NFYK15006U  Biophysics of Cells and Single Molecules

Volume 2018/2019
Education

MSc Programme in Nanoscience

MSc Programme in Physics

MSc Programme in Physics w. minor subject

Content

The course focuses on bio-mechanics and functions of biological systems on the nano- and micron-scale. We will explore the bio-mechanics of living cells and understand how force influences cellular decisions and life. There will be quantitative descriptions of biological polymers and of how these are part of intelligent tensegrity structures with parallels to human architecture.  Cellular dynamics and movement is often mediated by amazing single molecule motors and bio-polymerization, which is a process also relevant for development of wide-spread diseases as, e.g., Alzheimer's and Parkinson's diseases. The course also presents novel remarkable force-scope and microscopy techniques that allows for studying fundamental actions of the molecular building blocks of life. Emphasis is on how single molecule results complement, and in certain cases contradict, results obtained at the ensemble level. To correctly understand life at the the nano- or micro-scale, the course invokes and describes relevant recent non-equilibrium theories. The course deals with the most recent research results and is partly based on scientific papers. Hence, an important aspect of the course is a critical assessment of primary literature.

Learning Outcome

Knowledge:
The course participants will gain 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 and cellular biophysics research, going through the most important and remarkable results achieved also, for instance in the biomechanics of stem cells. Emphasis will be on how, in practice, to treat non-equilibrium nano-scale systems. In addition, the course participants will gain experience in reading, understanding and criticizing primary literature and will be trained in presenting and questioning research results.

 

Skills:
The course will enable the participant to

  • obtain knowledge about the physics of polymers. Be able to quantify the typical physical size, flexibility and elasticity of polymers. Utilize this knowledge on to understand the biomechancis of living cells and organisms.
  • understand the energetics of membrane bending, hereunder to predict the shape of self-assembled membrane structures. This knowledge is useful for understanding shape and function of cellular components and whole cells.  
  • understand how living organisms generate force and motion and how they respond to mechanical cues. This includes a physics based understanding of biopolymers and polymerization dynamics, an understanding of the action of molecular motors, and a thorough understanding of cellular micro-rheology.
  • gain knowledge about the most common single molecule techniques, 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 be able to apply non-equilibrium theories including Jarzynski's 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 understanding of complex biological systems. The course participants will understand how important force and mechanical properties are for development and life at all scales. The course participants will also gain competences in understanding the working method, capabilities, and limitations of single molecule techniques and they will be able to utilize non-equilibrium statistical physics for analyzing 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’ 2nd edition by David Boal. In addition, there will be primary literature in the form of scientific papers which will be provided during the course.

The participant is expected to have followed courses equivalent to a bachelor degree in biophysics, bio-medical physics, physics or nano-science. However, in the past also students with, e.g., a biochemical, chemical or biological background have successfully completed the course.
Lectures, theoretical exercises, student presentations of primary literature, a project.
Individual
Continuous feedback during the course of the semester
Credit
7,5 ECTS
Type of assessment
Oral examination, 20-30 minutes
Continuous assessment
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 the presentation and the mandatory 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