Computational Techniques for Materials at the Nano-scale (MAT 306)

2021 Spring
Faculty of Engineering and Natural Sciences
Materials Sci.& Nano Eng.(MAT)
6.00 / 6.00 ECTS (for students admitted in the 2013-14 Academic Year or following years)
Ali Rana At─▒lgan,
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Formal lecture,Interactive lecture,Group tutorial,Laboratory
Interactive,Learner centered,Communicative,Discussion based learning,Task based learning,Simulation
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Modeling techniques operative at the atomistic and mesoscopic time and length scales. All-atom methods; force fields. Conformational searching. Statistical mechanics concepts relevant for molecular simulations. Normal mode analysis in one- and two- dimensions and its relation to spectroscopy. Setting-up molecular dynamics simulations and basic analyses of the trajectories. Introduction to particle-based mesoscopic simulations. Self-organization at the molecular scale.


To introduce various modeling techniques operative at a broad range of time and length scales relevant to the understanding of the structure-property relationships of "materials" where a material is defined in the broad sense of anything that is utilized for a particular human defined purpose; to introduce a conceptual framework for the understanding of macroscopic observations of materials from a microscopic viewpoint.


Interpret the problem of time and length scales in molecular modeling by relating the type of the problem to the available modeling technique.
Sketch simple potential energy surfaces for systems of up to four particles and identify the global energy minimum and local energy minima on it.
Calculate the energy of conformations of simple molecules of up to six particles, given the parameters of a force field describing the molecule.
Relate the influence of conformations of a molecule on its properties by calculating the average properties of a given system based-on the Boltzmann distribution.
Perform conformational searching on systems of up to 10 particles by applying systematic and random search methods.
Perform normal mode analysis on systems of up to 10 particles in one and two-dimensions and relate the output to vibrational spectroscopy experiments.
Set-up and run molecular dynamics simulations on complex systems such as polymers and proteins.
Make physics-based descriptions of the main ingredients of a simulation such as the Verlet algorithm, periodic boundary conditions, selection of time step.
Calculate thermodynamic (e.g. temperature, pressure, heat capacity), and kinetic properties (diffusion constant, various relaxation times) from simulated trajectories.


  Percentage (%)
Exam 50
Assignment 50



A. R. Leach, Molecular Modelling 2nd ed. Prentice Hall (2001). ISBN: 0-582-38210-6