# Search result: Catalogue data in Autumn Semester 2016

Biomedical Engineering Master | ||||||

Track Courses | ||||||

Biomechanics | ||||||

Recommended Elective Courses These courses are particularly recommended for the Biomechanics track. Please consult your track advisor if you wish to select other subjects. | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |
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151-0255-00L | Energy Conversion and Transport in Biosystems | W | 4 credits | 2V + 1U | D. Poulikakos, A. Ferrari | |

Abstract | Theory and application of thermodynamics and energy conversion in biological systems with focus on the cellular level. | |||||

Objective | Theory and application of energy conversion at the cellular level. Understanding of the basic features governing solutes transport in the principal systems of the human cell. Connection of characteristics and patterns from other fields of engineering to biofluidics. Heat and mass transport processes in the cell, generation of forces, work and relation to biomedical technologies. | |||||

Content | Mass transfer models for the transport of chemical species in the human cell. Organization and function of the cell membrane and of the cell cytoskeleton. The role of molecular motors in cellular force generation and their function in cell migration. Description of the functionality of these systems and of analytical experimental and computational techniques for understanding of their operation. Introduction to cell metabolism, cellular energy transport and cellular thermodynamics. | |||||

Lecture notes | Material in the form of hand-outs will be distributed. | |||||

Literature | Lecture notes and references therein. | |||||

151-0524-00L | Continuum Mechanics I | W | 4 credits | 2V + 1U | E. Mazza | |

Abstract | The lecture deals with constitutive models that are relevant for design and calculation of structures. These include anisotropic linear elsticity, linear viscoelasticity, plasticity, viscoplasticity. Homogenization theories and laminate theory are presented. Theoretical models are complemented by examples of engineering applications and eperiments. | |||||

Objective | Basic theories for solving continuum mechanics problems of engineering applications, with particular attention to material models. | |||||

Content | Anisotrope Elastizität, Linearelastisches und linearviskoses Stoffverhalten, Viskoelastizität, mikro-makro Modellierung, Laminattheorie, Plastizität, Viscoplastizität, Beispiele aus der Ingenieuranwendung, Vergleich mit Experimenten. | |||||

Lecture notes | yes | |||||

151-0604-00L | Microrobotics Does not take place this semester. | W | 4 credits | 3G | B. Nelson | |

Abstract | Microrobotics is an interdisciplinary field that combines aspects of robotics, micro and nanotechnology, biomedical engineering, and materials science. The aim of this course is to expose students to the fundamentals of this emerging field. Throughout the course students are expected to submit assignments. The course concludes with an end-of-semester examination. | |||||

Objective | The objective of this course is to expose students to the fundamental aspects of the emerging field of microrobotics. This includes a focus on physical laws that predominate at the microscale, technologies for fabricating small devices, bio-inspired design, and applications of the field. | |||||

Content | Main topics of the course include: - Scaling laws at micro/nano scales - Electrostatics - Electromagnetism - Low Reynolds number flows - Observation tools - Materials and fabrication methods - Applications of biomedical microrobots | |||||

Lecture notes | The powerpoint slides presented in the lectures will be made available in hardcopy and as pdf files. Several readings will also be made available electronically. | |||||

Prerequisites / Notice | The lecture will be taught in English. | |||||

151-0605-00L | Nanosystems | W | 4 credits | 4G | A. Stemmer, J.‑N. Tisserant | |

Abstract | From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles. Intermolecular forces, their macroscopic manifestations, and ways to control such interactions. Self-assembly and directed assembly of 2D and 3D structures. Special emphasis on the emerging field of molecular electronic devices. | |||||

Objective | Familiarize students with basic science and engineering principles governing the nano domain. | |||||

Content | The course addresses basic science and engineering principles ruling the nano domain. We particularly work out the links between topics that are traditionally taught separately. Special emphasis is placed on the emerging field of molecular electronic devices, their working principles, applications, and how they may be assembled. Topics are treated in 2 blocks: (I) From Quantum to Continuum From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles. (II) Interaction Forces on the Micro and Nano Scale Intermolecular forces, their macroscopic manifestations, and ways to control such interactions. Self-assembly and directed assembly of 2D and 3D structures. | |||||

