Course Journal -- Nathan S Lachenmyer

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Week 1

Introductory Stuff

Statement of Objectives

My background is in physics and electrical engineering/computer science; primarily I've worked on feedback and control systems for physics experiments. My Master's research has been in building circuits for cell control using many of the same concepts as in feedback/control electronics, which has inspired an interest in biology.

My hope is that this class will help me learn to apply all of the theoretical techniques I've learned in coursework towards making useful instruments for measuring biological systems. I think that learning how to interface and control biological systems with computers is the key to making significant progress, and that's where I hope I will be able to contribute in the future.

In addition, having a solid understanding of how instrumentation works allows one to modify it to meet ones' needs. If I acquire a solid working knowledge of how bioinstrumentation works, that gives me the freedom to design or repurpose equipment to meet my particular needs. This is a particularly cost-effective approach to instrumentation that make the difference in enabling researchers to do work that would otherwise be outside of their budget.

I am also a frequent contributor to several open-source projects -- of particular note is Boston's DIY (Do-It-Yourself) Biology group based in Davis Square. I hope to be able to contribute many open-source, cheap instrumentation designs to their lab to help people perform biological research with a non-research budget.

Plan for Lab 1

  • Calibrations using PSD/Equipartition/Stokes Methods
  • E Coli Flagellar Motors
  • DNA Tethers

2012 02 14

  • DNA Tethers

Week 2

22 Feb 2012

  • Prepared sample of 3.2 um silica particles according to lab manual
    • 1k:1 dilution of 3.2 um in 1 M NaCl was already available in lab
    • Prepared 50k:1 dilution of particles by adding 100 uL of 10k:1 dilution to 400 uL H2O
  • Forgot to turn the laser diode on when I arrived, found it off <--- remember to do this in the future!

23 Feb 2012

  • One of the piezos isn't respond (blinking readout on controller)
    • Power cycle the piezos, start OTKB again
    • If this doesn't work, restart Matlab
  • Position Calibration
    • Acquired an okay x-calibration
    • y-calibration looks really odd, nonsensical
  • Asked Steve about it --> check it out again later
  • E Coli Spinning
    • Problem: Too many E Coli results in crowding, hard to trap just one
    • Problem: Hard to determine E Coli that are 'anchored' to the slide vs. free-floaters
      • Solution: Rinse the slide with DI Water, floaters get rinsed away with the fluid.
    • Problem: Many E Coli are anchored via multiple flagella -- they 'flip' rather than spin!
      • Solution: Pipette the E Coli multiple times in/out of a centrifuge tube; this 'cuts' many of their flagella so that they have less longer flagella to attach with. After pipetting multiple times, we incubate the E Coli on a slide to attach them.
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