2020 Faculty Courses School of Life Science and Technology Department of Life Science and Technology Graduate major in Life Science and Technology
Biomolecular Analysis
- Academic unit or major
- Graduate major in Life Science and Technology
- Instructor(s)
- Masaaki Fujii / Toshiya Osada / Yoshitaka Ishii / Shun-Ichi Ishiuchi
- Class Format
- Lecture (Zoom)
- Media-enhanced courses
- -
- Day of week/Period
(Classrooms) - Intensive
- Class
- -
- Course Code
- LST.A501
- Number of credits
- 200
- Course offered
- 2020
- Offered quarter
- 2Q
- Syllabus updated
- Jul 10, 2025
- Language
- English
Syllabus
Course overview and goals
This course is organized into four parts. The first part of the course deals with an AFM (atomic force microscopy). The AFM has become a powerful tool to study biological samples not only for imaging at the molecular level but also for measuring their mechanical properties. The course begins with an overview of AFM and then goes to applications of AFM to the study of the biological materials. The second part introduces nuclear magnetic resonance (NMR) spectroscopy. The third part describes the vibrational spectroscopy. It includes quantum chemical description of molecular vibrations, normal modes, principle and setup of infrared spectroscopy and Raman scattering, and their examples of several important molecules such as benzenes. The vibrational relaxation will also be shown with examples. In the fourth part, application of Raman, infrared and ultra fast spectroscopy biomolecules will be introduced. In addition, recent progress of ultra cold ion spectroscopy, which is a new methodology combining mass spectrometry and laser spectroscopy, will be introduced.
Course description and aims
By the end of this course, students will be able to:
1) gain understanding of the basic principles of AFM.
2) learn the broad applications of AFM in biological fields
3) understand molecular vibrations and normal modes
4) understand the experimental techniques to measure the molecular vibrations and its applications
5) learn theory and applications of NMR spectroscopy
Keywords
AFM, normal mode, molecular vibration, infrared and Raman spectroscopy, Laser spectroscopy, mass spectrometry, nuclear magnetic resonance, NMR
Competencies
- Specialist skills
- Intercultural skills
- Communication skills
- Critical thinking skills
- Practical and/or problem-solving skills
Class flow
The class starts with reviews of previous class. Towards the end of class, students are often given exercise problems related to the lecture given that day to solve. To prepare for the class, students should read the course schedule section and check what topics will be covered. Required learning should be completed outside the classroom for preparation and review purposes.
Classes are basically done in English, but if necessary we will provide supplementary explanation in Japanese.
Course schedule/Objectives
| Course schedule | Objectives | |
|---|---|---|
| Class 1 | Quantum chemical description of molecular vibrations | Understanding molecular vibration |
| Class 2 | Normal mode | Understanding normal mode description of molecular vibrations |
| Class 3 | Infrared absorption and Raman scattering | Understanding of 2-3D NMR and advanced applications of NMR spectroscopy and imaging to various systems |
| Class 4 | Infrared and Raman spectra and vibrational relaxation | Understanding relation between spectra and molecular vibrations |
| Class 5 | NMR spectroscopy: (1) Introduction to NMR spectroscopy | Understanding of basic theory and applications of NMR spectroscopy |
| Class 6 | NMR spectroscopy: (2) Classical theory and 1D NMR | Understanding of classical theory of NMR spectroscopy and 1D NMR |
| Class 7 | NMR spectroscopy: (3) 2-3D NMR and applications to small molecules, proteins, and imaging | Understanding of 2-3D NMR and advanced Understanding principle of infrared absorption and Raman effect |
| Class 8 | NMR spectroscopy: (4) Quantum theory in NMR spectroscopy | Understanding of quantum descriptions of NMR spectroscopy |
| Class 9 | Introduction to application of Raman spectroscopy to biomolecules | Understanding how to apply Raman spectroscopy to investigate biomolecules |
| Class 10 | Introduction to application of infrared spectroscopy to biomolecules | Understanding how to apply infrared spectroscopy to investigate biomolecules |
| Class 11 | Introduction to application of ultra fast spectroscopy to biomolecules | Understanding the principle of ultra fast spectroscopy and its application to biomolecules |
| Class 12 | Introduction to atomic force microscopy(AFM) | AFM instrumentation, Surface forces, Contact mechanics |
| Class 13 | Imaging modes of AFM | Acquiring an image, Image processing |
| Class 14 | AFM based single-molecule force spectroscopy AFM based single-cell force spectroscopy | Explain the principle and the application of AFM to single molecule. |
Study advice (preparation and review)
Textbook(s)
No textbook is set.
Reference books, course materials, etc.
Handouts will be distributed at the beginning of class when necessary and elaborated on using PowerPoint slides.
Evaluation methods and criteria
Final exams or reports 80%, exercise problems 20%.
Related courses
- LST.A409 ： Physical Biology of the Cell
Prerequisites
Students must have successfully completed Physical Chemistry I, II, and III (number) or have equivalent knowledge.