Syllabus for Molecular and Statistical Mechanics

Molekylär och statistisk mekanik

A revised version of the syllabus is available.

Syllabus

  • 5 credits
  • Course code: 1MB412
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Chemistry A1N, Biology A1N, Technology A1N

    Explanation of codes

    The code indicates the education cycle and in-depth level of the course in relation to other courses within the same main field of study according to the requirements for general degrees:

    First cycle
    G1N: has only upper-secondary level entry requirements
    G1F: has less than 60 credits in first-cycle course/s as entry requirements
    G1E: contains specially designed degree project for Higher Education Diploma
    G2F: has at least 60 credits in first-cycle course/s as entry requirements
    G2E: has at least 60 credits in first-cycle course/s as entry requirements, contains degree project for Bachelor of Arts/Bachelor of Science
    GXX: in-depth level of the course cannot be classified.

    Second cycle
    A1N: has only first-cycle course/s as entry requirements
    A1F: has second-cycle course/s as entry requirements
    A1E: contains degree project for Master of Arts/Master of Science (60 credits)
    A2E: contains degree project for Master of Arts/Master of Science (120 credits)
    AXX: in-depth level of the course cannot be classified.

  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2010-03-16
  • Established by: The Faculty Board of Science and Technology
  • Revised: 2017-10-31
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 30, 2018
  • Entry requirements:
  • Responsible department: Biology Education Centre

Learning outcomes

The course covers statistical mechanical theory and its applications to molecular systems as well as modern computer simulation methods for studying the dynamics and energetics of macromolecules. After completing the course the student should be able to

  • explain the foundations and concepts of statistical mechanics such as canonical distributions, ensembles and partition functions, as well as the statistical mechanical description of ideal and non-ideal gases and simple liquids
  • account for the molecular mechanical description for interacting systems , including the theoretical basis behind force fields, intramolecular and intermolecular interactions 
  • connect the theoretical basis with its implementation in computational methods such as molecular dynamics simulations, energy optimisation, Monte Carlo and free energy calculations based on thermodynamics cycles
  • use computer modelling methods (outlined above) for analysing biomolecular structure, function and dynamics.

Content

The course gives an introduction to statistical mechanical theory, and connects it with the foundation of computer simulations of biomolecular dynamics and energetics, methods which are then covered extensively from a theoretical and practical perspective. Tthe following elements are covered in this course:

Maxwell-Boltzmann distributions, ensembles, molecular and canonical partition functions, kinetic theory of gases, transition state theory, configurational distributions, non-ideal gases, simple liquids, analytical force fields for interacting systems, energy optimisation, Monte Carlo methods, molecular dynamics simulation and algorithms, thermodynamics cycles and free energy calculations, methodology and applications in computer-aided drug design.

Instruction

The schedule comprises lectures, classroom exercises och computer practicals.

Assessment

Written exam (4 credits) at the end of the course and passed written reports from computer practicals (1 credit). Credits are only awarded for the completely passed course.

Reading list

Reading list

Applies from: week 30, 2018

  • Atkins, P. W. Physical chemistry

    6. ed.: New York: Freeman, cop. 1998

    Find in the library

  • Grant, Guy H.; Richards, W. Graham Computational chemistry

    Oxford: Oxford Univ. Press, 1995

    Find in the library