Syllabus Application
MAT 306
Computational Techniques for Materials at the Nano-scale
Faculty
Faculty of Engineering and Natural Sciences
Semester
Spring 2025-2026
Course
MAT 306 -
Computational Techniques for Materials at the Nano-scale
Time/Place
Time
Week Day
Place
Date
08:40-10:30
Tue
FASS-1076
Feb 16-May 22, 2026
08:40-09:30
Thu
FENS-G059
Feb 16-May 22, 2026
Level of course
Undergraduate
Course Credits
SU Credit:3, ECTS:6, Basic:2, Engineering:4
Prerequisites
-
Corequisites
Course Type
Lecture
Instructor(s) Information
Canan Atılgan
- Email: canan@sabanciuniv.edu
Course Information
Catalog Course Description
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.
Course Learning Outcomes:
| 1. | Interpret the problem of time and length scales in molecular modeling by relating the type of the problem to the available modeling technique. |
|---|---|
| 2. | Sketch simplified potential energy surfaces of molecular systems, identify their functionally relevant conformations and calculate the energies, given the parameters of a force field describing the molecules. |
| 3. | Apply simple statistical models from machine learning to identify conformational states of molecules. |
| 4. | Apply probability and statistics concepts to derive the Boltzmann and Maxwell distributions. |
| 5. | 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. |
| 6. | Perform normal mode analysis on nanoparticles and relate the output to vibrational spectroscopy experiments and the function of the nanomaterial. |
| 7. | Set-up and run molecular dynamics simulations on complex systems such as polymers and proteins. |
| 8. | Make physics-based descriptions of the main ingredients of a simulation such as the Verlet algorithm, periodic boundary conditions, selection of time step. |
| 9. | Calculate thermodynamic (e.g. temperature, pressure, heat capacity), and kinetic properties (diffusion constant, various relaxation times) from simulated trajectories. |
Course Objective
To introduce various modeling techniques operative at the atomistic and mesoscopic 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; to include modeling and simulation on equal footing with experiments in attacking problems; to provide the background for choosing the appropriate technique suited to the system at hand.
Sustainable Development Goals (SDGs) Related to This Course:
| Affordable and Clean Energy |
Course Materials
Resources:
Supplementary Textbooks: Leach, Molecular Modelling 2nd ed. Prentice Hall (2001). ISBN: 0-582-38210-6
Hinchliffe, Molecular Modeling for Beginners 2nded. Wiley (2008). ISBN: 978-0-470-51314-9
Frenkel & Smit, Understanding Molecular Simulation 2nd ed. Academic Press (2002). ISBN: 0-12-267351-4
Hinchliffe, Molecular Modeling for Beginners 2nded. Wiley (2008). ISBN: 978-0-470-51314-9
Frenkel & Smit, Understanding Molecular Simulation 2nd ed. Academic Press (2002). ISBN: 0-12-267351-4
Technology Requirements:
laptops to be brought to all classes