Undergraduate Course: Molecular Dynamics (MATH10084)
Course Outline
School  School of Mathematics 
College  College of Science and Engineering 
Credit level (Normal year taken)  SCQF Level 10 (Year 4 Undergraduate) 
Availability  Available to all students 
SCQF Credits  10 
ECTS Credits  5 
Summary  Molecular dynamics is an area of high current interest throughout science and engineering, being used to simulate diverse applications (HIV drugs, DNA helices, liquid crystals, polymers, and carbon nanotubules, to name a few). The topic concerns the treatment of Hamiltonian mechanical systems, with or without constraints, and either in isolation or in contact with a stochastic thermal bath.
The course will start with Newton¿s equations for a system of interacting particles. Different potential energy functions are used to model the effects of shortranged repulsion, dispersion, Coulombic attraction, and bonding. These will be surveyed. The generic properties of molecular Nbody systems will then be considered from the perspective of dynamical systems, including equilibrium states, normal modes, variational equations, and Lyapunov exponents.
Geometric integrators based on the symplectic property of Hamiltonian flows will be constructed using splitting and these will be analyzed using the Lie series technique (BakerCampbellHausdorff expansion), providing justification for the long term stability of the methods and their approximate conservation of energy. These ideas will be extended to systems with holonomic constraints.
The last part of the course will examine the stochastic differential equations used to model heat baths in molecular modeling. The equations of motion will be discussed in terms of their diffusion properties beginning with an elementary derivation of random walks, Brownian dynamics, and FokkerPlanck equations. The focus here will be on the design and implementation of numerical methods without a detailed analysis of their properties.
The course will include a numerical project using MATLAB code to simulate a small molecular system. 
Course description 
1. Overview of molecular potentials: (bonds, van der Waals interactions, Coulomb potentials, and certain coarse grained models)
2. Overview of basic concepts in classical mechanics/ODEs: Lagrangian and Hamiltonian systems, first integrals, equilibrium, linearization, stability, variational equations
3. Numerical methods: convergence, concepts of accuracy, volume preserving methods, symplectic integrators. Error expansion using Lie derivative.
4. Microcanonical ensemble: Liouville's equation, evolution of phase space density, mixing property.
5. Canonical ensemble: Gibbs distribution, temperature, Brownian motion, SDEs, Ito Formula, Langevin dynamics. Numerical methods for canonical sampling. Invariant measure error. Examples of Langevin splitting methods.

Information for Visiting Students
Prerequisites  None 
Course Delivery Information
Not being delivered 
Learning Outcomes
Students will be able to
(1) describe the features of the most common potentials in classical molecular models, including those used in materials and biological modelling (although they probably would not be able to derive them),
(2) be able to demonstrate first integrals and the symplectic property for some classes of numerical methods,
(3) be able to describe numerical methods for constrained dynamical systems and their implementation,
(4) be able to use software to explore the chaotic dynamics of molecular models,
(5) understand and be able to use and to design splitting methods for Langevin dynamics for applications in molecular sampling.

Reading List
Recommended :
B. Leimkuhler and C. Matthews, Molecular Dynamics, Springer, to appear. [a prepublication draft will be provided if the book is not available at runtime]
M. Allen and D. Tildesley, Computer Simulation of Liquids, Clarendon Press, 1989
D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd Edition, Academic Press, 2002.
B. Leimkuhler and S. Reich, Simulating Hamiltonian Dynamics, Cambridge
University Press, 2005. 
Additional Information
Graduate Attributes and Skills 
Not entered 
Keywords  MDyn 
Contacts
Course organiser  Dr Martin Dindos
Tel:
Email: M.Dindos@ed.ac.uk 
Course secretary  Mrs Alison Fairgrieve
Tel: (0131 6)50 5045
Email: Alison.Fairgrieve@ed.ac.uk 