Literature | - Kuhn, Hans; Försterling, H.D.: Principles of Physical Chemistry. Understanding Molecules, Molecular Assemblies, Supramolecular Machines. 1999, Wiley, ISBN: 0-471-95902-2 - Chen, Gang: Nanoscale Energy Transport and Conversion. 2005, Oxford University Press, ISBN: 978-0-19-515942-4 - Ouisse, Thierry: Electron Transport in Nanostructures and Mesoscopic Devices. 2008, Wiley, ISBN: 978-1-84821-050-9 - Wolf, Edward L.: Nanophysics and Nanotechnology. 2004, Wiley-VCH, ISBN: 3-527-40407-4 - Israelachvili, Jacob N.: Intermolecular and Surface Forces. 2nd ed., 1992, Academic Press,ISBN: 0-12-375181-0 - Evans, D.F.; Wennerstrom, H.: The Colloidal Domain. Where Physics, Chemistry, Biology, and Technology Meet. Advances in Interfacial Engineering Series. 2nd ed., 1999, Wiley, ISBN: 0-471-24247-0 - Hunter, Robert J.: Foundations of Colloid Science. 2nd ed., 2001, Oxford, ISBN: 0-19-850502-7 | |||||

Prerequisites / Notice | Course format: Lectures and Mini-Review presentations: Thursday 10-13, ML F 36 Homework: Mini-Reviews Students select a paper (list distributed in class) and expand the topic into a Mini-Review that illuminates the particular field beyond the immediate results reported in the paper. | |||||

227-2037-00L | Physical Modelling and Simulation | W | 5 credits | 4G | C. Hafner, J. Leuthold, J. Smajic | |

Abstract | This module consists of (a) an introduction to fundamental equations of electromagnetics, mechanics and heat transfer, (b) a detailed overview of numerical methods for field simulations, and (c) practical examples solved in form of small projects. | |||||

Objective | Basic knowledge of the fundamental equations and effects of electromagnetics, mechanics, and heat transfer. Knowledge of the main concepts of numerical methods for physical modelling and simulation. Ability (a) to develop own simple field simulation programs, (b) to select an appropriate field solver for a given problem, (c) to perform field simulations, (d) to evaluate the obtained results, and (e) to interactively improve the models until sufficiently accurate results are obtained. | |||||

Content | The module begins with an introduction to the fundamental equations and effects of electromagnetics, mechanics, and heat transfer. After the introduction follows a detailed overview of the available numerical methods for solving electromagnetic, thermal and mechanical boundary value problems. This part of the course contains a general introduction into numerical methods, differential and integral forms, linear equation systems, Finite Difference Method (FDM), Boundary Element Method (BEM), Method of Moments (MoM), Multiple Multipole Program (MMP) and Finite Element Method (FEM). The theoretical part of the course finishes with a presentation of multiphysics simulations through several practical examples of HF-engineering such as coupled electromagnetic-mechanical and electromagnetic-thermal analysis of MEMS. In the second part of the course the students will work in small groups on practical simulation problems. For solving practical problems the students can develop and use own simulation programs or chose an appropriate commercial field solver for their specific problem. This practical simulation work of the students is supervised by the lecturers. | |||||

263-5001-00L | Introduction to Finite Elements and Sparse Linear System Solving | W | 4 credits | 2V + 1U | P. Arbenz | |

Abstract | The finite element (FE) method is the method of choice for (approximately) solving partial differential equations on complicated domains. In the first third of the lecture, we give an introduction to the method. The rest of the lecture will be devoted to methods for solving the large sparse linear systems of equation that a typical for the FE method. We will consider direct and iterative methods. | |||||

Objective | Students will know the most important direct and iterative solvers for sparse linear systems. They will be able to determine which solver to choose in particular situations. | |||||

