Strahlensyndrome, Krebsinduktion, Mutationsauslösung, pränatale Strahlenwirkung; Strahlenbiologische Grundlagen des Strahlenschutzes; NutzenRisikoAbwägungen bei der medizinischen Strahlenanwendung; Prädiktive strahlenbiologische Methoden zur Optimierung der therapeutischen Strahlenanwendung.  
Lecture notes  Beilagen mit zusammenfassenden Texten, Tabellen, Bild und Grafikdarstellungen werden abgegeben  
Literature  Literaturliste wird abgegeben. Für NDSAbsolventen empfohlen: Hall EJ; Giacchia A: Radiobiology for the Radiologist, 7th Edition, 2011 Basic Clinical Radiobiology, edited by Joiner, van der Kogel, 2018  
Prerequisites / Notice  The former number of this course unit is 465095100L.  
402034100L  Medical Physics I  W  6 credits  2V + 1U  P. Manser  
Abstract  Introduction to the fundamentals of medical radiation physics. Functional chain due to radiation exposure from the primary physical effect to the radiobiological and medically manifest secondary effects. Dosimetric concepts of radiation protection in medicine. Mode of action of radiation sources used in medicine and its illustration by means of Monte Carlo simulations.  
Learning objective  Understanding the functional chain from primary physical effects of ionizing radiation to clinical radiation effects. Dealing with dose as a quantitative measure of medical exposure. Getting familiar with methods to generate ionizing radiation in medicine and learn how they are applied for medical purposes. Eventually, the lecture aims to show the students that medical physics is a fascinating and evolving discipline where physics can directly be used for the benefits of patients and the society.  
Content  The lecture is covering the basic principles of ionzing radiation and its physical and biological effects. The physical interactions of photons as well as of charged particles will be reviewed and their consequences for medical applications will be discussed. The concept of Monte Carlo simulation will be introduced in the excercises and will help the student to understand the characteristics of ionizing radiation in simple and complex situations. Fundamentals in dosimetry will be provided in order to understand the physical and biological effects of ionizing radiation. Deterministic as well as stochastic effects will be discussed and fundamental knowledge about radiation protection will be provided. In the second part of the lecture series, we will cover the generation of ionizing radiation. By this means, the xray tube, the clinical linear accelarator, and different radioactive sources in radiology, radiotherapy and nuclear medicine will be addressed. Applications in radiolgoy, nuclear medicine and radiotherapy will be described with a special focus on the physics underlying these applications.  
Lecture notes  A script will be provided.  
Prerequisites / Notice  For students of the MAS in Medical Physics (Specialization A) the performance assessment is offered at the earliest in the second year of the studies.  
Recommended Elective Courses These courses are particularly recommended for the Medical Physics track. Please consult your track advisor if you wish to select other subjects.  
Number  Title  Type  ECTS  Hours  Lecturers  
402067400L  Physics in Medical Research: From Atoms to Cells  W  6 credits  2V + 1U  B. K. R. Müller  
Abstract  Scanning probe and diffraction techniques allow studying activated atomic processes during early stages of epitaxial growth. For quantitative description, rate equation analysis, meanfield nucleation and scaling theories are applied on systems ranging from simple metallic to complex organic materials. The knowledge is expanded to optical and electronic properties as well as to proteins and cells.  
