Search result: Catalogue data in Autumn Semester 2014
|Biomedical Engineering Master|
|Master Programme According to Programme Regulations 2013|
| Track Core Courses|
During the Master program, a minimum of 12 CP must be obtained from track core courses.
|151-0604-00L||Microrobotics||W||4 credits||3G||B. Nelson|
|Abstract||Microrobotics is an interdisciplinary field that combines aspects of robotics, micro and nanotechnology, biomedical engineering, and materials science. The aim of this course is to expose students to the fundamentals of this emerging field. Throughout the course students are expected to submit assignments. The course concludes with an end-of-semester examination.|
|Objective||The objective of this course is to expose students to the fundamental aspects of the emerging field of microrobotics. This includes a focus on physical laws that predominate at the microscale, technologies for fabricating small devices, bio-inspired design, and applications of the field.|
|Content||Main topics of the course include:|
- Scaling laws at micro/nano scales
- Low Reynolds number flows
- Observation tools
- Materials and fabrication methods
- Applications of biomedical microrobots
|Lecture notes||The powerpoint slides presented in the lectures will be made available in hardcopy and as pdf files. Several readings will also be made available electronically.|
|Prerequisites / Notice||The lecture will be taught in English.|
|151-0605-00L||Nanosystems||W||4 credits||4G||A. Stemmer|
|Abstract||From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles.|
Intermolecular forces, their macroscopic manifestations, and ways to control such interactions.
Self-assembly and directed assembly of 2D and 3D structures.
Special emphasis on the emerging field of molecular electronic devices.
|Objective||Familiarize students with basic science and engineering principles governing the nano domain.|
|Content||The course addresses basic science and engineering principles ruling the nano domain. We particularly work out the links between topics that are traditionally taught separately.|
Special emphasis is placed on the emerging field of molecular electronic devices, their working principles, applications, and how they may be assembled.
Topics are treated in 2 blocks:
(I) From Quantum to Continuum
From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles.
(II) Interaction Forces on the Micro and Nano Scale
Intermolecular forces, their macroscopic manifestations, and ways to control such interactions.
Self-assembly and directed assembly of 2D and 3D structures.
|Literature||- Kuhn, Hans; Försterling, H.D.: Principles of Physical Chemistry. Understanding Molecules, Molecular Assemblies, Supramolecular Machines. 1999, Wiley, ISBN: 0-471-95902-2|
- Chen, Gang: Nanoscale Energy Transport and Conversion. 2005, Oxford University Press, ISBN: 978-0-19-515942-4
- Ouisse, Thierry: Electron Transport in Nanostructures and Mesoscopic Devices. 2008, Wiley, ISBN: 978-1-84821-050-9
- Wolf, Edward L.: Nanophysics and Nanotechnology. 2004, Wiley-VCH, ISBN: 3-527-40407-4
- Israelachvili, Jacob N.: Intermolecular and Surface Forces. 2nd ed., 1992, Academic Press,ISBN: 0-12-375181-0
- Evans, D.F.; Wennerstrom, H.: The Colloidal Domain. Where Physics, Chemistry, Biology, and Technology Meet. Advances in Interfacial Engineering Series. 2nd ed., 1999, Wiley, ISBN: 0-471-24247-0
- Hunter, Robert J.: Foundations of Colloid Science. 2nd ed., 2001, Oxford, ISBN: 0-19-850502-7
|Prerequisites / Notice||Course format:|
Lectures: Thursday 10-12, ML F 36
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.
