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Course Catalog 2010-2011
FYS-7306 Molecular modeling of bio- and nanosystems, 5-8 cr |
Person responsible
Ilpo Vattulainen, Sami Paavilainen, Tomasz Rog
Lessons
| Study type | P1 | P2 | P3 | P4 | Summer | Implementations | Lecture times and places |
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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
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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. |
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 - Principles and Applications | Andrew R. Leach | Alternative to Schlick | English | |||
| Book | Molecular Modeling and Simulation - An Interdisciplinary Guide | Tamar Schlick | Springer, 2002 | English |
Prerequisite relations (Requires logging in to POP)
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 enough 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/
Suitable for postgraduate studies
More precise information per implementation
| Implementation | Description | Methods of instruction | Implementation |
| Lectures Excercises Practical works |
Contact teaching: 0 % Distance learning: 0 % Self-directed learning: 0 % |