Autumn Semester 2020 takes place in a mixed form of online and classroom teaching.
Please read the published information on the individual courses carefully.

Search result: Catalogue data in Autumn Semester 2014

Biomedical Engineering Master Information
Master Programme According to Programme Regulations 2013
Track Courses
Bioelectronics
Track Core Courses
During the Master program, a minimum of 12 CP must be obtained from track core courses.
NumberTitleTypeECTSHoursLecturers
151-0604-00LMicrorobotics Information W4 credits3GB. Nelson
AbstractMicrorobotics 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.
ObjectiveThe 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.
ContentMain 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 notesThe 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 / NoticeThe lecture will be taught in English.
151-0605-00LNanosystemsW4 credits4GA. Stemmer
AbstractFrom 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.
ObjectiveFamiliarize students with basic science and engineering principles governing the nano domain.
ContentThe 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 / NoticeCourse format:

Lectures: Thursday 10-12, 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.
151-0621-00LMicrosystems Technology Information W6 credits4GC. Hierold, M. Haluska
AbstractStudents are introduced to the basics of micromachining and silicon process technology and will learn about the fabrication of microsystems and -devices by a sequence of defined processing steps (process flow).
ObjectiveStudents are introduced to the basics of micromachining and silicon process technology and will understand the fabrication of microsystem devices by the combination of unit process steps ( = process flow).
Content- Introduction to microsystems technology (MST) and micro electro mechanical systems (MEMS)
- Basic silicon technologies: Thermal oxidation, photolithography and etching, diffusion and ion implantation, thin film deposition.
- Specific microsystems technologies: Bulk and surface micromachining, dry and wet etching, isotropic and anisotropic etching, beam and membrane formation, wafer bonding, thin film mechanical and thermal properties, piezoelectric and piezoresitive materials.
- Selected microsystems: Mechanical sensors and actuators, microresonators, thermal sensors and actuators, system integration and encapsulation.
Lecture notesHandouts (available online)
Literature- S.M. Sze: Semiconductor Devices, Physics and Technology
- W. Menz, J. Mohr, O.Paul: Microsystem Technology
- G. Kovacs: Micromachined Transducer Sourcebook
Prerequisites / NoticePrerequisites: Physics I and II
227-0385-00LBiomedical Imaging Information W4 credits3GS. Kozerke, U. Moser, M. Rudin
AbstractIntroduction and analysis of medical imaging technology including X-ray procedures, computed tomography, nuclear imaging techniques using single photon and positron emission tomography, magnetic resonance imaging and ultrasound imaging techniques.
ObjectiveUnderstand the physical and technical principles underlying X-ray imaging, computed tomography, single photon and positron emission tomography, magnetic resonance imaging, ultrasound and Doppler imaging techniques. Develop the mathematical framework to describe image encoding/decoding, point-spread function/modular transfer function, signal-to-noise ratio, contrast behavior for each of the methods.
ContentX-ray imaging
Computed tomography
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
Ultrasound/Doppler imaging
Lecture notesLecture notes and handouts: Biomedical Imaging
LiteratureIntroduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith,
Cambridge University Press
227-0386-00LBiomedical Engineering Information W4 credits3GJ. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong
AbstractIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The focus is on learning the concepts that govern common medical instruments and the most important organs from an engineering point of view. In addition, the most recent achievements and trends of the field of biomedical engineering are also outlined.
ObjectiveIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The course provides an overview of the various topics of the different tracks of the biomedical engineering master course and helps orienting the students in selecting their specialized classes and project locations.
ContentIntroduction into neuro- and electrophysiology. Functional analysis of peripheral nerves, muscles, sensory organs and the central nervous system. Electrograms, evoked potentials. Audiometry, optometry. Functional electrostimulation: Cardiac pacemakers. Function of the heart and the circulatory system, transport and exchange of substances in the human body, pharmacokinetics. Endoscopy, medical television technology. Lithotripsy. Electrical Safety. Orthopaedic biomechanics. Lung function. Bioinformatics and Bioelectronics. Biomaterials. Biosensors. Microcirculation.Metabolism.
Practical and theoretical exercises in small groups in the laboratory.
Lecture notesIntroduction to Biomedical Engineering
by Enderle, Banchard, and Bronzino

AND

https://www1.ethz.ch/lbb/Education/BME
227-0427-00LSignal and Information Processing: Modeling, Filtering, LearningW6 credits4GH.‑A. Loeliger
AbstractFundamentals in signal processing, detection/estimation, and machine learning.
I. Linear signal representation and approximation: Hilbert spaces, LMMSE estimation, regularization and sparseness.
II. Learning linear and nonlinear functions and filters: kernel methods, neural networks.
III. Structured statistical models: hidden Markov models, factor graphs, Kalman filter, parameter estimation.
ObjectiveThe course is an introduction to some basic topics in signal processing, detection/estimation theory, and machine learning.
ContentPart I - Linear Signal Representation and Approximation: Hilbert spaces, least squares and LMMSE estimation, projection and estimation by linear filtering, learning linear functions and filters, regularization and sparseness, singular-value decomposition and pseudo-inverse, principal-components analysis.
Part II - Learning Nonlinear Functions: fundamentals of learning, neural networks, kernel methods.
Part III - Structured Statistical Models and Message Passing Algorithms: hidden Markov models, factor graphs, Gaussian message passing, Kalman filter and recursive least squares, Monte Carlo methods, parameter estimation, expectation maximization.
Lecture notesLecture notes.
Prerequisites / NoticePrerequisites:
- local bachelors: course "Discrete-Time and Statistical Signal Processing" (5. Sem.)
- others: solid basics in linear algebra and probability theory
376-1714-00LBiocompatible MaterialsW4 credits3GK. Maniura, P. M. Kollmannsberger, J. Möller, M. Zenobi-Wong
AbstractIntroduction 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.
ObjectiveThe 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.
ContentIntroduction 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 notesHandouts can be accessed online.
LiteratureLiteratur
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.
402-0674-00LPhysics in Medical Research: From Atoms to Cells Information W6 credits2V + 1UB. K. R. Müller
AbstractScanning 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.
ObjectiveThe 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.
227-1037-00LIntroduction to Neuroinformatics Information W6 credits2V + 1UK. A. Martin, M. Cook, V. Mante, M. Pfeiffer
AbstractThe course provides an introduction to the functional properties of neurons. Particularly the description of membrane electrical properties (action potentials, channels), neuronal anatomy, synaptic structures, and neuronal networks. Simple models of computation, learning, and behavior will be explained. Some artificial systems (robot, chip) are presented.
Objective
ContentThis course considers the structure and function of biological neural networks at different levels. The function of neural networks lies fundamentally in their wiring and in the electro-chemical properties of nerve cell membranes. Thus, the biological structure of the nerve cell needs to be understood if biologically-realistic models are to be constructed. These simpler models are used to estimate the electrical current flow through dendritic cables and explore how a more complex geometry of neurons influences this current flow. The active properties of nerves are studied to understand both sensory transduction and the generation and transmission of nerve impulses along axons. The concept of local neuronal circuits arises in the context of the rules governing the formation of nerve connections and topographic projections within the nervous system. Communication between neurons in the network can be thought of as information flow across synapses, which can be modified by experience. We need an understanding of the action of inhibitory and excitatory neurotransmitters and neuromodulators, so that the dynamics and logic of synapses can be interpreted. Finally, the neural architectures of feedforward and recurrent networks will be discussed in the context of co-ordination, control, and integration of sensory and motor information in neural networks.
Recommended Elective Courses
These courses are particularly recommended for the Bioelectronics track. Please consult your track advisor if you wish to select other subjects.
NumberTitleTypeECTSHoursLecturers
227-0166-00LAnalog Integrated Circuits Information W6 credits2V + 2UQ. Huang
AbstractThis course provides a foundation in analog integrated circuit design based on bipolar and CMOS technologies.
ObjectiveIntegrated circuits are responsible for much of the progress in electronics in the last 50 years, particularly the revolutions in the Information and Communications Technologies we witnessed in recent years. Analog integrated circuits play a crucial part in the highly integrated systems that power the popular electronic devices we use daily. Understanding their design is beneficial to both future designers and users of such systems.
The basic elements, design issues and techniques for analog integrated circuits will be taught in this course.
ContentReview of bipolar and MOS devices and their small-signal equivalent circuit models; Building blocks in analog circuits such as current sources, active load, current mirrors, supply independent biasing etc; Amplifiers: differential amplifiers, cascode amplifier, high gain structures, output stages, gain bandwidth product of op-amps; Stability; Comparators; Second-order effects in analog circuits such as mismatch, noise and offset; A/D and D/A converters; Introduction to switched capacitor circuits.
The exercise sessions aim to reinforce the lecture material by well guided step-by-step design tasks. The circuit simulator SPECTRE is used to facilitate the tasks. There is also an experimental session on op-amp measurments.
Lecture notesHandouts of presented slides. No script but an accompanying textbook is recommended.
LiteratureGray, Hurst, Lewis, Meyer, "Analysis and Design of Analog Integrated Circuits", 5th Ed. Wiley, 2010.
227-0447-00LImage Analysis and Computer Vision Information W6 credits3V + 1UG. Székely, O. Göksel, L. Van Gool
AbstractLight and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation and deformable shape matching. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition.
ObjectiveOverview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.
ContentThe first part of the course starts off from 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 it is investigated how the parameters of the electromagnetic waves are related to our perception. Also the interaction of light with matter is considered. The most important hardware components of technical vision systems, such as cameras, optical devices and illumination sources are discussed. The course then turns to the steps that are necessary to arrive at the discrete images that serve as input to algorithms. The next part describes necessary preprocessing steps of image analysis, that enhance image quality and/or detect specific features. Linear and non-linear 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 depth as two important examples. The estimation of image velocities (optical flow) will get due attention and methods for object tracking will be presented. Several techniques are discussed to extract three-dimensional information about objects and scenes. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed.
Lecture notesCourse material Script, computer demonstrations, exercises and problem solutions
Prerequisites / NoticePrerequisites:
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
227-0963-00LStatistical Parametric Mapping (SPM)W2 credits1VK. Stephan
AbstractThis course provides a comprehensive coverage of state-of-the-art statistical methods for fMRI data analysis, focusing on tools provided by the open source software package SPM
ObjectiveKnowledge of modern statistical methods for fMRI data analysis
ContentSpatial preprocessing & physiological noise correction
Voxel-based morphometry
Mass-univariate & multivariate analyses of fMRI
'Resting state' fMRI
Bayesian analysis methods
Effective connectivity analyses (Dynamic Causal Modeling)
227-0981-00LCross-Disciplinary Research and Development in Medicine and Engineering Restricted registration - show details
A maximum of 8 medical degree students and 8 (biomedical) engineering degree students can be admitted, their number should be equal.
W4 credits2V + 2AV. Kurtcuoglu, D. de Julien de Zelicourt, M. Meboldt, M. Schmid Daners, O. Ullrich
AbstractCross-disciplinary collaboration between engineers and medical doctors is indispensable for innovation in health care. This course will bring together engineering students from ETH Zurich and medical students from the University of Zurich to experience the rewards and challenges of such interdisciplinary work in a project based learning environment.
ObjectiveThe main goal of this course is to demonstrate the differences in communication between the fields of medicine and engineering. Since such differences become the most evident during actual collaborative work, the course is based on a current project in physiology research that combines medicine and engineering. For the engineering students, the specific aims of the course are to:

