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Contact:Dr. Melik Demirel
Course Description
Students will learn the simulation techniques and the design rules of nanostructures.
Basic concepts of computer modeling will be introduced using quantum and
classical approaches. Fundamental physical phenomena encountered in the
molecular fields of computational physics, chemistry, and biology will be
studied. Applications are drawn from a broad range of fields including soft
and condensed matter to build an understanding of nanostructures.
Course Content
a. Overview of Computer Simulation
i. History of computer simulations
ii. Simulations at multi-length scale (nano, meso,
micro)
iii. Experimental observations and linking to simulations
b. Simulation Fundamentals:
i. Quantum Mechanics
ii. Pseudopotentials
iii. Force Fields from QM
iv. Empirical Force Fields
v. Molecular Dynamics Methods
vi. Monte Carlo Methods
vii. Coarse Grain Models
viii. System level approaches
c. Applications and Design Rules
i. Bio-molecular Systems: Proteins, Nucleic Acids,
Drug Design
ii. Reactions Selection Rules and Rates at Surfaces
iii. Polymers: Statistical approaches, network dynamics
iv. Semiconductors: Surfaces and Defects in Solids
v. Metals: Bonding in Bulk Metals, Metallic Alloys, Dislocations
vi. Carbon: Fullerenes and Nanotubes
vii. Nanotechnology and Self-Assembly
viii. Cellular systems biology: reaction diffusion equations, biological
networks
Major topics and time allotments
Time allotments and topic covered are given in Table 1. The period allocation
of Table 1 is based on a Tuesday/Thursday offering with 75 minute periods
Table 1.
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MAJOR TOPIC
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TIME ALLOTMENT*
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Overview of Computer Simulation
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2 periods
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Quantum Mechanics
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4 periods
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Molecular Mechanics
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2 periods
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Pseudopotentials, Empirical Force Fields, Force Fields from QM
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2 periods
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Molecular Dynamics Methods, Monte Carlo Methods
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2 periods
|
|
Coarse Grain Models, System level
approaches
|
2 periods
|
|
Bio-molecular Systems: Proteins,
Nucleic Acids, Drug Design
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2 periods
|
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Reactions Selection Rules and Rates
at Surfaces
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1 periods
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Polymers: Statistical approaches,
network dynamics
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2 periods
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Semiconductors: Surfaces and Defects
in Solids
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2 periods
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Metals: Bonding in Bulk Metals,
Metallic Alloys, Dislocations
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2 periods
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Carbon: Fullerenes and Nanotubes
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2 periods
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Nanotechnology and Self-Assembly
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1 periods
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Cellular systems biology: reaction
diffusion equations, biological networks
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2 periods
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Required Book:
Understanding Molecular Simulation
by Daan Frenkel, Berend Smit
Publisher: Academic Press; 2 edition
(October 15, 2001) ISBN: 0122673514
Suggested Books:
Molecular Modelling:
Principles and Applications (2nd Edition)
by Andrew
Leach
Publisher: Prentice Hall; 2 edition (March 30, 2001) ISBN:
0582382106
Protein Physics: A Course of
Lectures
by Alexei
V. Finkelstein, Oleg
Ptitsyn
Publisher: Harcourt; (May 14, 2002) ISBN:
0122567811
Introduction to Modern Statistical
Mechanics
by David
Chandler
Publisher: Oxford University
Press; (September 1, 1987) ISBN: 0195042778
Computer Simulation of Liquids
by M.P.
Allen, D.J.
Tildesley
Publisher: Oxford University Press; Reprint edition (August 1, 1989) ISBN:
0198556454
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