2016 Biomolecular Analysis

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Academic unit or major
Graduate major in Life Science and Technology
Fujii Masaaki  Ohtani Hiroyuki  Osada Toshiya  Sakai Makoto 
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
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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 is to be announced in the class. 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. The fourth part deals with a super-resolution microscopy (SRM) using 2-color laser spectroscopy. Due to the diffraction of light, the resolution of conventional laser (light) microscopy is limited, and is almost the same as a wavelength of light. The lecture begins with the principles of SRM beyond the diffraction limit by using 2-color laser spectroscopy, and then goes to the applications of SRM to the observation of biological samples including living cells.

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) understand the principles of super-resolution microscopy.
6) learn the applications of super-resolution microscopy.


AFM, normal mode, molecular vibration, infrared and Raman spectroscopy, Laser spectroscopy, Super-resolution microscopy

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.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Introduction to atomic force microscopy(AFM) AFM instrumentation, Surface forces, Contact mechanics
Class 2 Imaging modes of AFM Acquiring an image, Image processing
Class 3 AFM based single-molecule force spectroscopy Explain the principle and the application of AFM to single molecule.
Class 4 AFM based single-cell force spectroscopy Explain the principle and the application of AFM to single cell.
Class 5 Molecular energy levels and wavefunctions Understanding molecular wavefunctions
Class 6 Quantum mechanical description of optical transitions Understanding interaction between light and molecules
Class 7 Visible and ultraviolet absorption and emission Understanding electronic transitions
Class 8 Phosphorescence and excited triplet states Understanding triplet state and its optical property
Class 9 Quantum chemical description of molecular vibrations 分子振動の理解
Class 10 Normal mode Understanding normal mode description of molecular vibrations
Class 11 Infrared absorption and Raman scattering Understanding principle of infrared absorption and Raman effect
Class 12 Infrared and Raman spectra and vibrational relaxation Understanding relation between spectra and molecular vibrations
Class 13 Introduction to super-resolution microscopy using 2-color laser spectroscopy Understanding the principle of the super-resolution microscopy using 2-color laser spectroscopy
Class 14 Applications of super-resolution microscopy to the observation of biological samples Explain the applications of super-resolution microscopy
Class 15 Infrared super-resolution microscopy based on the non-linear optical technique Explain the principle and the application of Infrared super-resolution microscopy


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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