- Acquire a working understanding of the anatomy and physiology of the investigated system;
- Identify the engineering challenges in the project and communicate them to the medical students;
- Develop and implement, together with the medical students, solution strategies for the identified challenges;
- Present the found solutions to a cross-disciplinary audience.
ContentAfter a general introduction to interdisciplinary communication and detailed background on the collaborative project, the engineering students will receive tailored lectures on the anatomy and physiology of the relevant system. They will then team up with medical students who have received a basic introduction to engineering methodology to collaborate on said project. In the process, they will be coached both by lecturers from ETH Zurich and the University of Zurich, receiving lectures customized to the project. The course will end with each team presenting their solution to a cross-disciplinary audience.
Lecture notesHandouts and relevant literature will be provided.
227-1033-00LNeuromorphic Engineering I Information W6 credits2V + 3UT. Delbrück, G. Indiveri, S.‑C. Liu
AbstractThis course covers analog circuits with emphasis on neuromorphic engineering: MOS transistors in CMOS technology, static circuits, dynamic circuits, systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions.
ObjectiveUnderstanding of the characteristics of neuromorphic circuit elements and their interaction in parallel networks.
ContentNeuromorphic circuits are inspired by the structure, function and plasticity of biological neurons and neural networks. Their computational primitives are based on physics of semiconductor devices. Neuromorphic architectures often rely on collective computation in parallel networks. Adaptation, learning and memory are implemented locally within the individual computational elements. Transistors are often operated in weak inversion (below threshold), where they exhibit exponential I-V characteristics and low currents. These properties lead to the feasibility of high-density, low-power implementations of functions that are computationally intensive in other paradigms. The high parallelism and connectivity of neuromorphic circuits permit structures with massive feedback without iterative methods and convergence problems and real-time processing networks for high-dimensional signals (e.g. vision). Application domains of neuromorphic circuits include silcon retinas and cochleas, real-time emulations of networks of biological neurons, and the development of autonomous robotic systems. This course covers devices in CMOS technology (MOS transistor below and above threshold, floating-gate MOS transistor, phototransducers), static circuits (differential pair, current mirror, transconductance amplifiers, multipliers, power-law circuits, resistive networks, etc.), dynamic circuits (linear and nonlinear filters, adaptive circuits), systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions on the characterization of neuromorphic circuits, from elementary devices to systems.
LiteratureS.-C. Liu et al.: Analog VLSI Circuits and Principles; various publications.
Prerequisites / NoticeParticular: The course is highly recommended for those who intend to take the spring semester course 'Neuromorphic Engineering II', that teaches the conception and layout of such circuits with a set of inexpensive software tools, ending with an optional submission of a mini-project for CMOS fabrication.

Prerequisites: Background in basics of semiconductor physics helpful, but not required.
227-2037-00LPhysical Modelling and Simulation Information W5 credits4GC. Hafner, J. Smajic
AbstractPhysical modelling plays an important role in the analysis and design of new structures, especially for micro and nano devices where fabrication and measurement are difficult. After the fundamentals of electromagnetics, mechanics, and thermodynamics, an introduction to the main concepts and most widely used codes for physical modelling is given and commercial codes are applied.
ObjectiveBasic knowledge of the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics. Knowledge of the main concepts of numerical methods for physical modelling and simulation. Ability 1) to select appropriate software, 2) to apply it for solving given problems, 3) to validate the results, 4) to interactively improve the models until sufficiently accurate results are obtained.
ContentSince the fabrication and characterization of micro- and nanostructures is difficult, expensive, and time-consuming, numerical modelling drastically reduced the design process. Although many commercial software packages are available, it is important to know the drawbacks and difficulties of the numerical methods behind them and to be able to validate the results obtained with such packages.
First, an introduction to the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics is given. This is important for understanding the problems to be analyzed and for validating results obtained from software packages. After this, the main concepts of numerical methods and of the most widely used codes for physical modelling are outlined and compared, which is essential for the adequate selection of software for solving given problems. After this, prominent commercial software packages are applied to various types of problems, ranging from electrodynamics to multiphysics. For becoming able to select appropriate software and to validate the results obtained, different commercial software packages will be used and compared during the exercises in form of small projects.
151-0255-00LEnergy Conversion and Transport in Biosystems
Does not take place this semester.
W4 credits2V + 1UD. Poulikakos, A. Ferrari
AbstractTheory and application of thermodynamics, energy conversion and fluid dynamics in biological systems and biomedicine at the macro scale and the cellular level.
ObjectiveTheory and application of energy conversion at the macro scale and the cellular level. Understanding of the basic features governing fluid transport in the principal fluidic systems of the human body. Connection of characteristics and patterns from other fields of engineering to biofluidics. Heat and mass transport processes within the human body and relation to biomedical technologies.
ContentHeat and mass transfer models for the transport of thermal energy and chemical species in the human body. Physiology, pathology and biomedical intervention based on extreme temperatures (medical radio frequency therapy, tissue freezing and cryotherapy). Introduction to the main fluidic systems of the human body (cardiovascular, cerebrospinal etc.). Description of the functionality of these systems and of analytical experimental and computational techniques for understanding of their operation. Introduction to bioengineering approaches for the treatment of common pathogenic conditions of these systems. Introduction to cell metabolism, cellular energy transport and cellular thermodynamics.
Lecture notesScript as well as additional material in the form of hand-outs will be distributed.
LiteratureLecture notes and references therein.
252-0523-00LComputational Biology Information W6 credits3V + 2UG. H. Gonnet
AbstractStudy of computational techniques, algorithms and data structures used to solve problems in computational biology. Topics: basic biology, string alignment, phylogeny (distance, character, parsimony), molecular evolution, multiple sequence alignment, probabilistic and statistical models, Markov models, microarrays, dynamic programming, maximum likelihood and specialized DNA and protein analysis.
ObjectiveFamiliarize the students with the basic concepts of molecular biology and the models and algorithms used to understand, classify and predict behaviour of living organism. This course is at the most basic level, where the main issues, mostly of molecular sequences, are studied.
ContentThis course lies in the intersection between Computer Science and Molecular Biology. The main purpose is to study computational techniques, algorithms and data structures which are usually applied to solve problems in Molecular Biology and Biochemistry.
The following topics are likely to be covered: Introduction, mathematical models of evolution, protein and DNA sequence alignment and its meaning, phylogenetic tree construction, multiple sequence alignments, secondary structure prediction, molecular dynamics, threading, role of bioinformatics in drug design, etc. From the computer science point of view we concentrate our attention in practical solutions for the above problems. Biological knowledge is an asset but not a prerequisite.
376-1219-00LRehabilitation Engineering II: Rehabilitation of Sensory and Vegetative Functions Information W3 credits2VR. Riener, R. Gassert
AbstractRehab. Engineering 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.
ObjectiveProvide 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.
ContentIntroduction, 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
LiteratureIntroductory 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 / NoticeTarget 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
376-1351-00LMicro/Nanotechnology and Microfluidics for Biomedical ApplicationsW2 credits2VE. Delamarche
AbstractThis 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.
ObjectiveThe 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.
ContentMostly 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 / NoticeNanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations.
529-0837-00LBiomicrofluidic EngineeringW7 credits3GA. de Mello
AbstractMicrofluidics describes the behaviour, control and manipulation of fluids that are geometrically constrained within sub-microliter environments. The use of microfluidic devices offers an opportunity to control physical and chemical processes with unrivalled precision, and in turn provides a route to performing chemistry and biology in an ultra-fast and high-efficiency manner.
ObjectiveIn the course students will investigate the theoretical concepts behind microfluidic device operation, the methods of microfluidic device manufacture and the application of microfluidic architectures to important problems faced in modern day chemical and biological analysis. A design workshop will allow students to develop new microscale flow processes by appreciating the dominant physics at the microscale. The application of these basic ideas will primarily focus on biological problems and will include a treatment of diagnostic devices for use at the point-of-care, advanced functional material synthesis, DNA analysis, proteomics and cell-based assays. Lectures, assignments and the design workshop will acquaint students with the state-of-the-art in applied microfluidics.
ContentSpecific topics in the course include, but not limited to:

1. Theoretical Concepts
Features of mass and thermal transport on the microscale
Key scaling laws
2. Microfluidic Device Manufacture
Conventional lithographic processing of rigid materials
Soft lithographic processing of plastics and polymers
Mass fabrication of polymeric devices
3. Unit operations and functional components
Analytical separations (electrophoresis and chromatography)
Chemical and biological synthesis
Sample pre-treatment (filtration, SPE, pre-concentration)
Molecular detection
4. Design Workshop
Design of microfluidic architectures for PCR, distillation & mixing
5. Contemporary Applications in Biological Analysis
Microarrays
Cellular analyses (single cells, enzymatic assays, cell sorting)
Proteomics
6. System integration
Applications in radiochemistry, diagnostics and high-throughput experimentation
Lecture notesLecture handouts will be provided
Prerequisites / NoticeThis lecture will be recorded for Students of Basel (BSSE), details will be announced later.
636-0003-00LBiological Engineering and BiotechnologyW6 credits3GM. Fussenegger
AbstractBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
Objective1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development.
Lecture notesHandsout during the course.
Biology Courses
NumberTitleTypeECTSHoursLecturers
227-0945-00LCell and Molecular Biology for EngineersW6 credits4GC. Frei
AbstractThe 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.
ObjectiveAfter 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.
ContentLectures will include the following topics: DNA, chromosomes, RNA, protein, genetics, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer, development and stem cells.

In addition, three journal clubs will be held, where one/two publictions will be discussed. 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 25% for the final grade.
Lecture notesScripts of all lectures will be available.
Literature"Molecular Biology of the Cell" (5th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.
Bioimaging
Track Core Courses
During the Master program, a minimum of 12 CP must be obtained from track core courses.
NumberTitleTypeECTSHoursLecturers
227-0385-00LBiomedical Imaging Information W4 credits3GS. Kozerke, U. Moser, M. Rudin
AbstractIntroduction and analysis of medical imaging technology including X-ray procedures, computed tomography, nuclear imaging techniques using single photon and positron emission tomography, magnetic resonance imaging and ultrasound imaging techniques.
ObjectiveUnderstand the physical and technical principles underlying X-ray imaging, computed tomography, single photon and positron emission tomography, magnetic resonance imaging, ultrasound and Doppler imaging techniques. Develop the mathematical framework to describe image encoding/decoding, point-spread function/modular transfer function, signal-to-noise ratio, contrast behavior for each of the methods.
ContentX-ray imaging
Computed tomography
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
Ultrasound/Doppler imaging
Lecture notesLecture notes and handouts: Biomedical Imaging
LiteratureIntroduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith,
Cambridge University Press
227-0386-00LBiomedical Engineering Information W4 credits3GJ. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong
AbstractIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The focus is on learning the concepts that govern common medical instruments and the most important organs from an engineering point of view. In addition, the most recent achievements and trends of the field of biomedical engineering are also outlined.
ObjectiveIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The course provides an overview of the various topics of the different tracks of the biomedical engineering master course and helps orienting the students in selecting their specialized classes and project locations.
ContentIntroduction into neuro- and electrophysiology. Functional analysis of peripheral nerves, muscles, sensory organs and the central nervous system. Electrograms, evoked potentials. Audiometry, optometry. Functional electrostimulation: Cardiac pacemakers. Function of the heart and the circulatory system, transport and exchange of substances in the human body, pharmacokinetics. Endoscopy, medical television technology. Lithotripsy. Electrical Safety. Orthopaedic biomechanics. Lung function. Bioinformatics and Bioelectronics. Biomaterials. Biosensors. Microcirculation.Metabolism.
Practical and theoretical exercises in small groups in the laboratory.
Lecture notesIntroduction to Biomedical Engineering
by Enderle, Banchard, and Bronzino