Learning objective  The lecture series is motivated by an overview covering the skin of the crystals, roughness analysis, contact angle measurements, protein absorption/activity and monocyte behaviour. As the first step, real structures on clean surfaces including surface reconstructions and surface relaxations, defects in crystals are presented, before the preparation of clean metallic, semiconducting, oxidic and organic surfaces are introduced. The atomic processes on surfaces are activated by the increase of the substrate temperature. They can be studied using scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The combination with molecular beam epitaxy (MBE) allows determining the sizes of the critical nuclei and the other activated processes in a hierarchical fashion. The evolution of the surface morphology is characterized by the density and size distribution of the nanostructures that could be quantified by means of the rate equation analysis, the meanfield nucleation theory, as well as the scaling theory. The surface morphology is further characterized by defects and nanostructure's shapes, which are based on the strain relieving mechanisms and kinetic growth processes. Highresolution electron diffraction is complementary to scanning probe techniques and provides exact mean values. Some phenomena are quantitatively described by the kinematic theory and perfectly understood by means of the Ewald construction. Other phenomena need to be described by the more complex dynamical theory. Electron diffraction is not only associated with elastic scattering but also inelastic excitation mechanisms that reflect the electronic structure of the surfaces studied. Lowenergy electrons lead to phonon and highenergy electrons to plasmon excitations. Both effects are perfectly described by dipole and impact scattering. Thinfilms of rather complex organic materials are often quantitatively characterized by photons with a broad range of wavelengths from ultraviolet to infrared light. Asymmetries and preferential orientations of the (anisotropic) molecules are verified using the optical dichroism and second harmonic generation measurements. Recently, ellipsometry has been introduced to online monitor film thickness, and roughness with subnanometer precision. These characterisation techniques are vital for optimising the preparation of medical implants. Cellsurface interactions are related to the cell adhesion and the contractile cellular forces. Physical means have been developed to quantify these interactions. Other physical techniques are introduced in cell biology, namely to count and sort cells, to study cell proliferation and metabolism and to determine the relation between cell morphology and function. X rays are more and more often used to characterise the human tissues down to the nanometer level. The combination of highly intense beams only some micrometers in diameter with scanning enables spatially resolved measurements and the determination of tissue's anisotropies of biopsies.  
227094100L  Physics and Mathematics of Radiotherapy Planning (University of Zurich) No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH as an incoming student. UZH Module Code: PHY471 https://www.uzh.ch/cmsssl/en/studies/application/chmobilityin.html Mind the enrolment deadlines at UZH: https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html  W  6 credits  3G  University lecturers  
Abstract  This lecture will provide a detailed introduction to radiotherapy treatment planning. The course considers the physical interactions of radiation in tissue, the mathematical aspects of treatment planning and additional aspects of central importance for radiotherapy planning.  
Learning objective  Students shall develop a thorough understanding of the foundations of radiotherapy from a physics and mathematics perspective, focusing on algorithmic components. After completing the course students should be able to implement the main components of a radiotherapy treatment planning system.  
Content  Radiotherapy is one of the main treatment options against cancer. Today, more than 50% of cancer patients receive radiation as part of their treatment. Modern radiotherapy is a highly technology driven field. Research and development in medical physics has improved the precision of radiotherapy substantially. Using intensitymodulated radiotherapy (IMRT), radiation can be delivered precisely to tumors while minimizing radiation exposure of heathy organs surrounding the tumor. Thereby, medical physics has provided radiation oncologists with new curative treatment approaches where previously only palliative treatments were possible. This lecture will provide a detailed introduction to radiotherapy treatment planning and will consists of three blocks: 1. The first part of the course considers the physical interactions of radiation in tissue. The physical interactions give rise to dose calculation algorithms, which are used to calculate the absorbed radiation dose based on a CT scan of the patient. 2. The second part considers the mathematical aspects of treatment planning. Mathematical optimization techniques are introduced, which are used in intensitymodulated radiotherapy to determine the external radiation fields that optimally irradiate the tumor while minimizing radiation dose to healthy organs. 3. The third part deals with additional aspects of central importance for radiotherapy planning. This includes biomedical imaging techniques for treatment planning and target delineation as well as image registration algorithms. The lectures are followed by computational exercises where students implement the main components of a radiotherapy treatment planning systems in two dimensions in Matlab.  
Lecture notes  Lecture slides and handouts.  
Prerequisites / Notice  Basic programming skills in Matlab (or willingness to learn) are needed for the exercises. Basic knowledge of calculus is needed, approximately corresponding to the 3rd year of a bachelor degree in physics, mathematics, computer science, engineering or comparable discipline.  
Other Elective Courses These courses may be suitable for the Medical Physics track. Please consult your track advisor.  
Number  Title  Type  ECTS  Hours  Lecturers  
227044700L  Image Analysis and Computer Vision  W  6 credits  3V + 1U  E. Konukoglu, F. Yu  
Abstract  Light and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition. Deep learning and Convolutional Neural Networks.  
Learning objective  Overview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.  
