Introduction to Nano-biophotonics

Instructor: Chia-Fu Chou
Time: Wed. 9:10-12:00
Classroom: 2nd meeting room, 5F, Institute of Physics, Academia Sinica
Office hours: Mon. 10-12 @ P612, IoP

Introdution:　　　　　　　　　　　　　　　　　　　　　　　　　　

In this course, we will review the basics and recent developments of nanobiophotonics, an emerging field which is cross-displinary among nanoscience and nanotechnology, biology, and photonics. The course is comprised of lectures from several special topics given by experts in these areas, including micro/nanofluidics, single molecule biophysics, DNA microarray, polymer brush, optical tweezers, near-field optics, plasmonics (SPR, SERS), bioimaging techniques (fluorescence, confocal, multiphoton, TIRFM, FRET, X-ray nanobeam, cryo-EM etc.), image analysis, quantum dots, electron and energy transfer reactions, singleenzyme catalytic reactions, ultrafast electron diffraction and lab tours by AS instructors. Grades will be evaluated on term project based on literature review or experimental work.

Grade evaluation on term project:

Written report (no more than 10 pages, due 1/11/08)-50%
Presentation-50%

Speakers and topics to be covered: (classnote)

• Chou, Chia-Fu (6) – Introduction, micro/nanofluidics, SM biophys, bioimaging, Fluorescence microscopy, TIRFM, Term project assignment & evaluation
• Lee, Chau-Hwang (1) – Confocal, NIWOP-cell membrane imaging, image processing
• Dong, Chen-Yuan (1) (NTU) – Multiphoton imaging
• Wei, Pei-Kuen (1) – Near-field optics/SNOM, SERS, Nanoscale optical control and biosensing
• Cheng, Ji-Yen (1) – DNA microarrays-fabrication, detection, and analysis new
• Chang, Wei-Hau (1) – Nanoscale resolved CryoEM for structural biology
• Hwu, Yeu-Kuang (1) – X-ray nanoimaging
• Tang, Jau (1) – Studies of single molecules using confocal microscopy; photophysical properties of quantum dots; studies of electron and energy transfer reactions; single-enzyme catalytic reactions; ultrafast electron diffraction
• Gukassyan, Vladimir (1) (YMU) – Time-resolved fluorescence microscopy (FLIM, FRET, TCSPC)
• Juan, Wen-Tau (1) Polymer brush, optical tweezers

Class Schedule for Fall Semester, 2007

Week	Seminar (Wed.)	9:10-12:00	Week	Seminar (Wed.)	9:10-12:00
1	96/09/19	Chou, Chia-Fu	9	96/11/14	Chang, Wei-Hau
2	96/09/26	Chou, Chia-Fu	10	96/11/21	Hwu, Yeu-Kuang
3	96/10/03	Lee, Chau-Hwang	11	96/11/28	Tang, Jau 湯朝暉
4	96/10/10	國慶日 (放假一天)	12	96/12/05	Gukassyan, Vladimir
5	96/10/17	Dong, Chen Yuan	13	96/12/12	Juan, Wen-Tau
6	96/10/24	Cheng, Ji-Yen	14	97/12/19	Term project Chou, Chia-Fu
7	96/10/31	Wei, Pei-Kuen	15	97/12/26	Term project presentation Chou, Chia-Fu
8	96/11/07	期中考週- Term project assignment Chou, Chia-Fu	16	97/01/02	Term project presentation Chou, Chia-Fu

Term project presentation (Wed.)	9:10-12:00
96/12/19	Sub-diffraction-limit imaging II. (Judy, Jian-Der) Single-Molecule Analysis II. (Leo, Yu-Shuan, Yu-Yen)
96/12/26	Single-Molecule Analysis I. (Cheng-Hung, Nitin) Sub-diffraction-limit imaging III. (Po-Chieh, Pei-Yin, Jia-Wei) Stabilization of an optical microscope to 0.1 nm in 3D. (Min- Kung, Ya-Jay)
97/01/02	Sub-diffraction-limit imaging I. (Yii-Lih, Jie-Pan) Million-fold Preconcentration of Proteins and Peptides by Nanofluidic Filter. (Sriram, Sayeda) Biolabeling with QDs. (Shobhit)
Students reports: new

