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
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; 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 Atýlgan – office: 2058;
phone: 9523; e-mail: canan@sabanciuniv.edu
Assistant: TBA
– office: TBA; phone: TBA; e-mail: ???@sabanciuniv.edu
Hours:
Lecture - Mon 12:40 – 14:30 (2019), Tue 16:40 – 17:30 (L056); Discussion – Tue
18:40 – 19:30; Office – see schedule on my door
Textbook: Hinchliffe, Molecular Modelling
for Beginners 2nd ed. Wiley (2008). ISBN: 978-0-470-51314-9
Supplementary
Textbooks: Frenkel & Smit, Understanding
Molecular Simulation 2nd ed. Academic Press (2002). ISBN:
0-12-267351-4
Leach,
Molecular Modelling 2nd ed. Prentice Hall
(2001). ISBN: 0-582-38210-6
Course Organization: Structured
instruction with accompanying assignments.
Evaluation
will be based two midterms (20 % each), seven assignments (50 %) and
participation (10 %).
COURSE OUTLINE:
Week 1: The problem of time and
length scales; coordinate systems; potential energy surfaces; molecular
graphics. Degrees of freedom of a system. DS Visualizer tutorial
Aim:
Introduce tools operative at various time and length scales
Week 2: Tutorial on MatLab and other tools to be used in the Course (to be
moderated by Deniz Turgut).
HW1:
Molecule visualization practice
Week 3: Introduction to all-atom
methods; force fields for organic, inorganic, and
solid-state systems; reactive force fields; force field parameterization. HW2:
Calculation of internal coordinates
Aim:
How to choose a force field suitable for a particular system of interest.
Week 4-5: Energy minimization;
non-derivative, first- and second-derivative methods. HW 3: Coding interactions
Aim:
How and when to choose a minimization algorithm suitable for a particular
purpose. Introduce a method for the direct comparison of experiment and
simulation.
Week 5-6: Normal mode analysis.
Introduction to conformational searching; systematic and random search methods.
Derivation of the Boltzmann distribution. HW4: Conformational search
Aim:
Study of the conformations of a molecule and their influence on its properties.
Week 7: Systematic and random search methods. Review for the
midterm exam. HW5: Conformational search and NMA
Aim: Study of the conformations of a molecule and
their influence on its properties.
Week 8: Midterm I (Apr.
5) Derivation of the Boltzmann distribution.
Aim: Implement the idea of a trajectory and pave the
way for the calculation of simple thermodynamic properties.
Week 9: Monte Carlo simulations;
importance sampling. On- and off-lattice Monte Carlo,
applications to polymers and dense systems. HW6: Random number generation
Aim:
Introduce the concept of ergodicity, and sampling
from different ensembles.
____________________________________________________Spring
break HW7: Monte Carlo
Week 10: General comments on
“trajectory” methods; cut-offs on non-bonded energy terms; periodic boundary
conditions; some tricks for an efficient simulation. Introduction
to molecular dynamics simulations.
Aim:
Understand the capabilities and the limitations of a dynamic simulation method
based on first principles.
Weeks 11: Principles of molecular
dynamics simulations. HW8: Molecular Dynamics
Aim: To
establish concepts of equipartition, energy
conservation.
Week 12: MD continued & BD.
Prediction of system properties from simulations: Thermodynamic properties.
Aim:
Bridge theory and experiments that are based on the dynamics of molecules.
Week 13: Prediction of system
properties from simulations: Radial distribution functions, correlation
functions, diffusion coefficient.
Aim:
Bridge theory and experiments that are based on the dynamics of molecules.
Week 14: Midterm
II (May. 24) Introduction to coarse-graining; methods used on the mesoscale; dissipative particle dynamics. HW9: Dissipative Particle Dynamics
Aim:
Introduce relatively new methods operative on the mesoscale;
provide a link between microscopic scales and mesoscopic/macroscopic
phenomena. Show how a simplistic elastic model can reproduce equilibrium
properties of chain systems.
SOFTWARE:
o
Various
molecular visualization software (e.g. DS Visualizer:
http://accelrys.com/products/discovery-studio/visualization/index.html ; VMD: http://www.ks.uiuc.edu/Research/vmd/ )
o
NAMD (Molecular
Dynamics software: http://www.ks.uiuc.edu/Research/namd/ )
o
ESPResSo (Molecular
Dynamics software: www.espresso.mpg.de )
o
Some
programming of your own (nothing fancy – just basic programming to analyze data
you produce from the package programs above)