|151-0621-00L||Microsystems Technology||W||6 credits||4G||C. Hierold, M. Haluska|
|Abstract||Students 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).|
|Objective||Students 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 notes||Handouts (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 / Notice||Prerequisites: Physics I and II|
|227-0385-00L||Biomedical Imaging||W||4 credits||3G||S. Kozerke, U. Moser, M. Rudin|
|Abstract||Introduction 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.|
|Objective||Understand 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.|
|Content||X-ray imaging |
Single photon emission tomography
Positron emission tomography
Magnetic resonance imaging
|Lecture notes||Lecture notes and handouts: Biomedical Imaging|
|Literature||Introduction to Medical Imaging: Physics, Engineering and Clinical Applications by Andrew Webb, Nadine Barrie Smith, |
Cambridge University Press
|227-0386-00L||Biomedical Engineering||W||4 credits||3G||J. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong|
|Abstract||Introduction 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.|
|Objective||Introduction 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.|
|Content||Introduction 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 notes||Introduction to Biomedical Engineering|
by Enderle, Banchard, and Bronzino
|227-0427-00L||Signal and Information Processing: Modeling, Filtering, Learning||W||6 credits||4G||H.‑A. Loeliger|
|Abstract||Fundamentals 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.
|Objective||The course is an introduction to some basic topics in signal processing, detection/estimation theory, and machine learning.|
|Content||Part 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 notes||Lecture notes.|
|Prerequisites / Notice||Prerequisites: |
- local bachelors: course "Discrete-Time and Statistical Signal Processing" (5. Sem.)
- others: solid basics in linear algebra and probability theory
|376-1714-00L||Biocompatible Materials||W||4 credits||3G||K. Maniura, P. M. Kollmannsberger, J. Möller, M. Zenobi-Wong|
|Abstract||Introduction to molecules used for biomaterials, molecular interactions between different materials and biological systems (molecules, cells, tissues). The concept of biocompatibility is discussed and important techniques from biomaterials research and development are introduced.|
|Objective||The class consists of three parts: |
1. Introdcution into molecular characteristics of molecules involved in the materials-to-biology interface. Molecular design of biomaterials.
2. The concept of biocompatibility.
3. Introduction into methodology used in biomaterials research and application.
|Content||Introduction into native and polymeric biomaterials used for medical applications. The concepts of biocompatibility, biodegradation and the consequences of degradation products are discussed on the molecular level. Different classes of materials with respect to potential applications in tissue engineering and drug delivery are introduced. Strong focus lies on the molecular interactions between materials having very different bulk and/or surface chemistry with living cells, tissues and organs. In particular the interface between the materials surfaces and the eukaryotic cell surface and possible reactions of the cells with an implant material are elucidated. Techniques to design, produce and characterize materials in vitro as well as in vivo analysis of implanted and explanted materials are discussed.|
In addition, a link between academic research and industrial entrepreneurship is established by external guest speakers.
|Lecture notes||Handouts can be accessed online.|
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.
|402-0674-00L||Physics in Medical Research: From Atoms to Cells||W||6 credits||2V + 1U||B. K. R. Müller|
|Abstract||Scanning probe and diffraction techniques allow studying activated atomic processes during early stages of epitaxial growth. For quantitative description, rate equation analysis, mean-field nucleation and scaling theories are applied on systems ranging from simple metallic to complex organic materials. The knowledge is expanded to optical and electronic properties as well as to proteins and cells.|
|Objective||The lecture series is motivated by an overview covering the skin of the crystals, roughness analysis, contact angle measurements, protein absorption/activity and monocyte behaviour.|
As the first step, real structures on clean surfaces including surface reconstructions and surface relaxations, defects in crystals are presented, before the preparation of clean metallic, semiconducting, oxidic and organic surfaces are introduced.
The atomic processes on surfaces are activated by the increase of the substrate temperature. They can be studied using scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The combination with molecular beam epitaxy (MBE) allows determining the sizes of the critical nuclei and the other activated processes in a hierarchical fashion. The evolution of the surface morphology is characterized by the density and size distribution of the nanostructures that could be quantified by means of the rate equation analysis, the mean-field nucleation theory, as well as the scaling theory. The surface morphology is further characterized by defects and nanostructure's shapes, which are based on the strain relieving mechanisms and kinetic growth processes.
