Search result: Catalogue data in Autumn Semester 2024
Chemical and Bioengineering Master  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 Electives | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Biochemical Engineering | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 636-0108-00L | Biological Engineering and Biotechnology | W | 4 credits | 3V | M. Fussenegger | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Biological 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Biological 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | 1. 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 notes | Handout during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 636-0007-00L | Computational Systems Biology | W | 6 credits | 3V + 2U | J. Stelling | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Study of fundamental concepts, models and computational methods for the analysis of complex biological networks. Topics: Systems approaches in biology, biology and reaction network fundamentals, modeling and simulation approaches (topological, probabilistic, stoichiometric, qualitative, linear / nonlinear ODEs, stochastic), and systems analysis (complexity reduction, stability, identification). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Biology has witnessed an unprecedented increase in experimental data and, correspondingly, an increased need for computational methods to analyze this data. The explosion of sequenced genomes, and subsequently, of bioinformatics methods for the storage, analysis and comparison of genetic sequences provides a prominent example. Recently, however, an additional area of research, captured by the label "Systems Biology", focuses on how networks, which are more than the mere sum of their parts' properties, establish biological functions. This is essentially a task of reverse engineering. The aim of this course is to provide an introductory overview of corresponding computational methods for the modeling, simulation and analysis of biological networks. We will start with an introduction into the basic units, functions and design principles that are relevant for biology at the level of individual cells. Making extensive use of example systems, the course will then focus on methods and algorithms that allow for the investigation of biological networks with increasing detail. These include (i) graph theoretical approaches for revealing large-scale network organization, (ii) probabilistic (Bayesian) network representations, (iii) structural network analysis based on reaction stoichiometries, (iv) qualitative methods for dynamic modeling and simulation (Boolean and piece-wise linear approaches), (v) mechanistic modeling using ordinary differential equations (ODEs) and finally (vi) stochastic simulation methods. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | http://www.csb.ethz.ch/education/lectures.html | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006. Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2010. B. Ingalls, Mathematical modeling in systems biology: an introduction. MIT Press, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 376-1714-00L | Biocompatible Materials | W | 4 credits | 3V | K. Maniura, M. Rottmar, 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The course covers the follwing topics: 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. 4. Introduction to different material classes in use for medical applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Introduction into natural 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, drug delivery and for medical devices 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. A link between academic research and industrial entrepreneurship is demonstrated by external guest speakers, who present their current research topics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Handouts are deposited online (moodle). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Literature: - 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 and references therin. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 529-0615-01L | Biochemical and Polymer Reaction Engineering | W | 6 credits | 3G | P. Arosio, P. Fleckenstein | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Polymerization reactions and processes. Homogeneous and heterogeneous (emulsion) kinetics of free radical polymerization. Post treatment of polymer colloids. Bioprocesses for the production of molecules and therapeutic proteins. Kinetics and design of aggregation processes of macromolecules and proteins. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | The aim of the course is to learn how to design polymerization reactors and bioreactors to produce polymers and proteins with the specific product qualities that are required by different applications in chemical, pharmaceutical and food industry. This activity includes the post-treatment of polymer latexes, the downstream processing of proteins and the analysis of their colloidal behavior. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | We will cover the fundamental processes and the operation units involved in the production of polymeric materials and proteins. In particular, the following topics are discussed: Overview on the different polymerization processes. Kinetics of free-radical polymerization and use of population balance models. Production of polymers with controlled characteristics in terms of molecular weight distribution. Kinetics and control of emulsion polymerization. Surfactants and colloidal stability. Aggregation kinetics and aggregate structure in conditions of diffusion and reaction limited aggregation. Modeling and design of colloid aggregation processes. Physico-chemical characterization of proteins and description of enzymatic reactions. Operation units in bioprocessing: upstream, reactor design and downstream. Industrial production of therapeutic proteins. Characterization and engineering of protein aggregation. Protein aggregation in biology and in biotechnology as functional materials. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Scripts are available on the web page of the Arosio-group: http://www.arosiogroup.ethz.ch/education.html Additional handout of slides will be provided during the lectures. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | R.J. Hunter, Foundations of Colloid Science, Oxford University Press, 2nd edition, 2001 D. Ramkrishna, Population Balances, Academic Press, 2000 H.W. Blanch, D. S. Clark, Biochemical Engineering, CRC Press, 1995 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 529-0837-01L | Biomicrofluidic Engineering  | W | 6 credits | 3G | A. de Mello | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Microfluidics describes the behaviour, control and manipulation of fluids geometrically constrained within sub-uL environments. Microfluidic devices enable physical and chemical processes to be controlled with exquisite precision and in an fast and efficient manner. This course introduces the underlying concepts, features and applications of microfluidic systems in the chemical and life sciences. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | We 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 central component of this course is a research project. This will allow students to develop a practical understanding of the benefits of miniaturization in chemical and biological experimentation. Projects will be performed in groups of between four and six students and will include both experimental and simulation aspects. Each group, under the guidance of a mentor, will plan and execute a novel research project. The results of this activity will be disseminated through an 'academic-style" research article and a "conference-style" oral presentation. Course grades will be evaluated through both a written exam and the project grade. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Specific topics covered in the course include, but are not limited to: 1. Theoretical Concepts Scaling laws, features of thermal/mass transport, diffusion, basic description of fluid flow in small volumes, microfluidic mixing strategies. 2. Microfluidic Device Manufacture Basic principles of conventional lithography of rigid materials, ‘soft’ lithography, polymer machining (injection molding, hot embossing, and 3D-printing). 3. Electrokinetics Principles of electrophoresis, electroosmosis, high performance capillary electrophoresis, electrokinetic scaling laws, chip-based electrophoresis and isoelectric focusing. 4. Mass Transfer Phenomena Key features of mass transport in microfluidic systems, diffusive transport, diffusion-convection, Péclet number, Taylor-Aris diffusion, chaotic mixing and Damköhler numbers. 5. Heat Transfer Phenomena Key features of thermal transport in microfluidic systems, conduction, convection, heat transfer by convection in internal flows, heat transfer processes in microfluidic devices. 6. Microfluidic Systems for Materials Synthesis Microfluidic reactors for the controlled synthesis of colloidal nanomaterials, advanced automation for bespoke materials discovery & characterization. 7. Point-of-Care Diagnostics Microscale tools for diagnostics, challenges associated with point-of-care (PoC) diagnostic testing, requirements for PoC devices, common PoC device formats, applications of PoC diagnostics in the developing world. 8. Microscale DNA Amplification Amplification and analysis of nucleic acids using batch, continuous flow and droplet-based microfluidic reactors. 9. Small volume Molecular Detection Spectroscopic approaches for analyte detection in small volumes with a particular focus on single molecule detection. 10. Droplets and Segmented Flows Formation, manipulation and use of liquid/liquid segmented flows in chemical and biological experimentation. 11. Single Cell Analysis Applications of microfluidic tools in cellular analysis, flow cytometry, enzymatic assays and single cell analysis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture handouts, background literature, problem sheets and notes will be provided electronically through the course Moodle site. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | There is no set text for the course. All relevant literature will be provided electronically through the course Moodle site. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 551-0357-00L | Cellular Matters: Properties, Functions and Applications of Biomolecular Condensates The number of participants is limited to 30 and will only take place with a minimum of 6 participants. At the beginning of the course, student groups will be formed and assigned to the milestone papers. To facilitate this, students must confirm their registration by the beginning of the 3rd week of semester. | W | 4 credits | 2S | T. Michaels, F. Allain, P. Arosio, D. Hilvert, M. Jagannathan, T. Kleele, R. Mezzenga, G. Neurohr, R. Riek, A. E. Smith, K. Weis, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This Master level course delves into the emerging field of biomolecular condensates - membrane-less organelles in cells. Using interdisciplinary concepts from biology, chemistry, biophysics, and soft matter, we will explore the biological properties of these condensates, their functions in health and disease, and their potentiol as new biomimetic materials for various applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | In the last decade, a novel type of cell compartments called biomolecular condensates have been discovered. This discovery is radically changing our understanding of the cell, its organization, and dynamics. The emerging picture is that the cytoplasm and nucleoplasm are highly complex fluids that can (meta)stably segregate into membrane-less compartments, similary to emulsions. This interdisciplinary course encompasses milestone works and cutting-edge research questions in the young field of biomolecular condensates, including their properties, functions, and applications. The course begins with a lecture series that introduces the topic of condensates to an interdisciplinary audience and provides a theoretical foundation for understanding current research questions in the field. the lecturesprovide a base for student presentations of recent publications in the field, and for research seminars given by course lecturers, who are all active researchers with diverse expertise. Through this exciting interdisciplinary understanding of biomolecular condensates, bridging biology, chemistry, biophysics, and soft matter. Students will not only learn how to critically read and evaluate scientific literature but will also gain valuable experience in giving scientific presentations to an interdisciplinary audience. Each presentation will require an introduction, critical analysis of the results, and a discussion of their significance, allowing student to substantiate their statements with a critical mindset that considers the pros and cons of chosen approaches and methods, as well as any limitations or possible follow-up experiments. This process will enable student to ask relevant querions and actively participate in class discussions, further enhancing their scientific skills. In preparing the presentations, the students will have the unique opportunity to interact closely with each other and with the lecturers, who are all internationally well-established experts, and receive guidance in selectin a topic for the final presentaton and supporting literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The topic of biomolecular condensates goes beyond the boundaries of traditional disciplines and requires a multi-disciplinary approach that leverages and cross-fertilizes biology, physical chemistry, biophysics, and soft matter. This course will explore the properties, functions and potentioal applicatons of biomolecular condensates, including their role in neurodegenerative diseases such as Alzheimer's and Parkinson's, as well as their use as smart biomimetic materials. This course is divided into two parts. The fist part will introduce the basic concepts essentialto the study of biomolecular condensates and phase separation. Topics include: fundamental units and scales in soft matter, phase transitions in biology, biopolymers and molecular self-assembly, introduction to active matter. This will establish a foundation for the second part, which will explore milestone works and current research in the field of biomolecular condensates. Each lecture of this second part will consist of: 1) a short literature seminar, where student groups will present and discuss a milestone paper assigned in advance and 2) a research seminar, where one of the course lecturers will present their own state-of-the art research in the field, building upon the milestone literature. At the beginning of the course, student groups will be formed and assigned to the milestone papers. To facilitate this, students must confirm their registration by the beginning of the 3rd week of semester. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Lecture slides and some scripts will be provided. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | No compulsory textbooks. Literature will be provided during the course | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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