Content | I. THE FINITE ELEMENT METHOD (1) Introduction, model problems. (2) 1D problems. Piecewise polynomials in 1D. (3) 2D problems. Triangulations. Piecewise polynomials in 2D. (4) Variational formulations. Galerkin finite element method. (5) Implementation aspects. II. DIRECT SOLUTION METHODS (6) LU and Cholesky decomposition. (7) Sparse matrices. (8) Fill-reducing orderings. III. ITERATIVE SOLUTION METHODS (9) Stationary iterative methods, preconditioning. (10) Preconditioned conjugate gradient method (PCG). (11) Incomplete factorization preconditioning. (12) Multigrid preconditioning. (13) Nonsymmetric problems (GMRES, BiCGstab). (14) Indefinite problems (SYMMLQ, MINRES). | |||||

Literature | [1] M. G. Larson, F. Bengzon: The Finite Element Method: Theory, Implementation, and Applications. Springer, Heidelberg, 2013. [2] H. Elman, D. Sylvester, A. Wathen: Finite elements and fast iterative solvers. OUP, Oxford, 2005. [3] Y. Saad: Iterative methods for sparse linear systems (2nd ed.). SIAM, Philadelphia, 2003. [4] T. Davis: Direct Methods for Sparse Linear Systems. SIAM, Philadelphia, 2006. [5] H.R. Schwarz: Die Methode der finiten Elemente (3rd ed.). Teubner, Stuttgart, 1991. | |||||

Prerequisites / Notice | Prerequisites: Linear Algebra, Analysis, Computational Science. The exercises are made with Matlab. | |||||

376-1103-00L | Frontiers in Nanotechnology | W | 4 credits | 4V | V. Vogel, further lecturers | |

Abstract | Many disciplines are meeting at the nanoscale, from physics, chemistry to engineering, from the life sciences to medicine. The course will prepare students to communicate more effectively across disciplinary boundaries, and will provide them with deep insights into the various frontiers. | |||||

Objective | Building upon advanced technologies to create, visualize, analyze and manipulate nano-structures, as well as to probe their nano-chemistry, nano-mechanics and other properties within manmade and living systems, many exciting discoveries are currently made. They change the way we do science and result in so many new technologies. The goal of the course is to give Master and Graduate students from all interested departments an overview of what nanotechnology is all about, from analytical techniques to nanosystems, from physics to biology. Students will start to appreciate the extent to which scientific communities are meeting at the nanoscale. They will learn about the specific challenges and what is currently “sizzling” in the respective fields, and learn the vocabulary that is necessary to communicate effectively across departmental boundaries. Each lecturer will first give an overview of the state-of-the art in his/her field, and then describe the research highlights in his/her own research group. While preparing their Final Projects and discussing them in front of the class, the students will deepen their understanding of how to apply a range of new technologies to solve specific scientific problems and technical challenges. Exposure to the different frontiers will also improve their ability to conduct effective nanoscale research, recognize the broader significance of their work and to start collaborations. | |||||

Content | Starting with the fabrication and analysis of nanoparticles and nanostructured materials that enable a variety of scientific and technical applications, we will transition to discussing biological nanosystems, how they work and what bioinspired engineering principles can be derived, to finally discussing biomedical applications and potential health risk issues. Scientific aspects as well as the many of the emerging technologies will be covered that start impacting so many aspects of our lives. This includes new phenomena in physics, advanced materials, novel technologies and new methods to address major medical challenges. | |||||

Lecture notes | All the enrolled students will get access to a password protected website where they can find pdf files of the lecture notes, and typically 1-2 journal articles per lecture that cover selected topics. | |||||

376-1219-00L | Rehabilitation Engineering II: Rehabilitation of Sensory and Vegetative Functions | W | 3 credits | 2V | R. Riener, R. Gassert, L. Marchal Crespo | |

Abstract | Rehabilitation Engng is the application of science and technology to ameliorate the handicaps of individuals with disabilities to reintegrate them into society.The goal is to present classical and new rehabilitation engineering principles applied to compensate or enhance motor, sensory, and cognitive deficits. Focus is on the restoration and treatment of the human sensory and vegetative system. | |||||

