Course Catalog 2013-2014
Postgraduate

Basic Pori International Postgraduate Open University

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Course Catalog 2013-2014

FYS-7306 Molecular Modeling of Bio- and Nanosystems, 5-8 cr

Additional information

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://butler.cc.tut.fi/~vattula2/ The course is not lectured until further notice.
Suitable for postgraduate studies
Will not be lectured year 2013-2014

Person responsible

Ilpo Vattulainen, Oana Cramariuc, Sami Paavilainen, Tomasz Rog

Requirements

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

Principles and baselines related to teaching and learning

-

Learning Outcomes

The main learning outcome is obtaining an overall view of how to apply computational techniques to relevant many-body problems in the nano-regime and biological systems. After passing the course the student is able to use available software to calculate the electronic structure of a specified system, and to perform classical molecular dynamics simulations, with a focus on nano- and biomolecular systems. The student also knows how to interpret and verify the results.

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.     

Instructions for students on how to achieve the learning outcomes

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

Assessment scale:

Numerical evaluation scale (1-5) will be used on the course

Study material

Type Name Author ISBN URL Edition, availability, ... Examination material Language
Book   Electronic Structure Calculations for Solids and Molecules   Jorge Kohanoff       Cambridge, 2006   Yes    English  
Book   Molecular Modeling - Principles and Applications   Andrew R. Leach       Alternative to Schlick   No    English  
Book   Molecular Modeling and Simulation - An Interdisciplinary Guide   Tamar Schlick       Springer, 2002   Yes    English  

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Correspondence of content

Course Corresponds course  Description 
FYS-7306 Molecular Modeling of Bio- and Nanosystems, 5-8 cr FYS-7306 Molecular Modeling of Bio- and Nanosystems, 5-8 cr  

Last modified31.12.2013