課程名稱 |
分子模擬導論 Introduction to Molecular Modeling |
開課學期 |
108-1 |
授課對象 |
理學院 化學系 |
授課教師 |
鄭原忠 |
課號 |
Chem5075 |
課程識別碼 |
223 U1400 |
班次 |
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學分 |
3.0 |
全/半年 |
半年 |
必/選修 |
選修 |
上課時間 |
星期五6,7,8(13:20~16:20) |
上課地點 |
化210室 |
備註 |
本課程中文授課,使用英文教科書。 限學士班三年級以上 且 限本系所學生(含輔系、雙修生) 總人數上限:60人 |
Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1081IMM2019 |
課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
課程大綱
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課程概述 |
The course will focus on theoretical backgrounds for molecular modeling methods. We emphasize how to choose suitable simulation methods and correctly interpret outputs of molecular modeling packages. The outline of the course is:
* Atoms, Molecules, and Interactions
o Ab initio methods for many electron systems
o Electron correlation methods
o Density function theory
* Structures and Phases
o Solid state physics
o Simple statistical thermodynamics
o Empirical force field models and molecular mechanics
* Time-Evolution and State Transitions
o Molecular dynamics simulation methods
o Methods for exploring conformational space
o Free energy calculations
* Properties and Functions
o Brownian dynamics
o Monte Carlo simulation methods
o Coarse-graining approaches
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課程目標 |
This couse aims to provide a "multiscale" view of molecular modeling, which ranges from atomistic methods based on quantum mechanics and classical mechanics to coarse-grained statistical approaches. The goal is to provide students an overview of theoretical tools for molecular modeling that will be useful in physical chemistry researches. |
課程要求 |
Course Prerequisites:
* General Physics & General Chemistry
* Basic Quantum Mechanics (Physical Chemistry II)
* Linear Algebra
* Willingness to Learn How to Operate Computers
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預期每週課後學習時數 |
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Office Hours |
另約時間 備註: 使用 email 與教授約時間 |
指定閱讀 |
待補 |
參考書目 |
Textbook: Molecular Modelling, 2nd Edition by Andrew R. Leach, Prentice Hall.
Recommended reference book: Physical Chemistry, 4th Edition by Robert J. Silbey,
Robert A. Alberty, and Moungi G. Bawendi, Wiley. |
評量方式 (僅供參考) |
No. |
項目 |
百分比 |
說明 |
1. |
Final project |
50% |
This course puts a strong emphasis on being able to develop and complete a project pertaining to methods of molecular modeling. Each student taken the class must develop and solve a problem related to molecular modeling, based on a paper from a selected list of ~ 20 papers. |
2. |
Final exam |
20% |
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3. |
Midterm exams |
20% |
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4. |
Homework & class participants |
10% |
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週次 |
日期 |
單元主題 |
第1週 |
9/13 |
校慶停課 |
第2週 |
9/20 |
Class preparation, Division into groups |
第3週 |
9/27 |
H-like atoms, Helium atom, the Born-Oppenheimer approximation, The Hartree-Fock method, the Roothaan-Hall equations |
第5週 |
10/11 |
停課 (國慶日調整放假) |
第6週 |
10/18 |
Molecular mechanics, potential energy surface, long-range interactions |
第7週 |
10/25 |
Basic statistical mechanics, solvation model |
第8週 |
11/1 |
Midterm exam |
第9週 |
11/8 |
Classical force fields, pair distribution function |
第10週 |
11/15 |
校慶停課 |
第11週 |
11/22 |
Molecular dynamic simulation, Monte Carlo simulation methods, enhanced sampling methods |
第12週 |
11/29 |
Free energy calculations, free energy perturbation, thermodynamic integration |
第13週 |
12/6 |
Time correlation functions, linear response theory, transport phenomena |
第14週 |
12/13 |
停課 |
第15週 |
12/20 |
Multiscale coarse-grained models, Mesoscale dynamics |
第16週 |
12/27 |
Exam |
第17週 |
1/3 |
Final project presentations |
第18週 |
1/10 |
Final project presentations |
第4-1週 |
10/4 |
Electron correlation methods, Density functional theory |
第4-2週 |
10/5 |
Solid state physics (補課) |
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