Objective | Provide knowledge on the anatomy and physiology of the human sensory system, related dysfunctions and pathologies, and how rehabilitation engineering can provide sensory restoration and substitution. This lecture is independent from Rehabilitation Engineering I. Thus, both lectures can be visited in arbitrary order. | |||||

Content | Introduction, problem definition, overview Rehabilitation of visual function - Anatomy and physiology of the visual sense - Technical aids (glasses, sensor substitution) - Retina and cortex implants Rehabilitation of hearing function - Anatomy and physiology of the auditory sense - Hearing aids - Cochlea Implants Rehabilitation and use of kinesthetic and tactile function - Anatomy and physiology of the kinesthetic and tactile sense - Tactile/haptic displays for motion therapy (incl. electrical stimulation) - Role of displays in motor learning Rehabilitation of vestibular function - Anatomy and physiology of the vestibular sense - Rehabilitation strategies and devices (e.g. BrainPort) Rehabilitation of vegetative Functions - Cardiac Pacemaker - Phrenic stimulation, artificial breathing aids - Bladder stimulation, artificial sphincter Brain stimulation and recording - Deep brain stimulation for patients with Parkinson, epilepsy, depression - Brain-Computer Interfaces | |||||

Literature | Introductory Books: An Introduction to Rehabilitation Engineering. R. A. Cooper, H. Ohnabe, D. A. Hobson (Eds.). Taylor & Francis, 2007. Principles of Neural Science. E. R. Kandel, J. H. Schwartz, T. M Jessell (Eds.). Mc Graw Hill, New York, 2000. Force and Touch Feedback for Virtual Reality. G. C. Burdea (Ed.). Wiley, New York, 1996 (available on NEBIS). Human Haptic Perception, Basics and Applications. M. Grunwald (Ed.). Birkhäuser, Basel, 2008. The Sense of Touch and Its Rendering, Springer Tracts in Advanced Robotics 45, A. Bicchi et al.(Eds). Springer-Verlag Berlin, 2008. Interaktive und autonome Systeme der Medizintechnik - Funktionswiederherstellung und Organersatz. Herausgeber: J. Werner, Oldenbourg Wissenschaftsverlag 2005. Neural prostheses - replacing motor function after desease or disability. Eds.: R. Stein, H. Peckham, D. Popovic. New York and Oxford: Oxford University Press. Advances in Rehabilitation Robotics - Human-Friendly Technologies on Movement Assistance and Restoration for People with Disabilities. Eds: Z.Z. Bien, D. Stefanov (Lecture Notes in Control and Information Science, No. 306). Springer Verlag Berlin 2004. Intelligent Systems and Technologies in Rehabilitation Engineering. Eds: H.N.L. Teodorescu, L.C. Jain (International Series on Computational Intelligence). CRC Press Boca Raton, 2001. Selected Journal Articles and Web Links: Abbas, J., Riener, R. (2001) Using mathematical models and advanced control systems techniques to enhance neuroprosthesis function. Neuromodulation 4, pp. 187-195. Bach-y-Rita P., Tyler M., and Kaczmarek K (2003). Seeing with the brain. International journal of human-computer-interaction, 15(2):285-295. Burdea, G., Popescu, V., Hentz, V., and Colbert, K. (2000): Virtual reality-based orthopedic telerehabilitation, IEEE Trans. Rehab. Eng., 8, pp. 430-432 Colombo, G., Jörg, M., Schreier, R., Dietz, V. (2000) Treadmill training of paraplegic patients using a robotic orthosis. Journal of Rehabilitation Research and Development, vol. 37, pp. 693-700. Hayward, V. (2008): A Brief Taxonomy of Tactile Illusions and Demonstrations That Can Be Done In a Hardware Store. Brain Research Bulletin, Vol 75, No 6, pp 742-752 Krebs, H.I., Hogan, N., Aisen, M.L., Volpe, B.T. (1998): Robot-aided neurorehabilitation, IEEE Trans. Rehab. Eng., 6, pp. 75-87 Levesque. V. (2005). Blindness, technology and haptics. Technical report, McGill University. Available at: http://www.cim.mcgill.ca/~vleves/docs/VL-CIM-TR-05.08.pdf Quintern, J. (1998) Application of functional electrical stimulation in paraplegic patients. NeuroRehabilitation 10, pp. 205-250. Riener, R., Nef, T., Colombo, G. (2005) Robot-aided neurorehabilitation for the upper extremities. Medical & Biological Engineering & Computing 43(1), pp. 2-10. Riener, R. (1999) Model-based development of neuroprostheses for paraplegic patients. Royal Philosophical Transactions: Biological Sciences 354, pp. 877-894. The vOICe. http://www.seeingwithsound.com. VideoTact, ForeThought Development, LLC. http://my.execpc.com/?dwysocki/videotac.html | |||||

