Search result: Catalogue data in Autumn Semester 2014
|Biomedical Engineering Master|
|Master Programme According to Programme Regulations 2013|
| Recommended Elective Courses|
These courses are particularly recommended for the Biomechanics track. Please consult your track advisor if you wish to select other subjects.
|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.|
|151-0511-00L||Mechanics of Nano- and Micro-Materials||W||4 credits||2V + 1U||C. Daraio|
|Abstract||The 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.|
|Objective||Learn 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.|
|Lecture notes||Slides and notes from the course will be provided.|
|Literature||Relevant articles and reading materials will be provided. Various books will be recommended pertaining to the topics covered.|
|Prerequisites / Notice||Mechanics I, II, III|
|151-0524-00L||Continuum Mechanics for Engineers||W||4 credits||2V + 1U||E. Mazza|
|Abstract||The lecture deals with constitutive models that are relevant for design and calculation of structures. These include anisotropic linear elsticity, linear viscoelasticity, plasticity, viscoplasticity. Homogenization theories and laminate theory are presented. Theoretical models are complemented by examples of engineering applications and eperiments.|
|Objective||Basic theories for solving continuum mechanics problems of engineering applications, with particular attention to material models.|
|Content||Anisotrope Elastizität, Linearelastisches und linearviskoses Stoffverhalten, Viskoelastizität, mikro-makro Modellierung, Laminattheorie, Plastizität, Viscoplastizität, Beispiele aus der Ingenieuranwendung, Vergleich mit Experimenten.|
|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.
|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.
|263-5001-00L||Introduction to Finite Elements and Sparse Linear System Solving||W||4 credits||2V + 1U||P. Arbenz, T. Kaman|
|Abstract||The finite element (FE) method is the method of choice for (approximately) solving partial differential equations on complicated domains. In the first third of the lecture, we give an introduction to the method. The rest of the lecture will be devoted to methods for solving the large sparse linear systems of equation that a typical for the FE method. We will consider direct and iterative methods.|
|Objective||Students will know the most important direct and iterative solvers for sparse linear systems. They will be able to determine which solver to choose in particular situations.|
|Content||I. THE FINITE ELEMENT METHOD|
(1) Introduction, model problems.
(2) 1D problems. Piecewise polynomials in 1D.
(3) 2D problems. Triangulations. Piecewise polynomials in 2D.
(4) Variational formulations. Galerkin finite element method.
(5) Implementation aspects.
II. DIRECT SOLUTION METHODS
(6) LU and Cholesky decomposition.
(7) Sparse matrices.
(8) Fill-reducing orderings.
III. ITERATIVE SOLUTION METHODS
(9) Stationary iterative methods, preconditioning.
(10) Preconditioned conjugate gradient method (PCG).
(11) Incomplete factorization preconditioning.
(12) Multigrid preconditioning.
(13) Nonsymmetric problems (GMRES, BiCGstab).
(14) Indefinite problems (SYMMLQ, MINRES).
|Literature|| M. G. Larson, F. Bengzon: The Finite Element Method: Theory, Implementation, and Applications. Springer, Heidelberg, 2013.|
 H. Elman, D. Sylvester, A. Wathen: Finite elements and fast iterative solvers. OUP, Oxford, 2005.
 Y. Saad: Iterative methods for sparse linear systems (2nd ed.). SIAM, Philadelphia, 2003.
 T. Davis: Direct Methods for Sparse Linear Systems. SIAM, Philadelphia, 2006.
 H.R. Schwarz: Die Methode der finiten Elemente (3rd ed.). Teubner, Stuttgart, 1991.
|Prerequisites / Notice||Prerequisites: Linear Algebra, Analysis, Computational Science.|
The exercises are made with Matlab.
|376-1219-00L||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
|376-1279-00L||Virtual Reality in Medicine |
Does not take place this semester.
