Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
9101045842013Molecular Simulation IIElective128
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
1Learning the tricks of the molecular dynamics and Monte Carlo computer simulation methods.
2To able to analyse the results of the simulations.
3To be able to apply the simulation methods to the simple and complex liquids.
Mode of Delivery
Face to Face
Prerequisites and co-requisities
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, non-equilibrium molecular dynamics, Brownian dynamics, quantum simulations, some applications.
Weekly Detailed Course Contents
WeekTheoreticalPracticeLaboratory
1Some tricks of the simulations-1: the calculation of the forces, energies, and pressures, the shifted-force potentials.
2Some tricks of the simulations-2: For the calculation of the long-range forces, the ewald sum, the reaction field method, the particle-particle and particle-mesh algorithm for ionic systems.
3The initial configuration, the initial velocities, equilibration.
4Creation of the simulation-1: input/output files, structure files.
5Creation of the simulation-2: simulation details, program structure.
6Analysis of the results-1: time correlation function, estimating errors.
7Analysis of the results-1: correcting the results.
8Midterm exam
9Advanced simulation techniques-1: Free energy calculation.
10Advanced simulation techniques-2: smarter Monte Carlo, constant-temperature molecular dynamics, constant-pressure molecular Dynamics.
11Non-equilibrium molecular dynamics-1: shear flow, expansion and contraction.
12Non-equilibrium molecular dynamics-1: heat flow, diffusion, other perturbations.
13Brownian dynamics.
14Quantum simulations.
15Some Applications: liquid drop, melting, liquid crystals, rotational dynamics, interfaces.
16Final exam
Recommended or Required Reading
1. Michael P. Allen and Dominic J. Tildesley, Computer Simulation of Liquids, Clarendon Press-Oxford, 1991. 2. Daan Frenkel and Berend Smith, Understanding Molecular Simulation, Academic Press, 2002.
Planned Learning Activities and Teaching Methods
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
SUM0
End Of Term (or Year) Learning ActivitiesQuantityWeight
SUM0
SUM0
Language of Instruction
Turkish
Work Placement(s)
None
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination122
Final Examination122
Attending Lectures14342
Self Study148112
Individual Study for Homework Problems11010
Individual Study for Mid term Examination13030
Individual Study for Final Examination13030
Homework11010
TOTAL WORKLOAD (hours)238
Contribution of Learning Outcomes to Programme Outcomes
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1
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5
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6
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7
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9
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10
PO
11
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* 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 • e-mail: intrec@mail.ege.edu.tr