
Description of Individual Course UnitsCourse Unit Code  Course Unit Title  Type of Course Unit  Year of Study  Semester  Number of ECTS Credits  9101045842013  Molecular Simulation II  Elective  1  2  8 
 Level of Course Unit  Second Cycle  Objectives of the Course  The aim of the course is to teach how the simulations and the analyses will be done, to explain the advanced simulation techniques, and to give some applications of the simulation for simple and complex liquids.  Name of Lecturer(s)  Yard.Doç.Dr. E. Mine Çapar  Learning Outcomes  1  Learning the tricks of the molecular dynamics and Monte Carlo computer simulation methods.  2  To able to analyse the results of the simulations.  3  To be able to apply the simulation methods to the simple and complex liquids. 
 Mode of Delivery  Face to Face  Prerequisites and corequisities  None  Recommended Optional Programme Components   Course Contents  Some tricks of the simulations, the initial configurations and velocities, equilibration of the system, creation of the simulation, analysis of the results, advanced simulation techniques, nonequilibrium molecular dynamics, Brownian dynamics, quantum simulations, some applications.  Weekly Detailed Course Contents  
1  Some tricks of the simulations1: the calculation of the forces, energies, and pressures, the shiftedforce potentials.    2  Some tricks of the simulations2: For the calculation of the longrange forces, the ewald sum, the reaction field method, the particleparticle and particlemesh algorithm for ionic systems.    3  The initial configuration, the initial velocities, equilibration.    4  Creation of the simulation1: input/output files, structure files.    5  Creation of the simulation2: simulation details, program structure.    6  Analysis of the results1: time correlation function, estimating errors.    7  Analysis of the results1: correcting the results.    8  Midterm exam    9  Advanced simulation techniques1: Free energy calculation.    10  Advanced simulation techniques2: smarter Monte Carlo, constanttemperature molecular dynamics, constantpressure molecular Dynamics.    11  Nonequilibrium molecular dynamics1: shear flow, expansion and contraction.    12  Nonequilibrium molecular dynamics1: heat flow, diffusion, other perturbations.    13  Brownian dynamics.    14  Quantum simulations.    15  Some Applications: liquid drop, melting, liquid crystals, rotational dynamics, interfaces.    16  Final exam   
 Recommended or Required Reading  1. Michael P. Allen and Dominic J. Tildesley, Computer Simulation of Liquids, Clarendon PressOxford, 1991.
2. Daan Frenkel and Berend Smith, Understanding Molecular Simulation, Academic Press, 2002.
 Planned Learning Activities and Teaching Methods   Assessment Methods and Criteria   Language of Instruction  Turkish  Work Placement(s)  None 
 Workload Calculation 

Midterm Examination  1  2  2  Final Examination  1  2  2  Attending Lectures  14  3  42  Self Study  14  8  112  Individual Study for Homework Problems  1  10  10  Individual Study for Mid term Examination  1  30  30  Individual Study for Final Examination  1  30  30  Homework  1  10  10  
Contribution of Learning Outcomes to Programme Outcomes   * Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High 



Ege University, Bornova  İzmir / TURKEY • Phone: +90 232 311 10 10 • email: intrec@mail.ege.edu.tr 