AND

https://www1.ethz.ch/lbb/Education/BME
227-0447-00LImage Analysis and Computer Vision Information W6 credits3V + 1UG. Székely, O. Göksel, L. Van Gool
AbstractLight and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation and deformable shape matching. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition.
ObjectiveOverview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.
ContentThe first part of the course starts off from 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 it is investigated how the parameters of the electromagnetic waves are related to our perception. Also the interaction of light with matter is considered. The most important hardware components of technical vision systems, such as cameras, optical devices and illumination sources are discussed. The course then turns to the steps that are necessary to arrive at the discrete images that serve as input to algorithms. The next part describes necessary preprocessing steps of image analysis, that enhance image quality and/or detect specific features. Linear and non-linear 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 depth as two important examples. The estimation of image velocities (optical flow) will get due attention and methods for object tracking will be presented. Several techniques are discussed to extract three-dimensional information about objects and scenes. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed.
Lecture notesCourse material Script, computer demonstrations, exercises and problem solutions
Prerequisites / NoticePrerequisites:
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
227-0965-00LMicro and Nano-Tomography of Biological TissuesW4 credits3GM. Stampanoni, K. S. Mader
AbstractThe lecture introduces the physical and technical know-how of X-ray tomographic microscopy. Several X-ray 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.
ObjectiveIntroduction to the basic concepts of X-ray tomographic imaging, image analysis and data quantification at the micro and nano scale with particular emphasis on biological applications
ContentSynchrotron-based X-ray micro- and nano-tomography is today a powerful technique for non-destructive, high-resolution investigations of a broad range of materials. The high-brilliance and high-coherence of third generation synchrotron radiation facilities allow quantitative, three-dimensional imaging at the micro and nanometer scale and extend the traditional absorption imaging technique to edge-enhanced and phase-sensitive 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 X-ray nano-tomographic 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 notesAvailable online
LiteratureWill be indicated during the lecture.
Recommended Elective Courses
These courses are particularly recommended for the Bioimaging track. Please consult your track advisor if you wish to select other subjects.
NumberTitleTypeECTSHoursLecturers
227-0389-00LAdvanced Topics in Magnetic Resonance ImagingZ0 credits1VK. P. Prüssmann
AbstractThis course is geared towards master and PhD students with a focus on bioimaging. It covers advanced topics in magnetic resonance imaging in biennial rotation, including the electrodynamics of MR signal detection, noise mechanisms, image reconstruction, radiofrequency pulse design, RF pulse trains, as well as advanced contrast mechanisms.
Objectivesee above
227-0391-00LMedical Image AnalysisW3 credits2GP. C. Cattin, M. A. Reyes Aguirre
AbstractIt is the objective of this lecture to introduce the basic concepts used
in Medical Image Analysis. In particular the lecture focuses on shape
representation schemes, segmentation techniques, and the various image registration methods commonly used in Medical Image Analysis applications.
ObjectiveThis lecture aims to give an overview of the basic concepts of Medical Image Analysis and its application areas.
Prerequisites / NoticeBasic knowledge of computer vision would be helpful.
227-0963-00LStatistical Parametric Mapping (SPM)W2 credits1VK. Stephan
AbstractThis course provides a comprehensive coverage of state-of-the-art statistical methods for fMRI data analysis, focusing on tools provided by the open source software package SPM
ObjectiveKnowledge of modern statistical methods for fMRI data analysis
ContentSpatial preprocessing & physiological noise correction
Voxel-based morphometry
Mass-univariate & multivariate analyses of fMRI
'Resting state' fMRI
Bayesian analysis methods
Effective connectivity analyses (Dynamic Causal Modeling)
227-0967-00LComputational Neuroimaging Clinic Information W3 credits2VK. Stephan
AbstractThis seminar teaches problem solving skills for the design and analysis of neuroimaging data (fMRI, EEG). It deals with a wide variety of real-life problems that are brought to this meeting from the neuroimaging community at Zurich. Examples may include mass-univariate and multivariate analyses of fMRI data, dynamic causal modeling of fMRI and EEG data.
Objective1. Consolidation of theoretical knowledge (obtained in the 'Methods & models for fMRI data analysis' lecture) in a practical setting.
2. Acquisition of practical problem solving strategies for computational modeling of neuroimaging data.
ContentThis seminar teaches problem solving skills for the design and analysis of neuroimaging data (fMRI, EEG). It deals with a wide variety of real-life problems that are brought to this meeting from the euroimaging community at Zurich. Examples may include mass-univariate and multivariate analyses of fMRI data, dynamic causal modeling of fMRI and EEG data, or analyses of neuroimaging data on the basis of Bayesian models of behaviour.
227-0969-00LMethods & Models for fMRI Data Analysis Information W3 credits2VK. Stephan
AbstractThis course teaches methods and models for fMRI data analysis, covering all aspects of statistical parametric mapping (SPM), incl. preprocessing, the general linear model, statistical inference, multiple comparison corrections, event-related designs, and Dynamic Causal Modelling (DCM), a Bayesian framework for identification of nonlinear neuronal systems from neurophysiological data.
ObjectiveTo obtain in-depth knowledge of the theoretical foundations of SPM
and DCM and of their application to empirical fMRI data.
ContentThis course teaches state-of-the-art methods and models for fMRI data analysis. It covers all aspects of statistical parametric mapping (SPM), incl. preprocessing, the general linear model, frequentist and Bayesian inference, multiple comparison corrections, and event-related designs, and Dynamic Causal Modelling (DCM), a Bayesian framework for identification of nonlinear neuronal systems from neurophysiological data. A particular emphasis of the course will be on methodological questions arising in the context of neuroeconomic and clinical studies.
227-0971-00LComputational Psychiatry Information W3 credits2SK. Stephan
AbstractCurrent methods and concepts for deciphering mechanisms of maladaptive behaviour, such as aberrant learning and decision-making in healthy individuals and psychiatric patients.The key goal is to connect methodological training with biological and clinical knowledge about the phenomenology and pathophysiology of psychiatric and neurological diseases.
ObjectiveTo understand current concepts about computational and physiological mechanisms of maladaptive behaviour and psychiatric diseases.
ContentIn this seminar, we discuss current methods and concepts for deciphering mechanisms of maladaptive behaviour, such as aberrant learning and decision-making in healthy individuals and psychiatric patients. The key goal is to connect methodological training (in computational and statistical techniques for analyzing behavioural, fMRI and EEG data) with biological and clinical knowledge about the phenomenology and pathophysiology of psychiatric and neurological diseases. This seminar aims at bridging the gap between mathematical modelers and clinical neuroscientists, enabling more effective communication and joint translational research. To this end, each semester a novel topic is chosen which is examined both from clinical/biological and modeling perspectives.
227-2037-00LPhysical Modelling and Simulation Information W5 credits4GC. Hafner, J. Smajic
AbstractPhysical modelling plays an important role in the analysis and design of new structures, especially for micro and nano devices where fabrication and measurement are difficult. After the fundamentals of electromagnetics, mechanics, and thermodynamics, an introduction to the main concepts and most widely used codes for physical modelling is given and commercial codes are applied.
ObjectiveBasic knowledge of the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics. Knowledge of the main concepts of numerical methods for physical modelling and simulation. Ability 1) to select appropriate software, 2) to apply it for solving given problems, 3) to validate the results, 4) to interactively improve the models until sufficiently accurate results are obtained.
ContentSince the fabrication and characterization of micro- and nanostructures is difficult, expensive, and time-consuming, numerical modelling drastically reduced the design process. Although many commercial software packages are available, it is important to know the drawbacks and difficulties of the numerical methods behind them and to be able to validate the results obtained with such packages.
First, an introduction to the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics is given. This is important for understanding the problems to be analyzed and for validating results obtained from software packages. After this, the main concepts of numerical methods and of the most widely used codes for physical modelling are outlined and compared, which is essential for the adequate selection of software for solving given problems. After this, prominent commercial software packages are applied to various types of problems, ranging from electrodynamics to multiphysics. For becoming able to select appropriate software and to validate the results obtained, different commercial software packages will be used and compared during the exercises in form of small projects.
151-0105-00LQuantitative Flow VisualizationW4 credits2V + 1UT. Rösgen
AbstractThe course provides an introduction to digital image analysis in modern flow diagnostics. Different techniques which are discussed include image velocimetry, laser induced fluorescence, liquid crystal thermography and interferometry. The physical foundations and measurement configurations are explained. Image analysis algorithms are presented in detail and programmed during the exercises.
ObjectiveIntroduction to modern imaging techniques and post processing algorithms with special emphasis on flow analysis and visualization.
Understanding of hardware and software requirements and solutions.
Development of basic programming skills for (generic) imaging applications.
ContentFundamentals of optics, flow visualization and electronic image acquisition.
Frequently used mage processing techniques (filtering, correlation processing, FFTs, color space transforms).
Image Velocimetry (tracking, pattern matching, Doppler imaging).
Surface pressure and temperature measurements (fluorescent paints, liquid crystal imaging, infrared thermography).
Laser induced fluorescence.
(Digital) Schlieren techniques, phase contrast imaging, interferometry, phase unwrapping.
Wall shear and heat transfer measurements.
Pattern recognition and feature extraction, proper orthogonal decomposition.
Lecture notesavailable
Prerequisites / NoticePrerequisites: Fluiddynamics I, Numerical Mathematics, programming skills.
Language: German on request.
376-1279-00LVirtual Reality in Medicine Restricted registration - show details
Does not take place this semester.
W3 credits2VR. Riener
AbstractVirtual 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.
ObjectiveProvide theoretical and practical knowledge of new principles and applications of multi-modal simulation and interface technologies in medical education, therapy, and rehabilitation.
ContentVirtual 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!
LiteratureBook: Virtual Reality in Medicine. Riener, Robert; Harders, Matthias; 2012 Springer.
Prerequisites / NoticeThe course language is English.
Basic experience in Information Technology and Computer Science will be of advantage
More details will be announced in the lecture.
151-0605-00LNanosystemsW4 credits4GA. Stemmer
AbstractFrom 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.
ObjectiveFamiliarize students with basic science and engineering principles governing the nano domain.
ContentThe 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 / NoticeCourse format:

Lectures: Thursday 10-12, 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.
252-0543-01LComputer Graphics Information W6 credits3V + 2UM. Gross, O. Sorkine Hornung
AbstractThis course covers some of the fundamental concepts of computer graphics. The two main parts of the class are image synthesis and geometric modeling.
ObjectiveAt the end of the course students will be able to design and implement a rendering system based on raytracing. You will study the basic principles of modeling with splines and integrate spline-based representations into a rendering system. In addition we want to stimulate your curiosity to explore the field of computer graphics on your own or in future courses.
ContentThis course covers some of the fundamental concepts of computer graphics. The two main parts of the class are rendering and modeling. In the first part, we will discuss the basics of photorealistic image synthesis, i.e. how to generate a realistic image from a digital representation of a 3D scene. After introducing raytracing, we will briefly look at the physics of light transport, discuss the rendering equation, and investigate some advanced techniques to enhance the realism of rendered images. The second part will introduce the basics of modeling with curves and surfaces. We will discuss Bezier curves and surfaces, B-Splines and NURBS, and show how they can be used to design complex 3D geometry.
Lecture notesno
Prerequisites / NoticePrerequisites:
Fundamentals of calculus and linear algebra, basic concepts of algorithms and data structures, basic programming skills in C-like languages (we use JavaScript for exercises), Visual Computing core course recommended.
402-0674-00LPhysics in Medical Research: From Atoms to Cells Information W6 credits2V + 1UB. K. R. Müller
AbstractScanning 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.
ObjectiveThe 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.
227-1033-00LNeuromorphic Engineering I Information W6 credits2V + 3UT. Delbrück, G. Indiveri, S.‑C. Liu
AbstractThis course covers analog circuits with emphasis on neuromorphic engineering: MOS transistors in CMOS technology, static circuits, dynamic circuits, systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions.
ObjectiveUnderstanding of the characteristics of neuromorphic circuit elements and their interaction in parallel networks.
ContentNeuromorphic circuits are inspired by the structure, function and plasticity of biological neurons and neural networks. Their computational primitives are based on physics of semiconductor devices. Neuromorphic architectures often rely on collective computation in parallel networks. Adaptation, learning and memory are implemented locally within the individual computational elements. Transistors are often operated in weak inversion (below threshold), where they exhibit exponential I-V characteristics and low currents. These properties lead to the feasibility of high-density, low-power implementations of functions that are computationally intensive in other paradigms. The high parallelism and connectivity of neuromorphic circuits permit structures with massive feedback without iterative methods and convergence problems and real-time processing networks for high-dimensional signals (e.g. vision). Application domains of neuromorphic circuits include silcon retinas and cochleas, real-time emulations of networks of biological neurons, and the development of autonomous robotic systems. This course covers devices in CMOS technology (MOS transistor below and above threshold, floating-gate MOS transistor, phototransducers), static circuits (differential pair, current mirror, transconductance amplifiers, multipliers, power-law circuits, resistive networks, etc.), dynamic circuits (linear and nonlinear filters, adaptive circuits), systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions on the characterization of neuromorphic circuits, from elementary devices to systems.
LiteratureS.-C. Liu et al.: Analog VLSI Circuits and Principles; various publications.
Prerequisites / NoticeParticular: The course is highly recommended for those who intend to take the spring semester course 'Neuromorphic Engineering II', that teaches the conception and layout of such circuits with a set of inexpensive software tools, ending with an optional submission of a mini-project for CMOS fabrication.

