Daniel J. Müller: Catalogue data in Autumn Semester 2017

Name Prof. Dr. Daniel J. Müller
Professur für Biophysik
ETH Zürich, BSS F 43.2
Klingelbergstrasse 48
4056 Basel
Telephone+41 61 387 33 07
Fax+41 61 387 39 94
DepartmentBiosystems Science and Engineering
RelationshipFull Professor

636-0102-00LAdvanced Bioengineering4 credits3SS. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, D. J. Müller, R. Paro, R. Platt, T. Schroeder
AbstractThis course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications
ObjectiveStudents will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences.
ContentMolecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine.
Lecture notesHandouts during class
LiteratureWill be announced during the course
636-0104-00LNanomachines of the Cell
Attention: This course was offered in previous semesters with the number: 626-0010-00L "Nanomachines of the Cell (Part I): Principles". Students that already passed course 626-0010-00 cannot receive credits for course 636-0104-00.
4 credits3GD. J. Müller
AbstractMolecular biotechnology students will combine basic knowledge in molecular cell biology, biochemistry, proteomics, biophysics, bioinformatics, bionanotechnology and engineering to learn how the nanomachines of the cell works and to use this knowledge to address future molecular biotechnological and bionanotechnological questions. Particularly it will be addressed how biomolecular units can be char
ObjectiveGain of an interdisciplinary research and development competence, which qualifies for scientific work (master's or doctoral thesis) as well as for work in the research and development department of a biotechnological company. The module is of general use in nano- and biotechnological courses of study focusing modern biomolecular technologies.
ContentWhat are nanomachines of the cell? Understanding the cell as a complex factory. Are there engineering principles of the cell and if so what can we learn? Introducing new ways to understand and to apply engineering principles of cellular nanomachines in biotechnology and nanotechnology.
Introduction into factors and mechanisms that determine protein folding and stability. Inter- and intramolecular interactions. Understanding the concept of an energy landscape to describe protein folding, stabilization, destabilization, and unfolding. Mechanisms of protein stabilization, destabilization and aggregation in health and disease. Are there methods and ways to prevent protein destabilization and aggregation? Mechanisms of protein destabilization in biomaterials science, bioengineering, and in biotechnological and pharmacological applications. Protein stability in biotechnology. Biophysical methods that allow quantifying protein stability. Methods to prevent protein destabilization in biotechnological applications. Ways to adjust and manipulate the protein stability in biotechnology and medicine. Designing molecular compounds that stabilize specific proteins. Designing molecular compounds that lead to protein destabilization, misfolding and denaturation.
Biological and artificial membranes. Principles of membrane assembly, properties, stability and durability. Vesicles as containers for cargo. Engineering vesicles from native and synthetic components. Engineering ultrastable synthetic vesicles. Applying vesicles in biotechnology and medicine. Functionalizing vesicular membranes with proteins. Principles of membrane proteins. Structure and function relationship of membrane proteins. Importance of membrane proteins in pharmacology and biotechnology. Ways to structurally and functionally characterize membrane proteins. Bionanotechnological tools to handle and manipulate single membrane proteins. Membrane proteins as a toolbox to assemble nanoscopic functional vesicles. Designing multifunctional synthetic vesicles: Vesicles for drug delivery, vesicles for active transport, vesicles converting energy, vesicles switching their affinity, function, stability, and other properties.
Energy currencies of the cell. Energy conversion. Storable and transient forms of energy. Nature created a variety of light-driven ion pumps. How can we use this pumps, how can we modify them to our purpose? Employing light-driven ion pumps in biotechnology. Employing light-driven proton pumps adsorbing different wavelengths to boost the membrane gradient. How to create a synthetic membrane that allows no diffusion of ions. Transforming a proton into a chloride pump. Tuning the adsorption spectra of a light-driven ion pump. Engineering proton pumps as safety standards for credit cards and ID cards. Engineering proton pumps for holographic devices. Native and artificial light-activated ion channels. Engineering light-activated channels for their use in neuroscience: Optogenetics. ATP synthases convert transient into storable energies. Experimental approaches to explore the nanoscopic rotary machinery of single ATP synthases. Are there ways to engineer and to exchange the building blocks of the ATP synthase? Ways to change to gear of ATP synthases and to 'tune' its fuel consumption. Engineering an artificial vesicular system to convert light into ion gradients to synthesize ATP. Engineering ATP synthases as nanopropellers to move vesicles. Engineering a light-frequency tuned proton pumps to control the speed of nanopropelled vesicles. Engineering light-driven ion pumps to power the synthetic ATP propellers and to steer vesicles. Engineering and employing ATP synthases as molecular mixing devices.
Principles of signal transduction. The family of G-protein coupled receptors (GPCRs). Structure and function of GPCRs. Engineering (and other) possibilities to manipulate the functional state of GPCRs.
Lecture notesHand out will be given to students at lecture.
LiteratureAlberts et al: Molecular Biology of the cell
Biochemistry (5th edition), Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN 0-7167-4684-0, Freeman
Principles of Biochemistry, Nelson & Cox; ISBN: 1-57259-153-6, Worth Publishers, New York
Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania
Intermolecular & Surface Forces, Israelachvili; ISBN: 0-12-375181-0, Academic Press, London
Proteins: Biochemistry and Biotechnolgy, Walsh; ISBN: 0-471-899070, Wiley & Sons, New York
Textbook of Biochemistry with Clinical Correlations, Devlin; ISBN: 0-471-411361, Wiley & Sons, New York
Molecular Virology, Modrow et al.; ISBN: 3-8274-1086-X, Spektrum Verlag, Heidelberg
Prerequisites / NoticeThe module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher.
636-0301-00LCurrent Topics in Biosystems Science and Engineering2 credits1SR. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, P. Pantazis, R. Paro, S. Reddy, T. Schroeder, T. Stadler, J. Stelling
AbstractThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
ObjectiveTo provide an overview of current systems biology research.
ContentThe final list of topics will be available at http://www.bsse.ethz.ch/education/.