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Yanik Lab: Biosensing Hardware

Microfabricated Ti/Au biosensor chips, automated assay workflows, signal-delivery electronics, and optoelectronic diagnostic systems for antigen detection.

Role Undergraduate researcher — fabrication, hardware, automation
Status Active
Tags
Microfabrication PCB Design Optoelectronics Photolithography Opentrons Biosensing Signal Generation
Design doc (PDF)

Problem

Biosensing research requires consistent, repeatable chip fabrication and reliable signal delivery. Small variations in fabrication — resist thickness, exposure uniformity, metal deposition rate — produce chips with different baseline characteristics, which makes it hard to compare experimental results across runs or researchers.

Similarly, manually connecting bench equipment (function generators, oscilloscopes, pipettes) to chips during each experiment introduces variation and limits throughput. The lab needed both higher-quality chips and more automated workflows.

System overview

The project spans three interconnected areas: chip fabrication, signal delivery hardware, and assay automation. These are not separate projects — they form a pipeline where the quality of each stage affects the reliability of downstream measurements.

What I built

Ti/Au biosensor chip fabrication

I fabricate biosensor chips on glass substrates using a photolithography and lift-off process. The process flow:

  1. Substrate preparation — clean glass substrates are solvent-cleaned and plasma-cleaned to improve photoresist adhesion.
  2. Photoresist — spin-coat negative photoresist to a controlled thickness; soft-bake on hotplate.
  3. UV exposure — expose through chrome mask defining electrode geometry.
  4. Development — develop to remove exposed resist, leaving patterned windows for metal deposition.
  5. E-beam evaporation — deposit Ti adhesion layer (~5 nm) followed by Au sensing layer (~50–100 nm) under high vacuum.
  6. Lift-off — soak in acetone to dissolve remaining resist and remove unwanted metal, leaving clean Ti/Au electrodes.
  7. Inspection — optical microscope inspection for shorts, incomplete lift-off, or delamination.

The Ti/Au electrode geometry is designed for subsequent surface functionalization — attaching biological recognition elements (antibodies, aptamers) that bind target antigens selectively.

Signal-generation PCB

See the dedicated Signal-Generation PCB project page for full detail. The short version: I designed a compact PCB to deliver 50 Hz, 10 Vpp sinusoidal signal to biosensor chips during electrochemical measurements, replacing a bench function generator with an integrated, automation-compatible signal source.

Opentrons automation

I built and maintained liquid-handling protocols for the Opentrons OT-2 pipetting robot. The protocols handle:

  • Reagent preparation and dilution
  • Chip surface functionalization steps (incubation, wash cycles)
  • Sample loading
  • Buffer washes and final measurement preparation

Automating these steps reduces manual pipetting error, allows unattended runs, and enables parallelization across multiple chips simultaneously.

Optoelectronic diagnostic setup

Part of the lab’s work involves optical readout of biosensor chips — measuring changes in transmitted or reflected light as a function of surface binding events. I’ve supported the physical setup, sample positioning jigs, and documentation of imaging results for antigen detection experiments.

Undergraduate onboarding

I developed and delivered training materials for incoming undergraduate researchers covering cleanroom safety, gowning procedures, fabrication protocol documentation, and equipment operation basics.

Technical details

Process stepEquipment / method
Substrate cleanSolvent wash, plasma cleaner
PhotoresistSpin coater, hotplate
ExposureMask aligner (UV)
MetallizationE-beam evaporator
Metal layersTi (adhesion) / Au (sensing)
Lift-offAcetone soak + agitation
InspectionOptical microscope
AutomationOpentrons OT-2
Signal deliveryCustom PCB (50 Hz, 10 Vpp)

Fabrication yield and lessons

Yield is sensitive to process control. The most common failure modes I encountered:

  • Incomplete lift-off: resist remaining under metal at feature edges, usually from insufficient development time or inadequate acetone exposure during lift-off.
  • Delamination: Ti/Au peeling from glass, caused by insufficient plasma cleaning or vacuum excursion during deposition.
  • Shorts between electrodes: metal bridging across gaps, usually from dust particles on the substrate before exposure.

Each failure mode has a different root cause and a different fix. Tracking them carefully across fabrication runs allows incremental process improvement.

What I learned

Process documentation is load-bearing. Variation that seems random often traces to an undocumented step — a substrate handled without gloves, a develop time rounded to the nearest minute instead of timed precisely. Rigorous protocol recording is not bureaucracy; it is the only way to diagnose intermittent yield problems.

Automation is only as reliable as the protocol. The Opentrons robot executes exactly what it is told. Writing a protocol with an off-by-one error in tip assignments or a missing mix step produces consistent, reproducible bad results. Debugging automated protocols requires the same approach as debugging firmware.