Prerequisites: Background in basics of semiconductor physics helpful, but not required.
227-1037-00LIntroduction to Neuroinformatics Information W6 credits2V + 1UK. A. Martin, M. Cook, V. Mante, M. Pfeiffer
AbstractThe course provides an introduction to the functional properties of neurons. Particularly the description of membrane electrical properties (action potentials, channels), neuronal anatomy, synaptic structures, and neuronal networks. Simple models of computation, learning, and behavior will be explained. Some artificial systems (robot, chip) are presented.
Objective
ContentThis course considers the structure and function of biological neural networks at different levels. The function of neural networks lies fundamentally in their wiring and in the electro-chemical properties of nerve cell membranes. Thus, the biological structure of the nerve cell needs to be understood if biologically-realistic models are to be constructed. These simpler models are used to estimate the electrical current flow through dendritic cables and explore how a more complex geometry of neurons influences this current flow. The active properties of nerves are studied to understand both sensory transduction and the generation and transmission of nerve impulses along axons. The concept of local neuronal circuits arises in the context of the rules governing the formation of nerve connections and topographic projections within the nervous system. Communication between neurons in the network can be thought of as information flow across synapses, which can be modified by experience. We need an understanding of the action of inhibitory and excitatory neurotransmitters and neuromodulators, so that the dynamics and logic of synapses can be interpreted. Finally, the neural architectures of feedforward and recurrent networks will be discussed in the context of co-ordination, control, and integration of sensory and motor information in neural networks.
465-0953-00LBiostatisticsW2 credits2V + 1UB. Sick
AbstractThe 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, analysis of variance, logistic regression, survival analysis (Kaplan-Meier curves and Cox-regression).
Objective
551-1295-00LIntroduction to Bioinformatics: Concepts and Applications Information W6 credits4GW. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner
AbstractStorage, 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.
ObjectiveIntroduction 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.
ContentBioinformatics 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
Biology Courses
NumberTitleTypeECTSHoursLecturers
227-0945-00LCell and Molecular Biology for EngineersO6 credits4GC. Frei
AbstractThe 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.
ObjectiveAfter 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.
ContentLectures will include the following topics: DNA, chromosomes, RNA, protein, genetics, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer, development and stem cells.

In addition, three journal clubs will be held, where one/two publictions will be discussed. 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 25% for the final grade.
Lecture notesScripts of all lectures will be available.
Literature"Molecular Biology of the Cell" (5th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.
Biomechanics
Track Core Courses
During the Master program, a minimum of 12 CP must be obtained from track core courses.
NumberTitleTypeECTSHoursLecturers
227-0385-00LBiomedical Imaging Information W4 credits3GS. Kozerke, U. Moser, M. Rudin
AbstractIntroduction and analysis of medical imaging technology including X-ray procedures, computed tomography, nuclear imaging techniques using single photon and positron emission tomography, magnetic resonance imaging and ultrasound imaging techniques.
ObjectiveUnderstand the physical and technical principles underlying X-ray imaging, computed tomography, single photon and positron emission tomography, magnetic resonance imaging, ultrasound and Doppler imaging techniques. Develop the mathematical framework to describe image encoding/decoding, point-spread function/modular transfer function, signal-to-noise ratio, contrast behavior for each of the methods.
ContentX-ray imaging
Computed tomography
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
Ultrasound/Doppler imaging
Lecture notesLecture notes and handouts: Biomedical Imaging
LiteratureIntroduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith,
Cambridge University Press
227-0386-00LBiomedical Engineering Information W4 credits3GJ. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong
AbstractIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The focus is on learning the concepts that govern common medical instruments and the most important organs from an engineering point of view. In addition, the most recent achievements and trends of the field of biomedical engineering are also outlined.
ObjectiveIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The course provides an overview of the various topics of the different tracks of the biomedical engineering master course and helps orienting the students in selecting their specialized classes and project locations.
ContentIntroduction into neuro- and electrophysiology. Functional analysis of peripheral nerves, muscles, sensory organs and the central nervous system. Electrograms, evoked potentials. Audiometry, optometry. Functional electrostimulation: Cardiac pacemakers. Function of the heart and the circulatory system, transport and exchange of substances in the human body, pharmacokinetics. Endoscopy, medical television technology. Lithotripsy. Electrical Safety. Orthopaedic biomechanics. Lung function. Bioinformatics and Bioelectronics. Biomaterials. Biosensors. Microcirculation.Metabolism.
Practical and theoretical exercises in small groups in the laboratory.
Lecture notesIntroduction to Biomedical Engineering
by Enderle, Banchard, and Bronzino

AND

https://www1.ethz.ch/lbb/Education/BME
227-0447-00LImage Analysis and Computer Vision Information W6 credits3V + 1UG. Székely, O. Göksel, L. Van Gool
AbstractLight and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation and deformable shape matching. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition.
ObjectiveOverview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.
ContentThe first part of the course starts off from 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 it is investigated how the parameters of the electromagnetic waves are related to our perception. Also the interaction of light with matter is considered. The most important hardware components of technical vision systems, such as cameras, optical devices and illumination sources are discussed. The course then turns to the steps that are necessary to arrive at the discrete images that serve as input to algorithms. The next part describes necessary preprocessing steps of image analysis, that enhance image quality and/or detect specific features. Linear and non-linear 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 depth as two important examples. The estimation of image velocities (optical flow) will get due attention and methods for object tracking will be presented. Several techniques are discussed to extract three-dimensional information about objects and scenes. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed.
Lecture notesCourse material Script, computer demonstrations, exercises and problem solutions
Prerequisites / NoticePrerequisites:
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
227-0965-00LMicro and Nano-Tomography of Biological TissuesW4 credits3GM. Stampanoni, K. S. Mader
AbstractThe lecture introduces the physical and technical know-how of X-ray tomographic microscopy. Several X-ray 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.
ObjectiveIntroduction to the basic concepts of X-ray tomographic imaging, image analysis and data quantification at the micro and nano scale with particular emphasis on biological applications
ContentSynchrotron-based X-ray micro- and nano-tomography is today a powerful technique for non-destructive, high-resolution investigations of a broad range of materials. The high-brilliance and high-coherence of third generation synchrotron radiation facilities allow quantitative, three-dimensional imaging at the micro and nanometer scale and extend the traditional absorption imaging technique to edge-enhanced and phase-sensitive 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 X-ray nano-tomographic 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 notesAvailable online
LiteratureWill be indicated during the lecture.
376-1651-00LClinical and Movement BiomechanicsW4 credits3GS.  Lorenzetti, R. List, N. Singh
AbstractMeasurement and modeling of the human movement during daily activities and in a clinical environment.
ObjectiveThe students are able to analyse the human movement from a technical point of view, to process the data and perform modeling with a focus towards clinical application.
ContentThis course includes ethical considerations, measurement techniques, clinical testing, accessing movement data and anysis as well as modeling with regards to human movement.
376-1985-00LTrauma BiomechanicsW4 credits2V + 1UK.‑U. Schmitt, M. H. Muser
AbstractTrauma biomechanics in an interdisciplinary research field investigating the biomechanics of injuries and related subjects such as prevention. The lecture provides an introduction to the basic principles of trauma biomechanics.
ObjectiveIntroduction to the basic principles of trauma biomechanics.
ContentThis lecture serves as an introduction to the field of trauma biomechanics. Emphasis is placed on the interdisciplinary nature of impact biomechanics, which uses the combination of fundamental engineering principles and advanced medical technologies to develop injury prevention measures. Topics include: accident statistics and accident reconstruction, biomechanical response of the human to impact loading, injury mechanisms and injury criteria, test methods (including crash tests), computer simulations using multi-body and finite element modelling techniques, aspects of passive safety of vehicles (focusing on restraint systems and vehicle compatibility). Real world examples mainly from automobile safety are used to augment lecture material.
Lecture notesAvailable via homepage.
LiteratureSchmitt K-U, Niederer P, M. Muser, Walz F: "Trauma Biomechanics - An Introduction to Injury Biomechanics", Springer Verlag
Recommended Elective Courses
These courses are particularly recommended for the Biomechanics track. Please consult your track advisor if you wish to select other subjects.
NumberTitleTypeECTSHoursLecturers
151-0255-00LEnergy Conversion and Transport in Biosystems
Does not take place this semester.
W4 credits2V + 1UD. Poulikakos, A. Ferrari
AbstractTheory and application of thermodynamics, energy conversion and fluid dynamics in biological systems and biomedicine at the macro scale and the cellular level.
ObjectiveTheory and application of energy conversion at the macro scale and the cellular level. Understanding of the basic features governing fluid transport in the principal fluidic systems of the human body. Connection of characteristics and patterns from other fields of engineering to biofluidics. Heat and mass transport processes within the human body and relation to biomedical technologies.
ContentHeat and mass transfer models for the transport of thermal energy and chemical species in the human body. Physiology, pathology and biomedical intervention based on extreme temperatures (medical radio frequency therapy, tissue freezing and cryotherapy). Introduction to the main fluidic systems of the human body (cardiovascular, cerebrospinal etc.). Description of the functionality of these systems and of analytical experimental and computational techniques for understanding of their operation. Introduction to bioengineering approaches for the treatment of common pathogenic conditions of these systems. Introduction to cell metabolism, cellular energy transport and cellular thermodynamics.
Lecture notesScript as well as additional material in the form of hand-outs will be distributed.
LiteratureLecture notes and references therein.
151-0511-00LMechanics of Nano- and Micro-MaterialsW4 credits2V + 1UC. Daraio
AbstractThe course provides an introduction to the mechanics of nano- and micro-materials and devices, in the quasistatic and dynamic domains. It reviews scale effects in materials, surveys available characterization techniques and describes the effects of surfaces and microscale contacts. Recent applications of nano- and micro-materials in engineering systems will be discussed.
ObjectiveLearn the fundamental mechanical properties of nano- and micro-system. Understand the effects of scales on the response of materials. Explore applications and devices exploiting the response of materials at small scales.
Contentfollows soon
Lecture notesSlides and notes from the course will be provided.
LiteratureRelevant articles and reading materials will be provided. Various books will be recommended pertaining to the topics covered.
Prerequisites / NoticeMechanics I, II, III
151-0524-00LContinuum Mechanics for EngineersW4 credits2V + 1UE. Mazza
AbstractThe 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.
ObjectiveBasic theories for solving continuum mechanics problems of engineering applications, with particular attention to material models.
ContentAnisotrope Elastizität, Linearelastisches und linearviskoses Stoffverhalten, Viskoelastizität, mikro-makro Modellierung, Laminattheorie, Plastizität, Viscoplastizität, Beispiele aus der Ingenieuranwendung, Vergleich mit Experimenten.
Lecture notesyes
151-0604-00LMicrorobotics Information W4 credits3GB. Nelson
AbstractMicrorobotics 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.
ObjectiveThe 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.
ContentMain 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 notesThe 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 / NoticeThe lecture will be taught in English.
151-0605-00LNanosystemsW4 credits4GA. Stemmer
AbstractFrom 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.
ObjectiveFamiliarize students with basic science and engineering principles governing the nano domain.
ContentThe 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 / NoticeCourse format:

Lectures: Thursday 10-12, 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.
227-2037-00LPhysical Modelling and Simulation Information W5 credits4GC. Hafner, J. Smajic
AbstractPhysical modelling plays an important role in the analysis and design of new structures, especially for micro and nano devices where fabrication and measurement are difficult. After the fundamentals of electromagnetics, mechanics, and thermodynamics, an introduction to the main concepts and most widely used codes for physical modelling is given and commercial codes are applied.
ObjectiveBasic knowledge of the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics. Knowledge of the main concepts of numerical methods for physical modelling and simulation. Ability 1) to select appropriate software, 2) to apply it for solving given problems, 3) to validate the results, 4) to interactively improve the models until sufficiently accurate results are obtained.
ContentSince the fabrication and characterization of micro- and nanostructures is difficult, expensive, and time-consuming, numerical modelling drastically reduced the design process. Although many commercial software packages are available, it is important to know the drawbacks and difficulties of the numerical methods behind them and to be able to validate the results obtained with such packages.
First, an introduction to the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics is given. This is important for understanding the problems to be analyzed and for validating results obtained from software packages. After this, the main concepts of numerical methods and of the most widely used codes for physical modelling are outlined and compared, which is essential for the adequate selection of software for solving given problems. After this, prominent commercial software packages are applied to various types of problems, ranging from electrodynamics to multiphysics. For becoming able to select appropriate software and to validate the results obtained, different commercial software packages will be used and compared during the exercises in form of small projects.
263-5001-00LIntroduction to Finite Elements and Sparse Linear System Solving Information W4 credits2V + 1UP. Arbenz, T. Kaman
AbstractThe 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.
ObjectiveStudents 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.
ContentI. 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 / NoticePrerequisites: Linear Algebra, Analysis, Computational Science.
The exercises are made with Matlab.
376-1219-00LRehabilitation Engineering II: Rehabilitation of Sensory and Vegetative Functions Information W3 credits2VR. Riener, R. Gassert
AbstractRehab. Engineering 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.
ObjectiveProvide 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.
ContentIntroduction, 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
LiteratureIntroductory 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 / NoticeTarget 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
376-1279-00LVirtual Reality in Medicine Restricted registration - show details
Does not take place this semester.
W3 credits2VR. Riener
AbstractVirtual 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.
ObjectiveProvide theoretical and practical knowledge of new principles and applications of multi-modal simulation and interface technologies in medical education, therapy, and rehabilitation.
ContentVirtual 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!
LiteratureBook: Virtual Reality in Medicine. Riener, Robert; Harders, Matthias; 2012 Springer.
Prerequisites / NoticeThe course language is English.
Basic experience in Information Technology and Computer Science will be of advantage
More details will be announced in the lecture.
376-1714-00LBiocompatible MaterialsW4 credits3GK. Maniura, P. M. Kollmannsberger, J. Möller, M. Zenobi-Wong
AbstractIntroduction 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.
ObjectiveThe 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.
ContentIntroduction 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 notesHandouts can be accessed online.
LiteratureLiteratur
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.
376-1351-00LMicro/Nanotechnology and Microfluidics for Biomedical ApplicationsW2 credits2VE. Delamarche
AbstractThis 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.
ObjectiveThe 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.
ContentMostly 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 / NoticeNanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations.
376-1720-00LApplication of MATLAB in the Human Movement Sciences Information W2 credits2GR.  van de Langenberg
AbstractStudents 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).
ObjectiveStudents will acquire the ability to independently load, plot, and process kinematic, kinetic and electromyographical data using the MATLAB computing environment.
ContentDrawbacks 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.
LiteratureDuring the lecture, several electronically available MATLAB introductions are indicated. Course-specific scripts will be provided by the lecturer.
Prerequisites / NoticeA 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.
376-1974-00LColloquium in Biomechanics Information W2 credits2KB. Helgason, S. J. Ferguson, R. Müller, J. G. Snedeker, B. Taylor, M. Zenobi-Wong
AbstractCurrent topics in biomechanics presented by speakers from academia and industry.
ObjectiveGetting insight into actual areas and problems of biomechanics.
376-2017-00LBiomechanics of Sports Injuries and RehabilitationW3 credits2VK.‑U. Schmitt, J. Goldhahn
AbstractThis lectures introduces the basic principles of injury mechanics and rehabilitation focussing on sports injuries.
ObjectiveWithin 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.
ContentThis 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 notesHandouts can be downloaded.
LiteratureSchmitt K-U, Niederer P, M. Muser, Walz F: "Trauma Biomechanics - Accidental Injury in traffic and sports", Springer Verlag
Prerequisites / NoticeA 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.
402-0341-00LMedical Physics IW6 credits2V + 1UP. Manser
AbstractIntroduction 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.
ObjectiveUnderstanding 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.
ContentThe 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 notesA script will be provided.
402-0674-00LPhysics in Medical Research: From Atoms to Cells Information W6 credits2V + 1UB. K. R. Müller
AbstractScanning 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.
ObjectiveThe 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.
465-0953-00LBiostatisticsW2 credits2V + 1UB. Sick
AbstractThe 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, analysis of variance, logistic regression, survival analysis (Kaplan-Meier curves and Cox-regression).
Objective
551-1295-00LIntroduction to Bioinformatics: Concepts and Applications Information W6 credits4GW. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner
AbstractStorage, 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.
ObjectiveIntroduction 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.
ContentBioinformatics 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
Biology Courses
NumberTitleTypeECTSHoursLecturers
227-0945-00LCell and Molecular Biology for EngineersW6 credits4GC. Frei
AbstractThe 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.
ObjectiveAfter 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.
ContentLectures will include the following topics: DNA, chromosomes, RNA, protein, genetics, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer, development and stem cells.

