20.309:Learning outcomes

Course objective

Enable students to exploit instrumentation to its fullest potential in biological engineering research and development by introducing students to the underlying physical and engineering principles and their application to measurement problems.

Learning outcomes

After 20.309, you should be able to:

• Understand and apply advanced techniques for making quantitative measurements of biological systems
• Set up, align, calibrate, and operate electronic, mechanical, and optical instruments
  • Determine calibration factors, linear approximations
  • Compare multiple calibration methods
• Prepare samples
• Characterize instrument performance
• Measure operating parameters such as resolution, gain, magnification, …
• Make indirect measurements
  • Mechanical system excited by thermal noise
  • Micro-rheological properties by particle tracking
• Use computers to acquire and analyze experimental data
• Cope with real-world measurement obstacles
  • Noise
  • Drift

iii. Vibration iv. Loading (output/input impedance) v. Photobleaching h. Demonstrate conscientious work habits i. Use proper safety precautions ii. Use appropriate attention to detail and assiduousness iii. Show proper respect for lab equipment iv. Keep organized records v. Plan your time in the lab 2. Model and analyze simple electronic and optical systems a. Continuous time i. Use ideal linear elements to model electronic /mechanical/fluid/biological systems 1. Resistor, capacitor, independent source 2. Voltage divider, Wheatstone bridge 3. RC filters 4. Amplifier, feedback ii. Use Fourier transforms to solve linear, time-invariant systems 1. Transfer function 2. Frequency response 3. PSD 4. 2nd order system response iii. Use basic ideal nonlinear elements 1. Diode b. Discrete time i. Convolution ii. Discrete Fourier Transform c. Estimate theoretical measurements limits i. Thermal noise ii. Shot noise iii. Acoustic noise iv. Resolution v. Dynamic range and saturation d. Apply ray tracing and geometric optics to simple optical systems i. Convex and concave thin lenses ii. 4f system iii. Mirrors and dichroics 3. Design and construct prototypes of optical and mechanical instruments a. Use optical and electronic breadboards b. Identify and utilize common electronic and optical components i. Passive linear electronics (resistor, capacitor) ii. Passive nonlinear electronics (diode) iii. Active electronics (op amp, LED, voltage regulator) iv. Electronic sensors (RTD, photodiode) v. Simple lenses (plano-convex, plano-concave) vi. Filters, mirrors, and dichroics vii. Rigid optical construction (lens tubes, cubes, cage system) viii. Illumination sources (laser, LED) 4. Compare experimental data to theoretical models a. Fit experimental data to a model i. DNA melting curve ii. Cantilever frequency response 5. Understand and use instrumentation terminology a. SNR b. Resolution c. Dynamic range d. Saturation

Lab skills

• Use a disciplined approach to effeciently construct and debug optical and electronic instruments
  • Handle and clean optics (uncoated and coated)
  • Use rigid construction components to create a robust optical system
  • Use lasers, LEDs, CCD cameras, and kinematic mounts
  • Align an optical system
• Use an electronic breadboard to prototype a circuit
• Use common lab tools and equipment
  • DVM, oscilloscope, lab power supply, signal generator, amplifier, cabling and adapters
  • Use a PC data acquisition system to capture data

Model the behavior of optical and electronic systems

• Behavior of light
  • Wave equation
  • Plane and spherical wave solutions
  • Laws of refraction and reflection
  • Diffraction and interference
  • Relationship of classical and quantum mechanical descriptions of light

Optics

• Use the classical model of light to understand optical systems
  • Wave equation
  • Spherical and plane wave solutions
  • Diffraction and interference
  • Snell's law and the law of reflection
• Use ray tracing to model the behavior of systems of lenses and mirrors
  • Understand the relationship between rays and waves
  • Paraxial approximation
  • Thin lens approximation
• Understand the effect of optical aberrations
  • Spherical aberration
  • Chromatic aberration
  • Astigmatism
  • Coma
  • Field curvature
• Understand the theoretical performance of optical systems imposed by diffraction

Microscopy

• Understand how each microscope component contributes to image formation
  • Objective lens
    • Simple lens equivalent model
    • Corrections
    • Numerical aperture
    • Immersion
  • Illuminator
  • Condenser
  • Conjugate planes

Circuits

• Model electronic circuits with ideal lumped elements
  • Understand resistive divider
  • Determine Thevenin and Noron equivalent circuits
  • Use input and output impedance to determine the effect of connecting two systems

Systems

• Model electronic, mechanical, fluid, and thermal systems with lumped elements
• Determine the impulse and frequency response of a system of lumped elements
• Construct a Bode magnitude plot of a system transfer function