High-resolution electron diffraction is complementary to scanning probe techniques and provides exact mean values. Some phenomena are quantitatively described by the kinematic theory and perfectly understood by means of the Ewald construction. Other phenomena need to be described by the more complex dynamical theory. Electron diffraction is not only associated with elastic scattering but also inelastic excitation mechanisms that reflect the electronic structure of the surfaces studied. Low-energy electrons lead to phonon and high-energy electrons to plasmon excitations. Both effects are perfectly described by dipole and impact scattering.
Thin-films of rather complex organic materials are often quantitatively characterized by photons with a broad range of wavelengths from ultra-violet to infra-red light. Asymmetries and preferential orientations of the (anisotropic) molecules are verified using the optical dichroism and second harmonic generation measurements. These characterization techniques are vital for optimizing the preparation of medical implants and the determination of tissue's anisotropies within the human body.
Cell-surface interactions are related to the cell adhesion and the contractile cellular forces. Physical means have been developed to quantify these interactions. Other physical techniques are introduced in cell biology, namely to count and sort cells, to study cell proliferation and metabolism and to determine the relation between cell morphology and function.
3D scaffolds are important for tissue augmentation and engineering. Design, preparation methods, and characterization of these highly porous 3D microstructures are also presented.
Visiting clinical research in a leading university hospital will show the usefulness of the lecture series.
|227-1037-00L||Introduction to Neuroinformatics||W||6 credits||2V + 1U||K. A. Martin, M. Cook, V. Mante, M. Pfeiffer|
|Abstract||The 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.|
|Content||This 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.
|227-0166-00L||Analog Integrated Circuits||W||6 credits||2V + 2U||Q. Huang|
|Abstract||This course provides a foundation in analog integrated circuit design based on bipolar and CMOS technologies.|
|Objective||Integrated 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.
|Content||Review 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 notes||Handouts of presented slides. No script but an accompanying textbook is recommended.|
|Literature||Gray, Hurst, Lewis, Meyer, "Analysis and Design of Analog Integrated Circuits", 5th Ed. Wiley, 2010.|
|227-0447-00L||Image Analysis and Computer Vision||W||6 credits||3V + 1U||G. Székely, O. Göksel, L. Van Gool|
|Abstract||Light 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.|
|Objective||Overview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.|
|Content||The 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 notes||Course material Script, computer demonstrations, exercises and problem solutions|
|Prerequisites / Notice||Prerequisites: |
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
|227-0963-00L||Statistical Parametric Mapping (SPM)||W||2 credits||1V||K. Stephan|
|Abstract||This 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|
|Objective||Knowledge of modern statistical methods for fMRI data analysis|
|Content||Spatial preprocessing & physiological noise correction|
Mass-univariate & multivariate analyses of fMRI
'Resting state' fMRI
Bayesian analysis methods
Effective connectivity analyses (Dynamic Causal Modeling)
|227-0981-00L||Cross-Disciplinary Research and Development in Medicine and Engineering |
A maximum of 8 medical degree students and 8 (biomedical) engineering degree students can be admitted, their number should be equal.
|W||4 credits||2V + 2A||V. Kurtcuoglu, D. de Julien de Zelicourt, M. Meboldt, M. Schmid Daners, O. Ullrich|
|Abstract||Cross-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.|
|Objective||The 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.
|Content||After 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 notes||Handouts and relevant literature will be provided.|
|227-1033-00L||Neuromorphic Engineering I||W||6 credits||2V + 3U||T. Delbrück, G. Indiveri, S.‑C. Liu|
|Abstract||This 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.|
|Objective||Understanding of the characteristics of neuromorphic circuit elements and their interaction in parallel networks.|
|Content||Neuromorphic 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.|
|Literature||S.-C. Liu et al.: Analog VLSI Circuits and Principles; various publications.|
|Prerequisites / Notice||Particular: 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.
|227-2037-00L||Physical Modelling and Simulation||W||5 credits||4G||C. Hafner, J. Smajic|
|Abstract||Physical 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.|
|Objective||Basic 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.|
|Content||Since 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.