|W||3 credits||2V||R. Riener|
|Abstract||Virtual Reality has the potential to support medical training and therapy. This lecture will derive the technical principles of multi-modal (audiovisual, haptic, tactile etc.) input devices, displays and rendering techniques. Examples are presented in the fields of surgical training, intra-operative augmentation, and rehabilitation. The lecture is accompanied by practical courses and excursions.|
|Objective||Provide theoretical and practical knowledge of new principles and applications of multi-modal simulation and interface technologies in medical education, therapy, and rehabilitation.|
|Content||Virtual Reality has the potential to provide descriptive and practical information for medical training and therapy while relieving the patient and/or the physician. Multi-modal interactions between the user and the virtual environment facilitate the generation of high-fidelity sensory impressions, by using not only visual and auditory modalities, but also kinesthetic, tactile, and even olfactory feedback. On the basis of the existing physiological constraints, this lecture will derive the technical requirements and principles of multi-modal input devices, displays, and rendering techniques. Several examples are presented that are currently being developed or already applied for surgical training, intra-operative augmentation, and rehabilitation. The lecture will be accompanied by several practical courses on graphical and haptic display devices as well as excursions to facilities equipped with large-scale VR equipment. |
Students of higher semesters and PhD students of
- D-HEST, D-MAVT, D-ITET, D-INFK, D-PHYS
- Robotics, Systems and Control Master
- Biomedical Engineering/Movement Science and Sport
- Medical Faculty, University of Zurich
Students of other departments, faculties, courses are also welcome!
|Literature||Book: Virtual Reality in Medicine. Riener, Robert; Harders, Matthias; 2012 Springer.|
|Prerequisites / Notice||The course language is English. |
Basic experience in Information Technology and Computer Science will be of advantage
More details will be announced in the lecture.
|376-1714-00L||Biocompatible Materials||W||4 credits||3G||K. Maniura, 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.
|376-1351-00L||Micro/Nanotechnology and Microfluidics for Biomedical Applications||W||2 credits||2V||E. Delamarche|
|Abstract||This course is an introduction to techniques in micro/nanotechnology and to microfluidics. It reviews how many familiar devices are built and can be used for research and biomedical applications. Transistors for DNA sequencing, beamers for patterning proteins, hard-disk technology for biosensing and scanning microfluidics for analyzing tissue sections are just a few examples of the covered topics.|
|Objective||The main objective of the course is to introduce micro/nanotechnology and microfluidics to students having a background in the life sciences. The course should familiarize the students with the techniques used in micro/nanotechnology and show them how micro/nanotechnology pervades throughout life sciences. Microfluidics will be emphasized due to their increasing importance in research and medical applications. The second objective is to have life students less intimidated by micro/nanotechnology and make them able to link instruments and techniques to specific problems that they might have in their projects/studies. This will also help students getting access to the ETHZ/IBM Nanotech Center infrastructure if needed.|
|Content||Mostly formal lectures (2 × 45 min), with a 2 hour visit and introduction to cleanroom and micro/nanotechnology instruments, last 3 sessions would be dedicated to the presentation and evaluation of projects by students (3 students per team).|
|Prerequisites / Notice||Nanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations.|
|376-1720-00L||Application of MATLAB in the Human Movement Sciences||W||2 credits||2G||R. van de Langenberg|
|Abstract||Students will learn to import, process and graphically present experimental data using the MATLAB computing environment. Both the data and the methods of analysis will be typical for experiments in Human Movement Science (i.e. kinematics, kinetics and electromyography).|
|Objective||Students will acquire the ability to independently load, plot, and process kinematic, kinetic and electromyographical data using the MATLAB computing environment.|
|Content||Drawbacks of Excel; Possibilities in MATLAB; Import of several data formats; Plot of one and more signals; Removing of an offset and filtering of data based on self-written functions; Normalisation and parametrisation of data; Reliability; Interpolation, Differentiation and Integration in MATLAB.|
|Literature||During the lecture, several electronically available MATLAB introductions are indicated. Course-specific scripts will be provided by the lecturer.|
