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Course module: 8CM20
8CM20
Molecular modeling
Course info
Course module8CM20
Credits (ECTS)5
Category-
Course typeGraduate School
Language of instructionEnglish
Offered byEindhoven University of Technology; Biomedical Engineering; Computational Biology;
Is part of-
Contact persondr.ir. A.J. Markvoort
Telephone2661
E-maila.j.markvoort@tue.nl
Lecturer(s)
Co-lecturer
prof.dr. P.A.J. Hilbers
Other course modules lecturer
Responsible lecturer
dr.ir. A.J. Markvoort
Feedback and reachability
Other course modules lecturer
Contactperson for the course
dr.ir. A.J. Markvoort
Other course modules lecturer
Academic year2017
Period
GS4  (23/04/2018 to 08/07/2018)
Starting block
GS4
TimeslotA: A - Mo 1-4, We 9-10, Th 5-8
Course mode
Fulltime
Remarks-
Registration openfrom 15/11/2017 up to and including 25/03/2018
Application procedureYou apply via OSIRIS Student
Explanation-
Registration using OSIRISYes
Registration open for students from other department(s)Yes
Pre-registrationNo
Waiting listNo
Number of insufficient tests-
Number of groups of preference0
Learning objectives
  • Understanding knowledge of possibilities and impossibilities of various molecular simulation techniques
  • Understanding knowledge of the functioning of and theory behind the various molecular simulation techniques
  • Practical application of various molecular simulation techniques for studying relevant molecular systems

  • Content
    Next to theory and experiment, computer simulations are widely used in physical sciences to study diverse physical, chemical and biological problems. Such simulations are not only useful to study processes at time and length scales difficult to reach experimentally, like often the case in cellular processes, but can also be applied as a cheap alternative to time consuming experiments. Molecular simulation methods that we will treat, like (ab initio / atomistic / coarse grained) molecular dynamics, Monte Carlo, DPD and Brownian dynamics, are nice examples that can serve a wide range of applications, They are not only applied to investigate the shape or properties of chemical structures and their interactions in various physical and chemical processes, but can also be applied in the field of nano-technology. Also, we will consider computational modelling and analysis as they are increasingly often applied within computation biology for instance for de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. In this course, apart from the physical, chemical and numerical basis of these molecular simulation methods, the focus is on a number of practical applications
    Entrance requirements
    You must have completed the final examination bsc program exam
    Entrance requirements tests
    -
    Assumed previous knowledge
    • 8CB10 - Simulation of biochemical systems
    Previous knowledge can be gained by
    -
    Resources for self study
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    Short promotional description of the course
    Moleculaire simulaties en moleculaire modellering spelen een steeds prominentere rol in het begrijpen van, en (her)ontwerpen van, moleculaire structuren en de interacties tussen verschillende moleculen, zowel voor synthetische als biologische (macro)moleculen. In dit college wordt ingegaan op de achtergrond van verschillende simulatie- en modelleertechnieken en worden (door middel van opdrachten) verscheidene van die technieken toegepast voor het bestuderen van relevante moleculaire systemen.
    Short promotional description of the course
    Molecular simulations and molecular modelling play an increasingly prominent role in the understanding, and (re)designing, of molecular structures as well as interactions between molecules, both for synthetic and biological (macro) molecules. In this course the background of various simulation and modeling techniques will be discussed and several of those techniques will be applied (in the assignments) for studying relevant molecular systems.
    Required materials
    -
    Recommended materials
    Will be during lecture delivered.
    Instructional modes
    Guided selfstudy

    General
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    Remark
    -
    Lecture

    General
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    Remark
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    Tests
    Oral examination
    Test weight0
    Minimum grade6
    Test typeInterim examination
    Number of opportunities1
    OpportunitiesBlock GS4
    Test duration in minutes-

    Assessment
    -

    Remark
    -

    Assignment
    Test weight100
    Minimum grade6
    Test typeInterim examination
    Number of opportunities1
    OpportunitiesBlock GS4
    Test duration in minutes-

    Assessment
    -

    Remark
    -

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