2019 Biomolecular Analysis

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Academic unit or major
Graduate major in Life Science and Technology
Fujii Masaaki  Osada Toshiya  Ishii Yoshitaka  Ishiuchi Shun-Ichi 
Course component(s)
Day/Period(Room No.)
Mon3-4(B223,W831)  Thr3-4(B223,W831)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
Access Index

Course description and aims

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.

Student learning outcomes

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


AFM, normal mode, molecular vibration, infrared and Raman spectroscopy, Laser spectroscopy, mass spectrometry, nuclear magnetic resonance, NMR

Competencies that will be developed

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/Required learning

  Course schedule Required learning
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 Studies of biomolecules by ultra cold ion spectroscopy Understanding recent studies of biomolecules using ultra cold ion spectroscopy
Class 13 Introduction to atomic force microscopy(AFM) AFM instrumentation, Surface forces, Contact mechanics Understanding how to apply infrared spectroscopy to investigate biomolecules
Class 14 Imaging modes of AFM Acquiring an image, Image processing
Class 15 AFM based single-molecule force spectroscopy AFM based single-cell force spectroscopy Explain the principle and the application of AFM to single molecule. Explain the principle and the application of AFM to single cell.


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.

Assessment criteria and methods

Final exams or reports 80%, exercise problems 20%.

Related courses

  • LST.A409 : Physical Biology of the Cell

Prerequisites (i.e., required knowledge, skills, courses, etc.)

Students must have successfully completed Physical Chemistry I, II, and III (number) or have equivalent knowledge.

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