FYS-7306 Molecular modeling of bio- and nanosystems, 5 cr
Ilpo Vattulainen, Sami Paavilainen, Tomasz Rog
|Lecture times and places||Target group recommended to|
Luonnontieteiden ja ympäristötekniikan tiedekunta
Passing the exam; assignments; carrying out a molecular modeling research project whose topic will be chosen during the course.
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||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.|
Ability to perceive and apply the material needed in computational modeling of complex systems.
Numerical evaluation scale (1-5) will be used on the course
|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|
|FYS-1370 Statistinen fysiikka||Advisable|
|FYS-1610 Kvanttimekaniikka I||Advisable|
|FYS-4100 Laskennallinen fysiikka I||Advisable|
|FYS-4200 Laskennallinen fysiikka II||Advisable|
|FYS-6300 Molekyylien ja nanorakenteiden kvanttiteoria||Advisable|
|FYS-7100 Johdatus pehmeän aineen fysiikkaan||Advisable|
|FYS-7200 Biologinen fysiikka||Advisable|
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.
There is no equivalence with any other courses
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/
|Description||Methods of instruction||Implementation|
|Implementation 1|| Lectures
Contact teaching: 0 %
Distance learning: 0 %
Self-directed learning: 0 %