Prerequisites / Notice | Target Group: Students of higher semesters and PhD students of - D-MAVT, D-ITET, D-INFK, D-HEST - Biomedical Engineering, Robotics, Systems and Control - Medical Faculty, University of Zurich Students of other departments, faculties, courses are also welcome This lecture is independent from Rehabilitation Engineering I. Thus, both lectures can be visited in arbitrary order. | |||||

376-1279-00L | Virtual Reality in Medicine Does not take place this semester. | W | 3 credits | 2V | R. Riener | |

Abstract | Virtual Reality has the potential to support medical training and therapy. This lecture will derive the technical principles of multi-modal (audiovisual, haptic, tactile etc.) input devices, displays and rendering techniques. Examples are presented in the fields of surgical training, intra-operative augmentation, and rehabilitation. The lecture is accompanied by practical courses and excursions. | |||||

Objective | Provide theoretical and practical knowledge of new principles and applications of multi-modal simulation and interface technologies in medical education, therapy, and rehabilitation. | |||||

Content | Virtual Reality has the potential to provide descriptive and practical information for medical training and therapy while relieving the patient and/or the physician. Multi-modal interactions between the user and the virtual environment facilitate the generation of high-fidelity sensory impressions, by using not only visual and auditory modalities, but also kinesthetic, tactile, and even olfactory feedback. On the basis of the existing physiological constraints, this lecture will derive the technical requirements and principles of multi-modal input devices, displays, and rendering techniques. Several examples are presented that are currently being developed or already applied for surgical training, intra-operative augmentation, and rehabilitation. The lecture will be accompanied by several practical courses on graphical and haptic display devices as well as excursions to facilities equipped with large-scale VR equipment. Target Group: Students of higher semesters and PhD students of - D-HEST, D-MAVT, D-ITET, D-INFK, D-PHYS - Robotics, Systems and Control Master - Biomedical Engineering/Movement Science and Sport - Medical Faculty, University of Zurich Students of other departments, faculties, courses are also welcome! | |||||

Literature | Book: Virtual Reality in Medicine. Riener, Robert; Harders, Matthias; 2012 Springer. | |||||

Prerequisites / Notice | The course language is English. Basic experience in Information Technology and Computer Science will be of advantage More details will be announced in the lecture. | |||||

376-1714-00L | Biocompatible Materials | W | 4 credits | 3G | K. Maniura, J. Möller, M. Zenobi-Wong | |

Abstract | Introduction to molecules used for biomaterials, molecular interactions between different materials and biological systems (molecules, cells, tissues). The concept of biocompatibility is discussed and important techniques from biomaterials research and development are introduced. | |||||

Objective | The class consists of three parts: 1. Introdcution into molecular characteristics of molecules involved in the materials-to-biology interface. Molecular design of biomaterials. 2. The concept of biocompatibility. 3. Introduction into methodology used in biomaterials research and application. | |||||

