C9925 Introduction to soft matter models of membranes and proteins

Faculty of Science
Spring 2024
Extent and Intensity
2/0. 2 credit(s) (plus 1 credit for an exam). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Robert Vácha, PhD. (lecturer)
Sushmita Pal (assistant)
Guaranteed by
prof. RNDr. Robert Vácha, PhD.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Robert Vácha, PhD.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 19. 2. to Sun 26. 5. Mon 15:00–16:50 C04/211
Prerequisites
Calculus and physical chemistry at basic university level
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 34 fields of study the course is directly associated with, display
Course objectives
The course is focused on basics of coarse-grained models and their development. It also includes classification of models, their basic thermodynamics’ considerations, and commonly used Monte Carlo methods in their simulations.
The main objective of the course is to provide the students with:
- ability to classify and develop basic coarse-grained models
- describe and explain fundamental interactions in biomolecules
- introduction of soft matter
Learning outcomes
Student will be able to:
- analyze existing coarse grained models or develop a basic new ones
- identify a method and level of coarse graining in existing soft matter models
- calculate protein-protein, protein-membrane, and membrane-membrane interaction strengths and their distance dependence
- understand methods and phenomena in soft matter
Syllabus
  • 1) Introduction to coarse grained models
  • 2) Ideal chain approximation
  • 3) Ideal thin membrane
  • 4) Interaction of uncharged membrane and proteins
  • 5) Interaction of charged membrane and proteins I
  • 6) Interaction of charged membrane and proteins II
  • 7) Thermodynamic principles of self assembly
  • 8) Langmuir adsorption and grand canonical ensemble
  • 9) Dynamics and transport
  • 10) Advanced Monte Carlo
Literature
  • Intermolecular and Surface Forces 3rd edition by Jacob N. Israelachvili; Academic Press 2010
  • Giant Molecules: Here, There, and Everywhere 2nd edition by Alexander Y. Grosberg et al.; World Scientific Press 2010
  • Soft Condensed Matter Physics in Molecular and Cell Biology by W.C.K. Poon and D. Andelman; Taylor & Francis 2006
Teaching methods
Study of the provided literature, presentation and discussion at the classes
Assessment methods
One multiple choice test - about 20 questions with multiple correct answer possibility. Correct answer is +1 point, wrong answer is -1/2 point. Minimum to pass is 50% of available points.
Language of instruction
English
Further Comments
Study Materials
The course is taught once in two years.
The course is also listed under the following terms Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2020, Spring 2022, Spring 2023.
  • Enrolment Statistics (recent)
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