Content  This course aims at offering a selfcontained account of computer vision and its underlying concepts, including the recent use of deep learning. The first part starts with an overview of existing and emerging applications that need computer vision. It shows that the realm of image processing is no longer restricted to the factory floor, but is entering several fields of our daily life. First the interaction of light with matter is considered. The most important hardware components such as cameras and illumination sources are also discussed. The course then turns to image discretization, necessary to process images by computer. The next part describes necessary preprocessing steps, that enhance image quality and/or detect specific features. Linear and nonlinear filters are introduced for that purpose. The course will continue by analyzing procedures allowing to extract additional types of basic information from multiple images, with motion and 3D shape as two important examples. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed. A major part at the end is devoted to deep learning and AIbased approaches to image analysis. Its main focus is on object recognition, but also other examples of image processing using deep neural nets are given.  
Lecture notes  Course material Script, computer demonstrations, exercises and problem solutions  
Prerequisites / Notice  Prerequisites: Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Python and Linux. The course language is English.  
227096500L  Micro and NanoTomography of Biological Tissues  W  4 credits  3G  M. Stampanoni, F. Marone Welford  
Abstract  The lecture introduces the physical and technical knowhow of Xray tomographic microscopy. Several Xray imaging techniques (absorption, phase and darkfield contrast) will be discussed and their use in daily research, in particular biology, is presented. The course discusses the aspects of quantitative evaluation of tomographic data sets like segmentation, morphometry and statistics.  
Learning objective  Introduction to the basic concepts of Xray tomographic imaging, image analysis and data quantification at the micro and nano scale with particular emphasis on biological applications  
Content  Synchrotronbased Xray micro and nanotomography is today a powerful technique for nondestructive, highresolution investigations of a broad range of materials. The highbrilliance and highcoherence of third generation synchrotron radiation facilities allow quantitative, threedimensional imaging at the micro and nanometer scale and extend the traditional absorption imaging technique to edgeenhanced and phasesensitive measurements, which are particularly suited for investigating biological samples. The lecture includes a general introduction to the principles of tomographic imaging from image formation to image reconstruction. It provides the physical and engineering basics to understand how imaging beamlines at synchrotron facilities work, looks into the recently developed phase contrast methods, and explores the first applications of Xray nanotomographic experiments. The course finally provides the necessary background to understand the quantitative evaluation of tomographic data, from basic image analysis to complex morphometrical computations and 3D visualization, keeping the focus on biomedical applications.  
Lecture notes  Available online  
Literature  Will be indicated during the lecture.  
Biology Courses  
Number  Title  Type  ECTS  Hours  Lecturers  
227039910L  Physiology and Anatomy for Biomedical Engineers I  W  3 credits  2G  M. Wyss  
Abstract  Students will be able to identify and enumerate important anatomical structures to describe basic physiological processes of the human body to use a 3d animation database/software to use 'anatomical language' to retrieve anatomical structures to understand basic medical terminology  
Learning objective  To understand basic principles and structure of the human body in consideration of the clinical relevance and the medical terminology used in medical work and research.  
Content   The Human Body: nomenclature, orientations, tissues  Musculoskeletal system, Muscle contraction  Blood vessels, Heart, Circulation  Blood, Immune system  Respiratory system  AcidBaseHomeostasis  
Lecture notes  Lecture notes and handouts  
Literature  Silbernagl S., Despopoulos A. Color Atlas of Physiology; Thieme 2008 Faller A., Schuenke M. The Human Body; Thieme 2004 Netter F. Atlas of human anatomy; Elsevier 2014  
227094500L  Cell and Molecular Biology for Engineers I Does not take place this semester.  W  3 credits  2G  to be announced  
Abstract  The course gives an introduction into cellular and molecular biology, specifically for students with a background in engineering. The focus will be on the basic organization of eukaryotic cells, molecular mechanisms and cellular functions. Textbook knowledge will be combined with results from recent research and technological innovations in biology.  
Learning objective  After completing this course, engineering students will be able to apply their previous training in the quantitative and physical sciences to modern biology. Students will also learn the principles how biological models are established, and how these models can be tested.  
Content  Lectures will include the following topics (part I and II): DNA, chromosomes, genome engineering, RNA, proteins, genetics, synthetic biology, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer and stem cells. In addition, 4 journal clubs will be held, where recent publications will be discussed (2 journal clubs in part I and 2 journal clubs in part II). For each journal club, students (alone or in groups of up to three students) have to write a summary and discussion of the publication. These written documents will be graded and count as 40% for the final grade.  
Lecture notes  Scripts of all lectures will be available.  
Literature  "Molecular Biology of the Cell" (6th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.  
Competencies 

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