Reference:

1. Optical microscopy in general- http://micro.magnet.fsu.edu/
2. Stefan A. Maier: Plasmonics: Fundamentals and Applications (Springer, 2007)
3. Lukas Novotny and Bert Hecht: Principles of Nano-Optics (Cambridge University Press, 2006)
4. Joseph R. Lakowicz: Principles of Fluorescence Spectroscopy (3rd Ed., Springer, 2006)
5. Alastair Smith, Christopher Gell, and David Brockwell: Handbook of Single Molecule Fluorescence Spectroscopy (Oxford University Press, 2006)
6. Katrin Kneipp, Martin Moskovits, and Harald Kneipp: Surface- Enhanced Raman Scattering: Physics and Applications (Springer, 2006)
7. Wolfgang Becker: Advanced Time-Correlated Single Photon Counting Techniques (Springer Series in Chemical Physics, 2005)
8. Christof M. Niemeyer and Chad A. Mirkin (Editors): Nanobiotechnology: Concepts, Applications and Perspectives (Hardcover, Wiley-VCH, 2004)
9. Roland Glaser: Biophysics (Springer, 2004)
10. Paras N. Prasad: Introduction to Biophotonics (Wiley-Interscience, 2003)
11. West JL, Halas NJ: Engineered nanomaterials for biophotonics applications: Improving sensing, imaging, and therapeutics. Annual Review of Biomedical Engineering 5: 285-292 2003.
12. H. Berg, The Random Walk in Biology, Princeton University Press, 1993.

Term project topics:

Experimental work–

1. Optical tweezers
   (http://www.stanford.edu/group/blocklab/Optical Tweezers Introduction.htm)
2. Prism-based TIRFM (http://micro.magnet.fsu.edu/primer/techniques/fluorescence/tir
   f/tirfhome.html)
3. Nanometer Localization Analysis for Individual Fluorescent Probes (Biophys. J. 82, 2775–2783, 2002)

Literature review–

4. Sub-diffraction-limit imaging I: (Yii-Lih, Jie-Pan, 1/2/08)
   • Toward fluorescence nanoscopy. Nature Biotechnology 21 (11): 1347-1355 NOV 2003.
5. Sub-diffraction-limit imaging II: (Judy, Jian-Der, 12/19)
   • Imaging Intracellular Fluorescent Proteins at Nanometer Resolution. Science 313, 1642-1645, 2006.
6. Sub-diffraction-limit imaging III: (Po-Chieh, Pei-Yin, Jia-Wei, 12/26)
   • Sub-Diffraction-Limited Optical Imaging with a Silver Superlens. Science 308, 534-537, 2005.
   •Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods 3 (10): 793-795 OCT 2006.
7. Single-Molecule Analysis I: (Cheng-Hung Wei, Nitin, 12/26)
   • Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations. Science 299, 682-686, 2003.
8. Single-Molecule Analysis II: (Leo, Yu-Shuan, Yu-Yen, 12/19)
   • Single photons on demand from a single molecule at room temperature. Nature 407, 491-493, 2000.
   • Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS). Physical Review Letters 78, 1667-1670, 1997
9. Stabilization of an optical microscope to 0.1 nm in three dimensions. Applied Optics 46, 421-427, 2007. (Hsu Min-Kung, Lin Ya-Jay, 12/26)
10. Million-fold Preconcentration of Proteins and Peptides by Nanofluidic Filter. Analytical Chemistry 77 (14), 4293-4299, 2005. (Sriram, Sayeda, 1/2/08)
11. Biolabeling with QDs (Shobhit, 1/2/08)