Course Catalog 2009-2010 International Basic Pori International Postgraduate Open University |Degrees|     |Study blocks|     |Courses|

Person responsible

Ilpo Vattulainen, Sami Paavilainen, Tomasz Rog

Implementations

	Lecture times and places	Target group recommended to
Implementation 1	Per 1, 2 : Monday 15 - 17, SG209 Tuesday 15 - 18, SG209

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 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.

Evaluation criteria for the course

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		English
Book	Molecular Modeling and Simulation - An Interdisciplinary Guide	Tamar Schlick			Springer, 2002		English

Prerequisites

Additional information about prerequisites
The above list of recommended courses prior to this one 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.

Correspondence of content

There is no equivalence with any other courses

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. The course will be lectured provided that at least 6-8 students will participate in the course (which is very likely). Further information supporting the course is available at: http://alpha.cc.tut.fi/~vattula2/teaching-biomodeling/

More precise information per implementation

	Description	Methods of instruction	Implementation
Implementation 1		Lectures Seminar work Excercises Practical works	Contact teaching: 0 % Distance learning: 0 % Self-directed learning: 0 %

Last modified	11.01.2010
Modifier	Sami Paavilainen