Office hours
1-3 pm Wednesdays, 104 Keck
Lecture and lab schedule
1-3:55 pm Tuesdays and Thursdays, 108 Keck
- Jan 08
- Lecture 1: Overview of DNA-based logic circuits
- Lab 1: Design and analysis of a DNA-based square root circuit
- Jan 10
- Lecture 2: Overview of DNA-based neural networks
- Lab 2: Basic lab technique and measuring the rate of a DNA strand displacement reaction
- Jan 15
- Lecture 3: Programmable disorder in random DNA tilings
- Lab 3: Design and analysis of a smiley-shaped DNA origami
- Jan 17
- Student presentations: All students will present their designs of logic circuits, neural networks, and random tilings. A winner design will be selected for experimental demonstration.
- Lab 4: Sample preparation practice and spectrofluorometry
- Jan 22
- Lecture 4: A simple DNA gate motif
- Lab 5: Design and analysis of a molecular system for the student-designed logic circuit and neural network
- Jan 24
- Lecture 5: Finite DNA origami arrays
- Lab 6: Design and analysis of a molecular system for the student-designed random tiling
- Jan 29
- Lecture 6: Detective stories about debugging DNA circuits, part I
- Lab 7: Construction of a DNA-based catalyst for signal amplification
- Jan 31
- Lecture 7: Detective stories about debugging DNA circuits, part II
- Lab 8: Construction of a DNA-based catalyst with threshold for signal restoration
- Feb 05
- Student presentations: One student will represent each team and present progress in the past week, followed by discussions.
- Lab 9: Construction of a DNA-based logic gate
- Notes on Seesaw Compiler syntax and experimental protocols
- Mathematica notebook for generating protocols
- Feb 07
- Lecture 8: Detective stories about debugging DNA circuits, part III
- Lab 10a and Lab 10b: Construction of a DNA-based two-layer logic circuit
- Feb 12
- Student presentations
- Lab 11a and Lab 11b: Construction of the student-designed logic circuit
- Feb 14
- Lecture 9: Scaling up molecular pattern recognition, part I
- Lab 12: Construction of a DNA-based two-species winner-take-all circuit
- Feb 19
- Lecture 10: Scaling up molecular pattern recognition, part II
- Lab 13a and Lab 13b: Construction of a DNA-based neural network that has two 4-bit memories
- Feb 21
- Student presentations
- Lab 14: Construction of the student-designed neural network
- Feb 26
- Lecture 11: Detective stories about debugging DNA nanostructures
- Lab 15: Multi-channel pipetting practice and construction of a DNA origami tile
- Feb 28
- Lecture 12: Scaling up DNA nanostructures with arbitrary patterns
- Lab 16: Atomic force microscopy and data analysis of a DNA origami tile
- Gwyddion
- Yield Calculator (requires Matlab)
- Mar 05
- Student presentations
- Lab 17: Construction of the student-designed random tiling
- Mar 07
- Lecture 13: Algorithmic and architectural foundations for building molecular robots
- Lab 18: Atomic force microscopy and data analysis of the student-designed random tiling
- Mar 12
- Students working on final presentations
- Mar 19
- Final presentations (1-3 pm, 111 Keck)
Homework schedule
Email your homework and lab reports to the instructor and TAs by midnight of the due date.
- Jan 16
- Homework 1 due
- Jan 23
- Lab report 1 due
- Jan 30
- Homework 2 due
- Feb 15
- Lab report 2 due
- Feb 27
- Lab report 3 due
- Mar 11
- Lab report 4 due
- Mar 20
- A one-page perspective article due
Late penalty
1st and 2nd time late: no penalty for less than 12 hours late; -5 points per 24 hours after that. 3rd time late and above: -5 points per 24 hours.