20.309 Main Page

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20.309 This week and next

Week	Summary	Assignments due	Lab Manual	Resources
Week 11: Apr. 16 - 22	Continue DNA Melting 1 and prep for Quiz 2	Friday Apr. 21st: Quiz 2 in lecture	DNA Melting Part 1: Measuring Temperature and Fluorescence	Overview Lab Manual:Measuring DNA Melting Curves Code examples and simulations DNA Melting: Simulating DNA Melting - Basics DNA Melting: Simulating DNA Melting - Intermediate Topics DNA Melting: Model function and parameter estimation by nonlinear regression Reference materials DNA Melting Thermodynamics DNA Melting: DNA Sequences DINAMelt Web Server Background reading Electronics Primer
Week 12: Apr. 23 - 29	Finish DNA Melting 1, get started on PSet 4 and DNA Melting 2	Tuesday Apr. 25th: DNA Melting Part 1	DNA Melting Part 1: Measuring Temperature and Fluorescence
			DNA Melting Part 2: Lock-in Amplifier and Temperature Control	DNA melting: Identifying the unknown sample DNA Melting Part 2: Lock-in Amplifier and Temperature Control DNA Melting Report Requirements for Part 2

20.309 course information

• 20.309:Course Information
• 20.309:Lab Report Guidelines
• 20.309:Safety

Reserve a lab station here: Bioinstrumentation Lab reservation system

Optics bootcamp

Lab manual

• Optics Bootcamp

Background reading

• Geometrical optics and ray tracing
• Optical detectors, noise, and the limit of detection
• Manta G032 camera measurements

Optical microscopy lab

Code examples and simulations

• Converting Gaussian fit to Rayleigh resolution
• MATLAB: Estimating resolution from a PSF slide image
• Matlab: Scalebars
• Calculating MSD and Diffusion Coefficients

Background reading

• Geometrical optics and ray tracing
• Physical optics and resolution
• Optical aberrations
• Aperture and field stops
• Optical detectors, noise, and the limit of detection
• Manta G032 camera measurements
• Understanding log plots

Electronics bootcamp

Lab manual

• Electronics bootcamp

Background reading

• Electronics primer
• Khan Academy Material, esp. "Ideal Circuit Elements" and "Voltage Divider"
• Real electronics
• Impedance analysis
• Transfer functions and Bode plots
• Complex number review
• Input and output impedance

DNA melting lab

Lab manuals

• Lab Manual:Measuring DNA Melting Curves
• DNA Melting Part 1: Measuring Temperature and Fluorescence
• DNA Melting Report Requirements for Part 1
• DNA Melting: Model function and parameter estimation by nonlinear regression
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• DNA melting: Identifying the unknown sample
• DNA Melting Part 2: Lock-in Amplifier and Temperature Control
• DNA Melting Report Requirements for Part 2

Code examples and simulations

• DNA Melting: Simulating DNA Melting - Basics
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• DNA Melting: Model function and parameter estimation by nonlinear regression

Reference materials

• DNA Melting Thermodynamics
• DNA Melting: DNA Sequences
• DINAMelt Web Server

Background reading

• Electronics Primer

Limits of detection mini-lab

• Lab Manual: Limits of Detection
• Lab Manual: Atomic Force Microscopy (AFM)
• Limits of Detection: Data Sessions

MRI mini-lab

• MGH tabletop MRI

(Kept for historical reasons.)