In addition, three journal clubs will be held, where one/two publictions will be discussed. 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 25% for the final grade.
Lecture notesScripts of all lectures will be available.
Literature"Molecular Biology of the Cell" (5th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.
Medical Physics
Track Core Courses
During the Master program, a minimum of 12 CP must be obtained from track core courses.
NumberTitleTypeECTSHoursLecturers
227-0385-00LBiomedical Imaging Information W4 credits3GS. Kozerke, U. Moser, M. Rudin
AbstractIntroduction and analysis of medical imaging technology including X-ray procedures, computed tomography, nuclear imaging techniques using single photon and positron emission tomography, magnetic resonance imaging and ultrasound imaging techniques.
ObjectiveUnderstand the physical and technical principles underlying X-ray imaging, computed tomography, single photon and positron emission tomography, magnetic resonance imaging, ultrasound and Doppler imaging techniques. Develop the mathematical framework to describe image encoding/decoding, point-spread function/modular transfer function, signal-to-noise ratio, contrast behavior for each of the methods.
ContentX-ray imaging
Computed tomography
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
Ultrasound/Doppler imaging
Lecture notesLecture notes and handouts: Biomedical Imaging
LiteratureIntroduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith,
Cambridge University Press
402-0341-00LMedical Physics IW6 credits2V + 1UP. Manser
AbstractIntroduction 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.
ObjectiveUnderstanding 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.
ContentThe 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 notesA script will be provided.
402-0345-00LIntroduction to Medical Physics
Does not take place this semester.
W4 credits2VA. J. Lomax
AbstractMedical physics is a fascinating and worthwhile scientific discipline, providing many professional opportunities to apply physics to the care of patients, either in the clinic or in industry. It is also an area allowing for exciting, interesting and fulfilling areas of research.
ObjectiveIt is the aim of this course to give bachelor and master level students an insight into the wide spectrum of medical applications of physics, and to provide some insight into the work of the medical physicist in clinics, industry and research.
ContentThe lecture series will begin with a short historical overview of medical physics and an overview of the lecture series (lecture 1). This will be followed by two lectures on the physics of medical imaging. Medical imaging is one of the most important areas of preventative medicine and diagnostics, and in these two lectures, we will summarise the physics aspects of all the most important medical imaging modalities (X-ray, nuclear medicine, CT, MRI, Ultrasound imaging etc.). With lectures 4 and 5, we will move onto one of the other major areas of physics applied to medicine, radiotherapy. As the name implies, this is a physics 'heavy' discipline, being dependent as it is on both accelerator and particle physics. However, what is less well known is that this is also the second most successfu
l treatment of cancer after surgery and a great success story for the application of physics to medicine. In lectures 6 and 7 will then move on to a very different area, that of bio-photonics and bio-physics. Here we will look into the applications of lasers in medicine, from therapy to their use in particle acceleration for medical applications, as well as a variety of optical techniques for studying biological tissues, cells and structures.
In the second half of the lecture series (lectures 8-13) the style changes somewhat, and we will concentrate on professional aspects of medical physics and the role of the medical physicist in various professional scenarios. As such, lectures 8-11 will cover the role of the clinical medical physicist in diagnostic radiology, MRI, nuclear medicine and radiotherapy, whilst the last two lectures will concentrate on their role in industry and research. For many of this second set of lectures, external experts in the various areas will be invited in order to give the student the best possible insight into the life of a professional medical physicist.
227-0943-00LRadiobiologyW2 credits2VM. Pruschy
AbstractThe purpose of this course is to impart basic knowledge in radiobiology in order to handle ionizing rays and to provide a basis for predicting the radiation risk.
Objective
ContentEinführung 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, DNA-Defekte, Reparaturprozesse; Molekulare Strahlenbiologie: Bedeutung inter- und intrazellulärer Signalübermittlungsprozesse, Apoptose, Zellzyklus-Checkpoints; Strahlenrisiko: Strahlensyndrome, Krebsinduktion, Mutationsauslösung, pränatale Strahlenwirkung; Strahlenbiologische Grundlagen des Strahlenschutzes; Nutzen-Risiko-Abwägungen bei der medizinischen Strahlenanwendung; Prädiktive strahlenbiologische Methoden zur Optimierung der therapeutischen Strahlenanwendung.
Lecture notesBeilagen mit zusammenfassenden Texten, Tabellen, Bild- und Grafikdarstellungen werden abgegeben
LiteratureLiteraturliste wird abgegeben.
Für NDS-Absolventen empfohlen: Hall EJ: Radiobiology for the Radiologist, 5th Edition, Lippincott Williams&Wilkins, ISBN 0-7817-2649-2, 2000
Prerequisites / NoticeThe former number of this course unit is 465-0951-00L.
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.
NumberTitleTypeECTSHoursLecturers
402-0674-00LPhysics in Medical Research: From Atoms to Cells Information W6 credits2V + 1UB. K. R. Müller
AbstractScanning 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.
ObjectiveThe 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.
Other Elective Courses
These courses may be suitable for the Medical Physics track. Please consult your track advisor.
NumberTitleTypeECTSHoursLecturers
227-0447-00LImage Analysis and Computer Vision Information W6 credits3V + 1UG. Székely, O. Göksel, L. Van Gool
AbstractLight and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation and deformable shape matching. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition.
ObjectiveOverview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.
ContentThe first part of the course starts off from 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 it is investigated how the parameters of the electromagnetic waves are related to our perception. Also the interaction of light with matter is considered. The most important hardware components of technical vision systems, such as cameras, optical devices and illumination sources are discussed. The course then turns to the steps that are necessary to arrive at the discrete images that serve as input to algorithms. The next part describes necessary preprocessing steps of image analysis, that enhance image quality and/or detect specific features. Linear and non-linear 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 depth as two important examples. The estimation of image velocities (optical flow) will get due attention and methods for object tracking will be presented. Several techniques are discussed to extract three-dimensional information about objects and scenes. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed.
Lecture notesCourse material Script, computer demonstrations, exercises and problem solutions
Prerequisites / NoticePrerequisites:
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
Biology Courses
NumberTitleTypeECTSHoursLecturers
227-0945-00LCell and Molecular Biology for EngineersW6 credits4GC. Frei
AbstractThe 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.
ObjectiveAfter 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.
ContentLectures will include the following topics: DNA, chromosomes, RNA, protein, genetics, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer, development and stem cells.

In addition, three journal clubs will be held, where one/two publictions will be discussed. 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 25% for the final grade.
Lecture notesScripts of all lectures will be available.
Literature"Molecular Biology of the Cell" (5th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.
Molecular Bioengineering
Track Core Courses
During the Master program, a minimum of 12 CP must be obtained from track core courses.
NumberTitleTypeECTSHoursLecturers
376-1714-00LBiocompatible MaterialsW4 credits3GK. Maniura, P. M. Kollmannsberger, J. Möller, M. Zenobi-Wong
AbstractIntroduction 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.
ObjectiveThe 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.
ContentIntroduction 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 notesHandouts can be accessed online.
LiteratureLiteratur
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.
402-0674-00LPhysics in Medical Research: From Atoms to Cells Information W6 credits2V + 1UB. K. R. Müller
AbstractScanning 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.
ObjectiveThe 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.
465-0953-00LBiostatisticsW2 credits2V + 1UB. Sick
AbstractThe 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, analysis of variance, logistic regression, survival analysis (Kaplan-Meier curves and Cox-regression).
Objective
551-0103-00LFundamentals of Biology II: Cell Biology Information W5 credits5VU. Kutay, Y. Barral, E. Hafen, G. Schertler, U. Suter, S. Werner
AbstractThe goal of this course is to provide students with a wide general understanding in cell biology. With this material as a foundation, students have enough of a cell biological basis to begin their specialization not only in cell biology but also in related fields such as biochemistry, microbiology, pharmacological sciences, molecular biology, and others.
ObjectiveThe goal of this course is to provide students with a wide general understanding cell biology. With this material as a foundation, students have enough of a cell biological basis to begin their specialization not only in cell biology but also in related fields such as biochemistry, microbiology, pharmacological sciences, molecular biology, and others.
ContentThe focus is animal cells and the development of multicellular organisms with a clear emphasis on the molecular basis of cellular structures and phenomena. The topics include biological membranes, the cytoskeleton, protein sorting, energy metabolism, cell cycle and division, viruses, extracellular matrix, cell signaling, embryonic development and cancer research.
Lecture notesThe lectures are presented in the Powerpoint format. These are available on the WEB for ETH students over the nethz (https://sharepoint.biol.ethz.ch/sites/e-learn/551-0103-00L-H13/default.aspx). Some lectures are available on the ETH WEB site in a live format (Livestream) at the above WEB site.
LiteratureThe lectures follow Alberts et al. ‘Molecular Biology of the Cell’ Fifth edition, 2008 ISBN 978-0-8153-4105-5 (hard cover) and ISBN 978-0-8153-4106-2 (paperback).
Prerequisites / NoticeSome of the lectures are given in the English language.
551-1295-00LIntroduction to Bioinformatics: Concepts and Applications Information W6 credits4GW. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner
AbstractStorage, 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.
ObjectiveIntroduction 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.
ContentBioinformatics 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
636-0003-00LBiological Engineering and BiotechnologyW6 credits3GM. Fussenegger
AbstractBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
Objective1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development.
Lecture notesHandsout during the course.
Recommended Elective Courses
These courses are particularly recommended for the Molecular Bioengineering track. Please consult your track advisor if you wish to select other subjects.
NumberTitleTypeECTSHoursLecturers
151-0604-00LMicrorobotics Information W4 credits3GB. Nelson
AbstractMicrorobotics 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.
ObjectiveThe 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.
ContentMain 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 notesThe 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 / NoticeThe lecture will be taught in English.
227-0385-00LBiomedical Imaging Information W4 credits3GS. Kozerke, U. Moser, M. Rudin
AbstractIntroduction and analysis of medical imaging technology including X-ray procedures, computed tomography, nuclear imaging techniques using single photon and positron emission tomography, magnetic resonance imaging and ultrasound imaging techniques.
ObjectiveUnderstand the physical and technical principles underlying X-ray imaging, computed tomography, single photon and positron emission tomography, magnetic resonance imaging, ultrasound and Doppler imaging techniques. Develop the mathematical framework to describe image encoding/decoding, point-spread function/modular transfer function, signal-to-noise ratio, contrast behavior for each of the methods.
ContentX-ray imaging
Computed tomography
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
Ultrasound/Doppler imaging
Lecture notesLecture notes and handouts: Biomedical Imaging
LiteratureIntroduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith,
Cambridge University Press
227-0386-00LBiomedical Engineering Information W4 credits3GJ. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong
AbstractIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The focus is on learning the concepts that govern common medical instruments and the most important organs from an engineering point of view. In addition, the most recent achievements and trends of the field of biomedical engineering are also outlined.
ObjectiveIntroduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The course provides an overview of the various topics of the different tracks of the biomedical engineering master course and helps orienting the students in selecting their specialized classes and project locations.
ContentIntroduction into neuro- and electrophysiology. Functional analysis of peripheral nerves, muscles, sensory organs and the central nervous system. Electrograms, evoked potentials. Audiometry, optometry. Functional electrostimulation: Cardiac pacemakers. Function of the heart and the circulatory system, transport and exchange of substances in the human body, pharmacokinetics. Endoscopy, medical television technology. Lithotripsy. Electrical Safety. Orthopaedic biomechanics. Lung function. Bioinformatics and Bioelectronics. Biomaterials. Biosensors. Microcirculation.Metabolism.
Practical and theoretical exercises in small groups in the laboratory.
Lecture notesIntroduction to Biomedical Engineering
by Enderle, Banchard, and Bronzino

