Intended Audience: A junior/senior level course for MAT and BIO majors, PHYS minors, or anyone interested in understanding the microscopic basis of physically observed phenomena using modeling and simulation.

Aims: To introduce various modeling techniques operative at the atomistic and meso- 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.

Instructor: Canan Atılgan – office: 2058; phone: 9523; e-mail: canan@sabanciuniv.edu

Assistant: Gökçe Güven – office: 2102; phone: 2111; e-mail: gokceguven@sabanciuniv.edu

Hours: theory session – Wed 8:40 – 10:30 (L027); hands-on session – Wed 12:40 – 13:30 (G032)

Textbooks: Hinchliffe, Molecular Modelling for Beginners 2^nd ed. Wiley (2008). ISBN: 978-0-470-51314-9

Frenkel & Smit, Understanding Molecular Simulation 2^nd ed. Academic Press (2002). ISBN: 0-12-267351-4

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

Course Organization:, hands-on sessions (1 hr/wk), structured instruction (2 hrs/wk), off-class assignments

Evaluation will be based two midterms (20 % each), assignments (50 %) and participation (10 %).

COURSE OUTLINE:

Week 1: The problem of time and length scales in molecular modeling; coordinate systems; potential energy surfaces; molecular graphics.

Hands-on session: Tutorial for molecular graphics programs

Aim: Introduce computational tools operative at various time and length scales

Week 2: Introduction to all-atom methods; force fields and their parameterization.

Hands-on session: Defining NAMD coordinate and potential files

HW1: Molecule visualization

Aim: Learn how to choose a force field suitable for a particular system of interest.

Week 3: Calculation of forces from energies for simple potential functions.

Hands-on session: Running sample MD programs in NAMD and seeing the results of bad initial structures

Aim: First experience on the capabilities of molecular simulation.

Week 4: Energy minimization; non-derivative, first- and second-derivative methods. Degrees of freedom of a system.

Hands-on session: Calculating internal coordinates using a molecular graphics programs

Aim: How and when to choose a minimization algorithm suitable for a particular purpose.

Week 5: The Boltzmann distribution.

Hands-on session: Calculating the averages and distributions of internal coordinates

HW2: Random number generation

Aim: See why the Boltzmann distribution is central to molecular simulations.

Week 6: Introduction to conformational searching. Systematic and random search methods.

Hands-on session: Distorting structures leads to new conformations!

HW3: Conformational search

Aim: Identify the different conformations of a molecule.

Week 7: Normal mode analysis and its relation to spectroscopy.

Hands-on session: NMA using 1-D and 2-D molecules.

HW4: NMA on a simple 4-atom 2-D molecule

Aim: Study the influence of conformations of a molecule on its properties. Introduce a method for the direct comparison of experiment and simulation.

____________________________________________________Spring break

Week 8: Review for Midterm I and Midterm I (Apr. 11)

Week 9: Monte Carlo simulations; importance sampling. Ergodicity.

Hands-on session: Setting up a two dimensional simulation box for MC simulations.

HW5: Monte Carlo Simulations of the Ising Model

Aim: Implement the idea of a trajectory and pave the way for the calculation of simple thermodynamic properties.

Week 10: General comments on “trajectory” methods; periodic boundary conditions; some tricks for an efficient simulation.

Hands-on session: Setting up a two dimensional simulation box for MC simulations - continued.

Aim: Understand the capabilities and the limitations of a dynamic simulation method based on first principles.

Week 11: Molecular dynamics simulations: Setting up.

Hands-on session: Setting up an MD simulation.

HW6: Molecular Dynamics – simulating miscibility of two liquids

Aim: Establish the fundamentals of a molecular simulation.

Week 12: Molecular dynamics simulations: Prediction – Thermodynamic properties, radial distribution functions (RDFs).

Hands-on session: Analyzing an MD trajectory.

HW7: Molecular Dynamics – analyzing the simulations (diffusion coefficients, RDFs, heat capacity)

Aim: Bridge theory and experiments based on the dynamic simulations.

Week 13: Coarse graining: Dissipative Particle Dynamics (DPD).

Hands-on session: Setting up and analyzing a DPD simulation.

HW8: Dissipative Particle Dynamics for a surfactant system

Aim: Assess limitations and benefits of simulating larger systems.

Week 14: Review for Midterm II and Midterm II (May 23)

SOFTWARE:

o Various molecular visualization software (e.g. Accelrys DS Visualizer, VMD: http://www.ks.uiuc.edu/Research/vmd/)

o Molecular Dynamics software (NAMD: http://www.ks.uiuc.edu/Research/namd/; Materials Studio)

o Some programming of your own (nothing fancy – just basic programming to analyze data you produce from the package programs above)