|Prerequisites / Notice||A Laptop with MATLAB installed (v2009 or higher) and wireless internet access is mandatory. Two students can share a laptop if necessary. A MATLAB student version can be obtained at Stud-IDES for free.|
|376-1974-00L||Colloquium in Biomechanics||W||2 credits||2K||B. Helgason, S. J. Ferguson, R. Müller, J. G. Snedeker, B. Taylor, M. Zenobi-Wong|
|Abstract||Current topics in biomechanics presented by speakers from academia and industry.|
|Objective||Getting insight into actual areas and problems of biomechanics.|
|376-2017-00L||Biomechanics of Sports Injuries and Rehabilitation||W||3 credits||2V||K.‑U. Schmitt, J. Goldhahn|
|Abstract||This lectures introduces the basic principles of injury mechanics and rehabilitation focussing on sports injuries.|
|Objective||Within the scope of this lecture you will learn the basic principles of trauma biomechanics. Based on examples from sports, you will get to know different mechanisms that can possibly result in injury. Investigating the background and cause of injury should allow you to assess the injury risk for sports activities. Furthermore you should be able to develop measures to prevent such injury.|
|Content||This lecture deals with the basic principles of injury mechanics and rehabilitation. Mechanisms that can result in injury are presented. Furthermore possibilities to prevent injuries are discussed. Thereby the lecture focuses on sports injuries.|
|Lecture notes||Handouts can be downloaded.|
|Literature||Schmitt K-U, Niederer P, M. Muser, Walz F: "Trauma Biomechanics - Accidental Injury in traffic and sports", Springer Verlag|
|Prerequisites / Notice||A course work is required. The mark of this course work contributes to the final credits for this lecture. Details will be given during the first lecture.|
|402-0341-00L||Medical Physics I||W||6 credits||2V + 1U||P. Manser|
|Abstract||Introduction to the fundamentals of medical radiation physics. Functional chain due to radiation exposure from the primary physical effect to the radiobiological and medically manifest secondary effects. Dosimetric concepts of radiation protection in medicine. Mode of action of radiation sources used in medicine and its illustration by means of Monte Carlo simulations.|
|Objective||Understanding the functional chain from primary physical effects of ionizing radiation to clinical radiation effects. Dealing with dose as a quantitative measure of medical exposure. Getting familiar with methods to generate ionizing radiation in medicine and learn how they are applied for medical purposes. Eventually, the lecture aims to show the students that medical physics is a fascinating and evolving discipline where physics can directly be used for the benefits of patients and the society.|
|Content||The lecture is covering the basic principles of ionzing radiation and its physical and biological effects. The physical interactions of photons as well as of charged particles will be reviewed and their consequences for medical applications will be discussed. The concept of Monte Carlo simulation will be introduced in the excercises and will help the student to understand the characteristics of ionizing radiation in simple and complex situations. Fundamentals in dosimetry will be provided in order to understand the physical and biological effects of ionizing radiation. Deterministic as well as stochastic effects will be discussed and fundamental knowledge about radiation protection will be provided. In the second part of the lecture series, we will cover the generation of ionizing radiation. By this means, the x-ray tube, the clinical linear accelarator, and different radioactive sources in radiology, radiotherapy and nuclear medicine will be addressed. Applications in radiolgoy, nuclear medicine and radiotherapy will be described with a special focus on the physics underlying these applications.|
|Lecture notes||A script will be provided.|
|402-0674-00L||Physics in Medical Research: From Atoms to Cells||W||6 credits||2V + 1U||B. K. R. Müller|
|Abstract||Scanning probe and diffraction techniques allow studying activated atomic processes during early stages of epitaxial growth. For quantitative description, rate equation analysis, mean-field nucleation and scaling theories are applied on systems ranging from simple metallic to complex organic materials. The knowledge is expanded to optical and electronic properties as well as to proteins and cells.|
|Objective||The lecture series is motivated by an overview covering the skin of the crystals, roughness analysis, contact angle measurements, protein absorption/activity and monocyte behaviour.|
As the first step, real structures on clean surfaces including surface reconstructions and surface relaxations, defects in crystals are presented, before the preparation of clean metallic, semiconducting, oxidic and organic surfaces are introduced.
