Search result: Catalogue data in Spring Semester 2021

MAS in Medical Physics Information
Specialisation in General Medical Physics
Major in Molecular Biology and Biophysics
Electives
NumberTitleTypeECTSHoursLecturers
151-0622-00LMeasuring on the Nanometer ScaleW2 credits2GA. Stemmer
AbstractIntroduction to theory and practical application of measuring techniques suitable for the nano domain.
ObjectiveIntroduction to theory and practical application of measuring techniques suitable for the nano domain.
ContentConventional techniques to analyze nano structures using photons and electrons: light microscopy with dark field and differential interference contrast; scanning electron microscopy, transmission electron microscopy. Interferometric and other techniques to measure distances. Optical traps. Foundations of scanning probe microscopy: tunneling, atomic force, optical near-field. Interactions between specimen and probe. Current trends, including spectroscopy of material parameters.
Lecture notesSlides and recordings available via Moodle (registered participants only).
376-1392-00LMechanobiology: Implications for Development, Regeneration and Tissue EngineeringW3 credits2GG. Shivashankar
AbstractThis course will emphasize the importance of mechanobiology to cell determination and behavior. Its importance to regenerative medicine and tissue engineering will also be addressed. Finally, this course will discuss how age and disease adversely alter major mechanosensitive developmental programs.
ObjectiveThe goal of this course is to provide an introduction to the emerging field of “Mechanobiology”.
ContentWe will focus on cells and tissues and introduce the major methods employed in uncovering the principles of mechanobiology. We will first discuss the cellular mechanotransduction mechanisms and how they regulate genomes. This will be followed by an analysis of the mechanobiological underpinnings of cellular differentiation, cell-state transitions and homeostasis. Developing on this understanding, we will then introduce the mechanobiological basis of cellular ageing and its impact on tissue regeneration, including neurodegeneration and musculoskeletal systems. We will then highlight the importance of tissue organoid models as routes to regenerative medicine. We will also discuss the impact of mechanobiology on host-pathogen interactions. Finally, we will introduce the broad area of mechanopathology and the development of cell-state biomarkers as readouts of tissue homeostasis and disease pathologies. Collectively, the course will provide a quantitate framework to understand the mechanobiological processes at cellular scale and how they intersect with tissue function and diseases.

Lecture 1: Introduction to the course: forces, signalling and cell behaviour
Lecture 2: Methods to engineer and sense mechanobiological processes
Lecture 3: Mechanisms of cellular mechanosensing and cytoskeletal remodelling
Lecture 4: Nuclear mechanotransduction pathways
Lecture 5: Genome organization, regulation and genome integrity
Lecture 6: Differentiation, development and reprogramming
Lecture 7: Tissue microenvironment, cell behaviour and homeostasis
Lecture 8: Cellular aging and tissue regeneration
Lecture 9: Neurodegeneration and regeneration
Lecture 10: Musculoskeletal systems and regeneration
Lecture 11: Tissue organoid models and regenerative medicine
Lecture 12: Microbial systems and host-pathogen interactions
Lecture13: Mechanopathology and cell-state biomarkers
Lecture14: Concluding lecture and case studies
Lecture notesn/a
LiteratureTopical Scientific Manuscripts
636-0016-00LComputational Systems Biology: Stochastic Approaches Information W4 credits3GM. H. Khammash, A. Gupta
AbstractThis course is concerned with the development of computational methods for modeling, simulation, and analysis of stochasticity in living cells. Using these tools, the course explores the richness of stochastic phenomena, how it arises from the interactions of dynamics and noise, and its biological implications.
ObjectiveTo understand the origins and implications of stochastic noise in living cells, and to learn the computational tools for the modeling, simulation, analysis, and identification of stochastic biochemical reaction networks.
ContentThe cellular environment is abuzz with noise. A key source of this noise is the randomness that characterizes the motion of cellular constituents at the molecular level. Cellular noise not only results in random fluctuations (over time) within individual cells, but it is also a main source of phenotypic variability among clonal cell populations.

Review of basic probability and stochastic processes; Introduction to stochastic gene expression; deterministic vs. stochastic models; the stochastic chemical kinetics framework; a rigorous derivation of the chemical master equation; moment computations; linear vs. nonlinear propensities; linear noise approximations; Monte Carlo simulations; Gillespie's Stochastic Simulation Algorithm (SSA) and variants; direct methods for the solution of the Chemical Master Equation; moment closure methods; intrinsic and extrinsic noise in gene expression; parameter identification from noise; propagation of noise in cell networks; noise suppression in cells; the role of feedback; exploiting noise; bimodality and stochastic switches.
LiteratureLiterature will be distributed during the course as needed.
Prerequisites / NoticeStudents are expected to have completed the course `Mathematical modeling for systems biology (BSc Biotechnology) or `Computational systems biology (MSc Computational biology and bioinformatics). Concurrent enrollment in `Computational Systems Biology: Deterministic Approaches is recommended.
551-1616-00LMethods for Studies of Biological Macromolecules by NMRW1 credit2SA. D. Gossert
AbstractIn this course topics relevant to structure determination of biological macromolecules by solution state NMR spectroscopy are discussed. The course is tailored to advanced students, mainly PhD students and postdocs in structural biology who have experience with applications of NMR spectroscopy. The individual participants present various topics in form of a seminar.
ObjectiveThe students will actively participate in the course which is held in the form of a seminar. Individual students will prepare particular topics of the course based on literature references and present the material in form of a seminar to their fellow students. In short, the students learn to actively participate in discussions and to prepare a presentation of a scientific topic which was mostly unknown to them before.
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