NFYK15006U  Biophysics of Cells and Single Molecules

Volume 2017/2018
Education

MSc Programme in Nanoscience

MSc Programme in Physics

MSc Programme in Physics w. minor subject

Content

The course will focus on relevant mechanical properties and functions of biological systems on the nano- and micron-scale. One focus is on biological polymers and on how these are part of intelligent and material economic tensegrity structures. The principle behind tensegrity structures is similar to the architectural principles behind the construction of, e.g., bridges and skyscrapers. In addition, there will be focus on cellular movement, this involving single molecule motors and bio-polymerization, which is a topic that is also relevant for development of wide-spread diseases as, e.g., Alzheimer's and Parkinson's diseases. The course also goes through novel remarkable force-scope and microscopy techniques that allows for studying fundamental actions of the molecular building blocks of life. Emphasis will be on how the single molecule results are obtained, how they complement, and in certain cases contradict, results obtained at the ensemble level. The course will invoke the most recent non-equilibrium theories to correctly describe and understand results obtained at the nano-scale level. As the course deals with very recent research results, it is also based on scientific papers, and an important aspect of the course is a critical assessment of primary literature.

Learning Outcome

Knowledge:
The course participants will gain thorough knowledge about fundamental aspects of single molecule systems such as molecular motors, proteins, RNA and DNA, and nano-machines. Also, the course participants will gain deep knowledge of the most commonly used single molecule methodolgies,their capabilities, possibilities and limitations. These methodologies including optical tweezers, magnetic tweezers, AFM, single molecule fluorescence, and super-resolution microscopy.   The course will take the course participant to the front line of single molecule research, going through the most important and remarkable results achieved. Emphasis will also be on how, in practice, to treat non-equilibrium nano-scale systems. In addition, the course participants will gain important knowledge of how to read, understand and criticize primary literature and they will be trained in presenting and questioning research results.

 

Skills:
The course will enable the participant to

  • obtain knowledge about the physics of polymers. Being able to theoretically predict the typical physical size of a polymer under given conditions and predict flexibility and elasticity of polymer chains. Utilize this knowledge on the most commonly encountered biological polymers inside a living system.
  • predict the composition and self-assembled structuring of bio-membranes. Also, using energetics, the student should be able to predict the shapes of simple organisms under a variety of conditions and apply this knowledge to e.g. blood cells and simple bacteria.
  • know the forces arising from electrostatic interactions within a living organism. These forces include van der Walls and electrostatic interactions and entropic repulsion of sheets and polymers. To be able to apply these results to, e.g., adhesion processes.
  • understand how simple motion of living organisms come about. This includes understanding the polymerization of basic biopolymers such as actin and tubulin, the action of molecular motors, and the ability to calculate quantitatively the forces exerted.
  • gain knowledge about the most common single molecule techniques, these including optical tweezers, magnetic tweezers, single molecule flourescent techniques, super resolution microscopy, and AFM.
  • be aware of the fundamental problems encountered when studying nature at the single molecule level. This includes the role of thermal fluctuations and the fact that most of single molecule experiments are performed in a non-equilibrium fashion, thus rendering conventional statistical mechanics inadequate.
  • understand and being able to apply the most recent non-equilibrium theories these including the Jarzynski Equality and Crooks theorem.
  • perform a thorough and critical reading of a scientific manuscript.
  • have a general overview of the entire field with some knowledge of the status of research internationally.
     

Competencies:
The course participants will gain competencies in applying methods of physics to obtain a quantitative description of complex biological systems. Through this, knowledge will be gained concerning mechanical properties of living cells and their molecular building blocks. The course participants will also gain competences in understanding the working method, capabilities, and limitations of the most wide spread single molecule techniques and they will be able to utilize the most novel results of non-equilibrium statistical physics on nano-scale systems. Finally, the students will gain the competencies to critically read a scientific paper, to find the background material needed to fully understand the paper, and to perform a presentation of primary literature.

See Absalon for final course material. The following is an example of expected course literature.

 

‘Mechanics of the Cell’ by David Boal plus primary literature in the form of scientific papers that will be provided during the course.

The student is expected to have folowed courses equivalent to a bachelor degree in biophysics, bio-medical physics, physics or nanoscience
Lectures, theoretical exercises, student presentations of primary literature, a project.
Credit
7,5 ECTS
Type of assessment
Oral examination, 20-30 minutes
The mandatory project will be in the middle of the course period and will be based on answering questions in connection to scientific papers. The oral exam will take place in the exam week after the course period; the students will beforehand receive the questions for the oral exam and there will be no preparation time at the exam.
Exam registration requirements

Each student must have presented one scientific paper during the course and must have completed the mandatory project in order to register for the oral exam.

Aid
Without aids

no aids allowed for the oral exam

Marking scale
7-point grading scale
Censorship form
No external censorship
Internal examiners (normally two internal co-examiners)
Re-exam

Same as the regular exam. It will be possible to re-submit presentation and project before the re-exam; please contact the course responsible.

Criteria for exam assesment

see learning outcome

  • Category
  • Hours
  • Lectures
  • 30
  • Theory exercises
  • 20
  • Project work
  • 30
  • Colloquia
  • 20
  • Preparation
  • 105
  • Exam
  • 1
  • Total
  • 206