| Week | Date | Lecture Topic | Reference | Due |
| 1 | Aug. 23 | Biophotonics introduction | Ch. 1 | |
| Aug. 25 | Optics overview | Sec. 2.1, 7.3.4 | ||
| 2 | Aug. 30 | Quantized states of matter | Sec. 2.2 | |
| Sept. 1 | Biopolymers | Sec. 2.2 - 2.4, 3.4, 3.5 | ||
| 3 | Sept. 6 | Interaction between light & matter | Sec. 3.5, 4.1, 4.3 | |
| Sept. 8 | Absorption and Fluorescence | Sec. 4.2-4.6 | ||
| 4 | Sept. 13 | Fluorescence quenching | Paper | HW #1 |
| Sept. 15 | No Class | |||
| 5 | Sept. 20 | Fluorescence energy transfer | Sec. 9.2.4-9.2.5, 8.2 | |
| Sept. 22 | Fluorescence beacons, resonance energy transfer | Sec. 9.2.4-9.2.5, 8.2 | ||
| 6 | Sept. 27 | Fluorescence correlation spectroscopy | Sec. 4.9 | |
| Sept. 29 | No Class | |||
| 7 | Oct. 4 | Fluorescent probes | Sec. 8.1 | |
| Oct. 6 | Vibrational/IR/Raman spectroscopy | Sec. 4.7, 5.4.4 | ||
| Oct. 11 | Fall Break | |||
| Oct. 13 | Fall Break | |||
| 8 | Oct. 18 | Optical microscopy - overview | Sec. 7.1-7.3 | HW #2 |
| Oct. 20 | Optical microscopy - imaging, magnifier, objective | Sec. 7.1-7.3 | ||
| 9 | Oct. 25 | Presentations Ia | ||
| Oct. 27 | Presentations Ib | |||
| 10 | Nov. 1 | Optical microscopy - basic methods | Sec. 7.3 | |
| Nov. 3 | Optical microscopy - fluorescence/confocal | Sec. 7.4-7.5, 7.7-7.8, PPTs | ||
| 11 | Nov. 8 | 4pi/STED microscopy | Sec. 7.16 | |
| Nov. 10 | Near-field microscopy | Sec. 7.11 | ||
| 12 | Nov. 15 | TIRF microscopy | Sec. 7.10 | |
| Nov. 17 | SPR microscopy | Sec. 9.8 | ||
| 13 | Nov. 22 | Biosensors | Sec. 9.1-9.3 | |
| Nov. 24 | No Class - Thanksgiving | |||
| 14 | Nov. 29 | Biosensors - optical transduction | Sec. 9.4-9.8 | |
| Dec. 1 | DNA & protein microarrays | Sec. 10.1-10.3 | ||
| 15 | Dec. 6 | DNA & protein microarrays | Sec. 10.1-10.3 | |
| Dec. 8 | Campbell seminar, noon-1pm | HSEB 2120 | ||
| Final Exam | Dec. 12 | Presentations II (10:30-12:30) | HW #3 | |