|151-0255-00L||Energy Conversion and Transport in Biosystems|
Does not take place this semester.
|W||4 credits||2V + 1U||D. Poulikakos, A. Ferrari|
|Abstract||Theory and application of thermodynamics, energy conversion and fluid dynamics in biological systems and biomedicine at the macro scale and the cellular level.|
|Objective||Theory 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.|
|Content||Heat 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 notes||Script as well as additional material in the form of hand-outs will be distributed.|
|Literature||Lecture notes and references therein.|
|252-0523-00L||Computational Biology||W||6 credits||3V + 2U||G. H. Gonnet|
|Abstract||Study 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.|
|Objective||Familiarize 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.|
|Content||This 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.
|376-1219-00L||Rehabilitation Engineering II: Rehabilitation of Sensory and Vegetative Functions||W||3 credits||2V||R. Riener, R. Gassert|
|Abstract||Rehab. 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.|
|Objective||Provide knowledge on the anatomy and physiology of the human sensory system, related dysfunctions and pathologies, and how rehabilitation engineering can provide sensory restoration and substitution.|
|Content||Introduction, problem definition, overview |
Rehabilitation of visual function
- Anatomy and physiology of the visual sense
- Technical aids (glasses, sensor substitution)
- Retina and cortex implants
Rehabilitation of hearing function
- Anatomy and physiology of the auditory sense
- Hearing aids
- Cochlea Implants
Rehabilitation and use of kinesthetic and tactile function
- Anatomy and physiology of the kinesthetic and tactile sense
- Tactile/haptic displays for motion therapy (incl. electrical stimulation)
- Role of displays in motor learning
Rehabilitation of vestibular function
- Anatomy and physiology of the vestibular sense
- Rehabilitation strategies and devices (e.g. BrainPort)
Rehabilitation of vegetative Functions
- Cardiac Pacemaker
- Phrenic stimulation, artificial breathing aids
- Bladder stimulation, artificial sphincter
Brain stimulation and recording
- Deep brain stimulation for patients with Parkinson, epilepsy, depression
- Brain-Computer Interfaces
An Introduction to Rehabilitation Engineering. R. A. Cooper, H. Ohnabe, D. A. Hobson (Eds.). Taylor & Francis, 2007.
Principles of Neural Science. E. R. Kandel, J. H. Schwartz, T. M Jessell (Eds.). Mc Graw Hill, New York, 2000.
Force and Touch Feedback for Virtual Reality. G. C. Burdea (Ed.). Wiley, New York, 1996 (available on NEBIS).
Human Haptic Perception, Basics and Applications. M. Grunwald (Ed.). Birkhäuser, Basel, 2008.
The Sense of Touch and Its Rendering, Springer Tracts in Advanced Robotics 45, A. Bicchi et al.(Eds). Springer-Verlag Berlin, 2008.
Interaktive und autonome Systeme der Medizintechnik - Funktionswiederherstellung und Organersatz. Herausgeber: J. Werner, Oldenbourg Wissenschaftsverlag 2005.
Neural prostheses - replacing motor function after desease or disability. Eds.: R. Stein, H. Peckham, D. Popovic. New York and Oxford: Oxford University Press.
Advances in Rehabilitation Robotics - Human-Friendly Technologies on Movement Assistance and Restoration for People with Disabilities. Eds: Z.Z. Bien, D. Stefanov (Lecture Notes in Control and Information Science, No. 306). Springer Verlag Berlin 2004.
Intelligent Systems and Technologies in Rehabilitation Engineering. Eds: H.N.L. Teodorescu, L.C. Jain (International Series on Computational Intelligence). CRC Press Boca Raton, 2001.
Selected Journal Articles and Web Links:
Abbas, J., Riener, R. (2001) Using mathematical models and advanced control systems techniques to enhance neuroprosthesis function. Neuromodulation 4, pp. 187-195.
Bach-y-Rita P., Tyler M., and Kaczmarek K (2003). Seeing with the brain. International journal of human-computer-interaction, 15(2):285-295.