Content | Introduction into native and polymeric biomaterials used for medical applications. The concepts of biocompatibility, biodegradation and the consequences of degradation products are discussed on the molecular level. Different classes of materials with respect to potential applications in tissue engineering and drug delivery are introduced. Strong focus lies on the molecular interactions between materials having very different bulk and/or surface chemistry with living cells, tissues and organs. In particular the interface between the materials surfaces and the eukaryotic cell surface and possible reactions of the cells with an implant material are elucidated. Techniques to design, produce and characterize materials in vitro as well as in vivo analysis of implanted and explanted materials are discussed. In addition, a link between academic research and industrial entrepreneurship is established by external guest speakers. | |||||

Lecture notes | Handouts can be accessed online. | |||||

Literature | Literatur Biomaterials Science: An Introduction to Materials in Medicine, Ratner B.D. et al, 3rd Edition, 2013 Comprehensive Biomaterials, Ducheyne P. et al., 1st Edition, 2011 (available online via ETH library) Handouts provided during the classes and references therin. | |||||

376-1351-00L | Micro/Nanotechnology and Microfluidics for Biomedical Applications | W | 2 credits | 2V | E. Delamarche | |

Abstract | This course is an introduction to techniques in micro/nanotechnology and to microfluidics. It reviews how many familiar devices are built and can be used for research and biomedical applications. Transistors for DNA sequencing, beamers for patterning proteins, hard-disk technology for biosensing and scanning microfluidics for analyzing tissue sections are just a few examples of the covered topics. | |||||

Objective | The main objective of the course is to introduce micro/nanotechnology and microfluidics to students having a background in the life sciences. The course should familiarize the students with the techniques used in micro/nanotechnology and show them how micro/nanotechnology pervades throughout life sciences. Microfluidics will be emphasized due to their increasing importance in research and medical applications. The second objective is to have life students less intimidated by micro/nanotechnology and make them able to link instruments and techniques to specific problems that they might have in their projects/studies. This will also help students getting access to the ETHZ/IBM Nanotech Center infrastructure if needed. | |||||

Content | Mostly formal lectures (2 × 45 min), with a 2 hour visit and introduction to cleanroom and micro/nanotechnology instruments, last 3 sessions would be dedicated to the presentation and evaluation of projects by students (3 students per team). | |||||

Prerequisites / Notice | Nanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations. | |||||

376-1720-00L | Application of MATLAB in the Human Movement Sciences | W | 2 credits | 2G | R. van de Langenberg | |

Abstract | Students will learn to import, process and graphically present experimental data using the MATLAB computing environment. Both the data and the methods of analysis will be typical for experiments in Human Movement Science (i.e. kinematics, kinetics and electromyography). | |||||

Objective | Students will acquire the ability to independently load, plot, and process kinematic, kinetic and electromyographical data using the MATLAB computing environment. | |||||

Content | Drawbacks of Excel; Possibilities in MATLAB; Import of several data formats; Plot of one and more signals; Removing of an offset and filtering of data based on self-written functions; Normalisation and parametrisation of data; Reliability; Interpolation, Differentiation and Integration in MATLAB. | |||||

Literature | During the lecture, several electronically available MATLAB introductions are indicated. Course-specific scripts will be provided by the lecturer. | |||||

Prerequisites / Notice | A Laptop with MATLAB installed (v2009 or higher) and wireless internet access is mandatory. Two students can share a laptop if necessary. A MATLAB student version can be obtained at Stud-IDES for free. | |||||

376-1974-00L | Colloquium in Biomechanics | W | 2 credits | 2K | B. Helgason, S. J. Ferguson, R. Müller, J. G. Snedeker, B. Taylor, K. Würtz-Kozak, M. Zenobi-Wong | |

Abstract | Current topics in biomechanics presented by speakers from academia and industry. | |||||

Objective | Getting insight into actual areas and problems of biomechanics. | |||||

376-2017-00L | Biomechanics of Sports Injuries and Rehabilitation | W | 3 credits | 2V | K.‑U. Schmitt, J. Goldhahn | |

Abstract | This lectures introduces the basic principles of injury mechanics and rehabilitation focussing on sports injuries. | |||||