The atomic processes on surfaces are activated by the increase of the substrate temperature. They can be studied using scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The combination with molecular beam epitaxy (MBE) allows determining the sizes of the critical nuclei and the other activated processes in a hierarchical fashion. The evolution of the surface morphology is characterized by the density and size distribution of the nanostructures that could be quantified by means of the rate equation analysis, the mean-field nucleation theory, as well as the scaling theory. The surface morphology is further characterized by defects and nanostructure's shapes, which are based on the strain relieving mechanisms and kinetic growth processes.
High-resolution electron diffraction is complementary to scanning probe techniques and provides exact mean values. Some phenomena are quantitatively described by the kinematic theory and perfectly understood by means of the Ewald construction. Other phenomena need to be described by the more complex dynamical theory. Electron diffraction is not only associated with elastic scattering but also inelastic excitation mechanisms that reflect the electronic structure of the surfaces studied. Low-energy electrons lead to phonon and high-energy electrons to plasmon excitations. Both effects are perfectly described by dipole and impact scattering.
Thin-films of rather complex organic materials are often quantitatively characterized by photons with a broad range of wavelengths from ultra-violet to infra-red light. Asymmetries and preferential orientations of the (anisotropic) molecules are verified using the optical dichroism and second harmonic generation measurements. These characterization techniques are vital for optimizing the preparation of medical implants and the determination of tissue's anisotropies within the human body.
Cell-surface interactions are related to the cell adhesion and the contractile cellular forces. Physical means have been developed to quantify these interactions. Other physical techniques are introduced in cell biology, namely to count and sort cells, to study cell proliferation and metabolism and to determine the relation between cell morphology and function.
3D scaffolds are important for tissue augmentation and engineering. Design, preparation methods, and characterization of these highly porous 3D microstructures are also presented.
Visiting clinical research in a leading university hospital will show the usefulness of the lecture series.
|465-0953-00L||Biostatistics||W||2 credits||2V + 1U||B. Sick|
|Abstract||The course deals with simple quantitative and graphical as well as more complex methods of biostatistics. Contents: Descriptive statistics, probability theory and design of experiments, testing hypotheses, confidence intervals, correlation, simple and multiple linear regression, analysis of variance, logistic regression, survival analysis (Kaplan-Meier curves and Cox-regression).|
|551-1295-00L||Introduction to Bioinformatics: Concepts and Applications||W||6 credits||4G||W. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner|
|Abstract||Storage, handling and analysis of large datasets have become essential in biological research. The course will introduce students to a number of applications of bioinformatics in biology. Freely accessible software tools and databases will be explained and explored in theory and praxis.|
|Objective||Introduction to Bioinformatics I: Concepts and Applications (formerly Bioinformatics I) will provide students with the theoretical background of approaches to store and retrieve information from large databases. Concepts will be developed how DNA sequence information can be used to understand phylogentic relationships, how RNA sequence relates to structure, and how protein sequence information can be used for genome annotation and to predict protein folding and structure. Students will be introduced to quantitative methods for measuring gene expression and how this information can be used to model gene networks. Methods will be discussed to construct protein interaction maps and how this information can be used to simulate dynamic molecular networks.|
In addition to the theoretical background, the students will develop hands-on experiences with the bioinformatics methods through guided exercises. The course provides students from different backgrounds with basic training in bioinformatics approaches that have impact on biological, chemical and physics experimentation. Bioinformatics approaches draw significant expertise from mathematics, statistics and computational science.
Although "Intoduction to Bioinformatics I" will focus on theory and praxis of bioinformatics approaches, the course provides an important foundation for the course "Introduction to Bioinformatics II: Fundamentals of computer science, modeling and algorithms" that will be offered in the following semester.
|Content||Bioinformatics I will cover the following topics:|
From genes to databases and information
Prediction of gene function and regulation
RNA structure prediction
Gene expression analysis using microarrays
Protein sequence and structure databases
WWW for bioinformatics
Protein sequence comparisons
Proteomics and de novo protein sequencing
Protein structure prediction
Cellular and protein interaction networks
Molecular dynamics simulation
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