Course Catalog 2007-2008

FYS-7306 MOLECULAR MODELING OF BIO- AND NANOSYSTEMS, 5-8 cr
Molecular modeling of bio- and nanosystems

Courses persons responsible
Ilpo Vattulainen

Lecturers
Sami Paavilainen
Tapio Rantala
Ilpo Vattulainen
Emppu Salonen

Language of Instruction
The course will be lectured in English.

Lecturetimes and places
Per I,II: Monday 14 - 17, TC133
Per I,II: Thursday 14 - 16, TB224

Objectives
The main objective of the course is to provide the students with an overall view of how to apply computational techniques to relevant many-body problems in the nano-regime and biological systems. For the same reason, the lectures will be complemented by a significant fraction of hands-on exercises where the techniques are applied to practical problems.

Content
Content Core content Complementary knowledge Specialist knowledge
1. Principles of electronic structure calculations: density-functional theory and alternatives. Connection to classical modeling techniques. General aspects of numerical solutions to the electronic Schrödinger equation.

Practical approaches to electronic structure calculations of finite, periodic and complex structures: basis sets, pseudopotentials and PAWs. Software and applications.
 		      
2. Understanding of classical modeling techniques for dealing with larger scales in nano- and biological systems: force fields, integrators, long-range interactions, ensembles, constraints. Software packages and development of own simulation codes with a variety of applications.       
3. More coarse-grained techniques to probe scales beyond the atomistic regime.       
4. Practical hands-on exercises and project assignments where the above techniques are applied in practice to relevant and topical problems related to nanostructures, biological molecules, etc.       

Requirements for completing the course
Passing the exam; assignments; carrying out a molecular modeling research project whose topic will be chosen during the course.

Evaluation criteria for the course

  • Ability to perceive and apply the material needed in computational modeling of complex systems.

  • Used assessment scale is numeric (1-5)

    • Study material
    Type Name Auhor ISBN URL Edition, availability... Exam material Language
    Book Electronic Structure Calculations for Solids and Molecules Jorge Kohanoff     Cambridge, 2006 Yes  English 
    Book Molecular Modeling and Simulation - An Interdisciplinary Guide Tamar Schlick     Springer, 2002 Yes  English 

    Prerequisites
    Code Course Credits M/R
    FYS-1370 FYS-1370 Statistical Physics 3 Recommendable
    FYS-1610 FYS-1610 Quantum Mechanics I 5 Recommendable
    FYS-4100 FYS-4100 Computational Physics I 5 Recommendable
    FYS-4200 FYS-4200 Computational Physics II 5 Recommendable
    FYS-6300 FYS-6300 Quantum Theory of Molecules and Nanostructures 6 Recommendable
    FYS-7100 FYS-7100 Introduction to Soft Matter Physics 5 Recommendable
    FYS-7200 FYS-7200 Biological Physics 5 Recommendable

    Prequisite relations (Sign up to TUT Intranet required)

    Additional information about prerequisites
    The above list should not be taken literally. Though, overall, some sort of background is recommendable to maximize learning and the impact of the course. Having passed most of the above proposed courses is not really a condition for participating in the course, however.

    Remarks

    The above two books will be covered only in part. Additional study material will include the lectures notes, and possibly sections from Andrew R. Leach: Molecular Modelling: Principles and Applications, 2nd Edition (Prentice Hall, 2001). All material will be available for becoming acquainted with it.

  • The course is suitable for postgraduate studies.

    • Distance learning

  • ITC utilized during the course

    • - In information distribution via homepage, newsgroups or mailing lists, e.g. current issues, timetables
    - In compiling teaching material, particularly for online use or other electronic media
    - In compiling exercise, group or laboratory work
    - In the visualization of objects and phenomena, e.g. animations, demonstrations, simulations, video clips

  • Estimate as a percentage of the implementation of the course

    • - Contact teaching: 40 %
    - Distance learning: 20 %
    - Proportion of a student's independent study: 40 %

  • Description of the course implementation from ICT point of view

    • Lectures, exercises, project work.

    Scaling
    Methods of instructionHours
    Lectures 36
    Exercises 96
    Assignments 80
    Seminar reports 10
    Total sum 222

    Principles and starting points related to the instruction and learning of the course

  • The lectures will be complemented by exercises where practical simulation problems are considered as case studies. Some understanding and experience of programming is hence desirable. The course also includes a recommended final project, where some well-defined molecular system is studied in detail through one of the simulation techniques discussed during the course.

    • Additional information related to course
    The number of credit units (to be granted) depends on the scope and difficulty of the project work assignments. The largest number of credits (8) will be granted to those who have successfully conducted a rather major project study.

    Further information supporting the course is available at: http://www.tut.fi/~trantala/opetus/

    Correspondence of content
    FYS-7300 FYS-7300

    Course homepage

    Last modified 26.02.2007
    Modified byIlpo Vattulainen