Objective | Within the scope of this lecture you will learn the basic principles of trauma biomechanics. Based on examples from sports, you will get to know different mechanisms that can possibly result in injury. Investigating the background and cause of injury should allow you to assess the injury risk for sports activities. Furthermore you should be able to develop measures to prevent such injury. | |||||

Content | This lecture deals with the basic principles of injury mechanics and rehabilitation. Mechanisms that can result in injury are presented. Furthermore possibilities to prevent injuries are discussed. Thereby the lecture focuses on sports injuries. | |||||

Lecture notes | Handouts will be made available. | |||||

Literature | Schmitt K-U, Niederer P, M. Muser, Walz F: "Trauma Biomechanics - Accidental Injury in traffic and sports", Springer Verlag | |||||

Prerequisites / Notice | A course work is required. The mark of this course work contributes to the final credits for this lecture. Details will be given during the first lecture. | |||||

402-0341-00L | 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. | |||||

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 x-ray 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. | |||||

402-0674-00L | 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, mean-field 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. | |||||

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 mean-field 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. High-resolution 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. Low-energy electrons lead to phonon and high-energy electrons to plasmon excitations. Both effects are perfectly described by dipole and impact scattering. Thin-films of rather complex organic materials are often quantitatively characterized by photons with a broad range of wavelengths from ultra-violet to infra-red light. Asymmetries and preferential orientations of the (anisotropic) molecules are verified using the optical dichroism and second harmonic generation measurements. These characterization techniques are vital for optimizing the preparation of medical implants and the determination of tissue's anisotropies within the human body. Cell-surface 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. 3D scaffolds are important for tissue augmentation and engineering. Design, preparation methods, and characterization of these highly porous 3D microstructures are also presented. Visiting clinical research in a leading university hospital will show the usefulness of the lecture series. | |||||

465-0953-00L | Biostatistics | W | 4 credits | 2V + 1U | B. Sick | |

Abstract | The course deals with simple quantitative and graphical as well as more complex methods of biostatistics. Contents: Descriptive statistics, probability theory and design of experiments, testing hypotheses, confidence intervals, correlation, simple and multiple linear regression, classification and prediction, diagnostic tests, measurement of agreement. | |||||

Objective | ||||||

551-1295-00L | Introduction to Bioinformatics: Concepts and Applications | W | 6 credits | 4G | W. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner | |

Abstract | Storage, handling and analysis of large datasets have become essential in biological research. The course will introduce students to a number of applications of bioinformatics in biology. Freely accessible software tools and databases will be explained and explored in theory and praxis. | |||||

Objective | Introduction to Bioinformatics I: Concepts and Applications (formerly Bioinformatics I) will provide students with the theoretical background of approaches to store and retrieve information from large databases. Concepts will be developed how DNA sequence information can be used to understand phylogentic relationships, how RNA sequence relates to structure, and how protein sequence information can be used for genome annotation and to predict protein folding and structure. Students will be introduced to quantitative methods for measuring gene expression and how this information can be used to model gene networks. Methods will be discussed to construct protein interaction maps and how this information can be used to simulate dynamic molecular networks. In addition to the theoretical background, the students will develop hands-on experiences with the bioinformatics methods through guided exercises. The course provides students from different backgrounds with basic training in bioinformatics approaches that have impact on biological, chemical and physics experimentation. Bioinformatics approaches draw significant expertise from mathematics, statistics and computational science. Although "Intoduction to Bioinformatics I" will focus on theory and praxis of bioinformatics approaches, the course provides an important foundation for the course "Introduction to Bioinformatics II: Fundamentals of computer science, modeling and algorithms" that will be offered in the following semester. | |||||

Content | Bioinformatics I will cover the following topics: From genes to databases and information BLAST searches Prediction of gene function and regulation RNA structure prediction Gene expression analysis using microarrays Protein sequence and structure databases WWW for bioinformatics Protein sequence comparisons Proteomics and de novo protein sequencing Protein structure prediction Cellular and protein interaction networks Molecular dynamics simulation |

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