Burdea, G., Popescu, V., Hentz, V., and Colbert, K. (2000): Virtual reality-based orthopedic telerehabilitation, IEEE Trans. Rehab. Eng., 8, pp. 430-432
Colombo, G., Jörg, M., Schreier, R., Dietz, V. (2000) Treadmill training of paraplegic patients using a robotic orthosis. Journal of Rehabilitation Research and Development, vol. 37, pp. 693-700.
Hayward, V. (2008): A Brief Taxonomy of Tactile Illusions and
Demonstrations That Can Be Done In a Hardware Store. Brain Research Bulletin, Vol 75, No 6, pp 742-752
Krebs, H.I., Hogan, N., Aisen, M.L., Volpe, B.T. (1998): Robot-aided neurorehabilitation, IEEE Trans. Rehab. Eng., 6, pp. 75-87
Levesque. V. (2005). Blindness, technology and haptics. Technical report, McGill University. Available at: http://www.cim.mcgill.ca/~vleves/docs/VL-CIM-TR-05.08.pdf
Quintern, J. (1998) Application of functional electrical stimulation in paraplegic patients. NeuroRehabilitation 10, pp. 205-250.
Riener, R., Nef, T., Colombo, G. (2005) Robot-aided neurorehabilitation for the upper extremities. Medical & Biological Engineering & Computing 43(1), pp. 2-10.
Riener, R. (1999) Model-based development of neuroprostheses for paraplegic patients. Royal Philosophical Transactions: Biological Sciences 354, pp. 877-894.
The vOICe. http://www.seeingwithsound.com.
VideoTact, ForeThought Development, LLC. http://my.execpc.com/?dwysocki/videotac.html
|Prerequisites / Notice||Target Group: |
Students of higher semesters and PhD students of
- D-MAVT, D-ITET, D-INFK, D-HEST
- Biomedical Engineering, Robotics, Systems and Control
- Medical Faculty, University of Zurich
Students of other departments, faculties, courses are also welcome
|376-1351-00L||Micro/Nanotechnology and Microfluidics for Biomedical Applications||W||2 credits||2V||E. Delamarche|
|Abstract||This course is an introduction to techniques in micro/nanotechnology and to microfluidics. It reviews how many familiar devices are built and can be used for research and biomedical applications. Transistors for DNA sequencing, beamers for patterning proteins, hard-disk technology for biosensing and scanning microfluidics for analyzing tissue sections are just a few examples of the covered topics.|
|Objective||The main objective of the course is to introduce micro/nanotechnology and microfluidics to students having a background in the life sciences. The course should familiarize the students with the techniques used in micro/nanotechnology and show them how micro/nanotechnology pervades throughout life sciences. Microfluidics will be emphasized due to their increasing importance in research and medical applications. The second objective is to have life students less intimidated by micro/nanotechnology and make them able to link instruments and techniques to specific problems that they might have in their projects/studies. This will also help students getting access to the ETHZ/IBM Nanotech Center infrastructure if needed.|
|Content||Mostly formal lectures (2 × 45 min), with a 2 hour visit and introduction to cleanroom and micro/nanotechnology instruments, last 3 sessions would be dedicated to the presentation and evaluation of projects by students (3 students per team).|
|Prerequisites / Notice||Nanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations.|
|529-0837-00L||Biomicrofluidic Engineering||W||7 credits||3G||A. de Mello|
|Abstract||Microfluidics 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.|
|Objective||In 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.|
|Content||Specific 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)
4. Design Workshop
Design of microfluidic architectures for PCR, distillation & mixing
5. Contemporary Applications in Biological Analysis
Cellular analyses (single cells, enzymatic assays, cell sorting)
6. System integration
Applications in radiochemistry, diagnostics and high-throughput experimentation
|Lecture notes||Lecture handouts will be provided|
|Prerequisites / Notice||This lecture will be recorded for Students of Basel (BSSE), details will be announced later.|
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