AND

https://www1.ethz.ch/lbb/Education/BME
227-0965-00LMicro and Nano-Tomography of Biological TissuesW4 credits3GM. Stampanoni, K. S. Mader
AbstractThe lecture introduces the physical and technical know-how of X-ray tomographic microscopy. Several X-ray 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.
ObjectiveIntroduction to the basic concepts of X-ray tomographic imaging, image analysis and data quantification at the micro and nano scale with particular emphasis on biological applications
ContentSynchrotron-based X-ray micro- and nano-tomography is today a powerful technique for non-destructive, high-resolution investigations of a broad range of materials. The high-brilliance and high-coherence of third generation synchrotron radiation facilities allow quantitative, three-dimensional imaging at the micro and nanometer scale and extend the traditional absorption imaging technique to edge-enhanced and phase-sensitive 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 X-ray nano-tomographic 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 notesAvailable online
LiteratureWill be indicated during the lecture.
327-0505-00LSurfaces, Interfaces & their Applications I Information W3 credits2V + 1UN. Spencer, M. P. Heuberger, L. Isa
AbstractAfter being introduced to the physical/chemical principles and importance of surfaces and interfaces, the student is introduced to the most important techniques that can be used to characterize surfaces. Later, liquid interfaces are treated, followed by an introduction to the fields of tribology (friction, lubrication, and wear) and corrosion.
ObjectiveTo gain an understanding of the physical and chemical principles, as well as the tools and applications of surface science, and to be able to choose appropriate surface-analytical approaches for solving problems.
ContentIntroduction to Surface Science
Physical Structure of Surfaces
Surface Forces (static and dynamic)
Adsorbates on Surfaces
Surface Thermodynamics and Kinetics
The Solid-Liquid Interface
Electron Spectroscopy
Vibrational Spectroscopy on Surfaces
Scanning Probe Microscopy
Introduction to Tribology
Introduction to Corrosion Science
Lecture notesScript Download:
Link
LiteratureScript (20 CHF)
Book: "Surface Analysis--The Principal Techniques", Ed. J.C. Vickerman, Wiley, ISBN 0-471-97292
Prerequisites / NoticeChemistry:
General undergraduate chemistry
including basic chemical kinetics and thermodynamics

Physics:
General undergraduate physics
including basic theory of diffraction and basic knowledge of crystal structures
327-1101-00LBiomineralization Information W2 credits2VK.‑H. Ernst
AbstractThe course addresses undergraduate and graduate students interested in getting introduced into the basic concepts of biomineralization.
ObjectiveThe course aims to introduce the basic concepts of biomineralization and the underlying principles, such as supersaturation, nucleation and growth of minerals, the interaction of biomolecules with mineral surfaces, and cell biology of inorganic materials creation. An important part of this class is the independent study and the presentation of original literature from the field.
ContentBiomineralization is a multidisciplinary field. Topics dealing with biology, molecular and cell biology, solid state physics, mineralogy, crystallography, organic and physical chemistry, biochemistry, dentistry, oceanography, geology, etc. are addressed. The course covers definition and general concepts of biomineralization (BM)/ types of biominerals and their function / crystal nucleation and growth / biological induction of BM / control of crystal morphology, habit, shape and orientation by organisms / strategies of compartmentalization / the interface between biomolecules (peptides, polysaccharides) and the mineral phase / modern experimental methods for studying BM phenomena / inter-, intra, extra- and epicellular BM / organic templates and matrices for BM / structure of bone, teeth (vertebrates and invertebrates) and mollusk shells / calcification / silification in diatoms, radiolaria and plants / calcium and iron storage / impact of BM on lithosphere and atmosphere/ evolution / taxonomy of organisms.

1. Introduction and overview
2. Biominerals and their functions
3. Chemical control of biomineralization
4. Control of morphology: Organic templates and additives
5. Modern methods of investigation of BM
6. BM in matrices: bone and nacre
7. Vertebrate teeth
8. Invertebrate teeth
9. BM within vesicles: calcite of coccoliths
10. Silica
11. Iron storage and mineralization
Lecture notesScript with more than 600 pages with many illustrations will be distributed free of charge.
Literature1) S. Mann, Biomineralization, Oxford University Press, 2001, Oxford, New York
2) H. Lowenstam, S. Weiner, On Biomineralization, Oxford University Press, 1989, Oxford
3) P. M. Dove, J. J. DeYoreo, S. Weiner (Eds.) Biomineralization, Reviews in Mineralogoy & Geochemistry Vol. 54, 2003
Prerequisites / NoticeEach attendee is required to present a publication from the field. The selection of key papers is provided by the lecturer.
No special requirements are needed for attending. Basic knowledge in chemistry and cell biology is expected.
402-0341-00LMedical Physics IW6 credits2V + 1UP. Manser
AbstractIntroduction 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.
ObjectiveUnderstanding 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.
ContentThe 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 notesA script will be provided.
535-0423-00LDrug Delivery and Drug TargetingW2 credits2VJ.‑C. Leroux, P. Luciani
AbstractThe students gain an overview on current principles, methodologies and systems for controlled delivery and targeting of drugs. This enables the students to understand and evaluate the field in terms of scientific criteria.
ObjectiveThe students dispose of an overview on current principles and systems for the controlled delivery and targeting of drugs. The focus of the course lies on developing a capacity to understand the involved technologies and methods, as well as an appreciation of the chances and constraints of their therapeutic usage, with prime attention on anticancer drugs, therapeutic peptides, proteins, nucleic acids and vaccines.
ContentThe course covers the following topics: drug targeting and delivery principles, radiopharmaceuticals, macromolecular drug carriers, liposomes, micelles, micro/nanoparticles, gels and implants, administration of vaccines, delivery of active agents in tissue engineeering, targeting at the gastrointestinal level, synthetic carriers for nucleic acid drugs, ophthalmic devices and novel trends in transdermal and nasal drug delivery.
Lecture notesSelected lecture notes, documents and supporting material will be directly provided or may be downloaded using

http://www.galenik.ethz.ch/teaching/drug_del_drug_targ

The website also displays additional information on peroral delivery systems, transdermal systems and systems for alternative routes (nasal, pulmonary) of delivery. These fields are covered in detail in the course Galenische Pharmazie II (Galenical Pharmacy II).
LiteratureA.M. Hillery, A.W. Lloyd, J. Swarbrick (Hrsg). Drug Delivery and Targeting, Taylor & Francis, London and New York 2001.

Y. Perrie, T. Rhades. Pharmaceutics - Drug Delivery and Targeting, Pharmaceutical Press, London and Chicago, 2010.

Further references will be provided in the course.
636-0507-00LSynthetic Biology II Restricted registration - show details W4 credits4AS. Panke, Y. Benenson, J. Stelling
Abstract7 months biological design project, during which the students are required to give presentations on advanced topics in synthetic biology (specifically genetic circuit design) and then select their own biological system to design. The system is subsequently modeled, analyzed, and experimentally implemented. Results are presented at an international student competition at the MIT (Cambridge).
ObjectiveThe students are supposed to acquire a deep understanding of the process of biological design including model representation of a biological system, its thorough analysis, and the subsequent experimental implementation of the system and the related problems.
ContentPresentations on advanced synthetic biology topics (eg genetic circuit design, adaptation of systems dynamics, analytical concepts, large scale de novo DNA synthesis), project selection, modeling of selected biological system, design space exploration, sensitivity analysis, conversion into DNA sequence, (DNA synthesis external,) implementation and analysis of design, summary of results in form of scientific presentation and poster, presentation of results at the iGEM international student competition (www.igem.org).
Lecture notesHandouts during course
Prerequisites / NoticeThe final presentation of the project is typically at the MIT (Cambridge, US). Other competing schools include regularly Imperial College, Cambridge University, Harvard University, UC Berkeley, Princeton Universtiy, CalTech, etc.

This project takes place between end of Spring Semester and beginning of Autumn Semester. Registration in April.

Please note that the number of ECTS credits and the actual work load are disconnected.
Other Elective Courses
These courses may be suitable for the Molecular Bioengineering track. Please consult your track advisor.
NumberTitleTypeECTSHoursLecturers
551-0313-00LMicrobiology (Part I) Information W3 credits2VW.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis concept class will be based on common concepts (Grundlagen der Biologie IIB, Teil Mikrobiologie) and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
The lecture "Grundlagen der Biologie IIB", Mikrobiologie is the basis for this advanced lecture.
551-1103-00LMicrobial Biochemistry Information W4 credits2VJ. Vorholt-Zambelli, T. J. Erb, J. Piel
AbstractThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. Emphasis is on processes that are specific to bacteria and archaea and that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest.
ObjectiveThe lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms.
ContentImportant biochemical processes specific to bacteria and archaea will be presented that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. Emphasis is on concepts of energy generation and assimilation.

List of topics:
Eating sugars and letting them in
Challenging: Aromatics, xenobiotics, and oil
Complex: (Ligno-)Cellulose and in demand for bioenergy
Living on a diet and the anaplerotic provocation
Of climate relevance: The microbial C1 cycle
What are AMO and Anammox?
20 amino acids: the making of
Extending the genetic code
The 21st and 22nd amino acid
Some exotic biochemistry: nucleotides, cofactors
Ancient biochemistry? Iron-sulfur clusters, polymers
Secondary metabolites: playground of evolution
Lecture notesA script will be provided during the course.
Biology Courses
NumberTitleTypeECTSHoursLecturers
227-0945-00LCell and Molecular Biology for EngineersW6 credits4GC. Frei
AbstractThe 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.
ObjectiveAfter 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.
ContentLectures will include the following topics: DNA, chromosomes, RNA, protein, genetics, gene expression, membrane structure and function, vesicular traffic, cellular communication, energy conversion, cytoskeleton, cell cycle, cellular growth, apoptosis, autophagy, cancer, development and stem cells.

In addition, three journal clubs will be held, where one/two publictions will be discussed. 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 25% for the final grade.
Lecture notesScripts of all lectures will be available.
Literature"Molecular Biology of the Cell" (5th edition) by Alberts, Johnson, Lewis, Raff, Roberts, and Walter.