Yanik Lab: Biosensing Hardware and Automation

Cleanroom work during UV mask alignment and inspection.

Intro

My work in Yanik Lab spans the physical side of biosensing research: chip fabrication, deposition hardware, lab automation, signal delivery, electrochemical workflow development, optical inspection, data collection, and documentation.

The best way to describe the work is not as one project, but as a set of connected systems built around experimental bottlenecks.

Purpose

The purpose of this work is to make biosensing workflows more repeatable, automated, and usable. That includes fabricating chips, building supporting hardware, replacing fragile manual steps, documenting methods, and designing tools that can be used by other researchers.

Much of my role is practical support at the bench: setting up equipment, cleaning substrates, fabricating chips, inspecting results, labeling data, and building the hardware needed when the existing workflow gets in the way.

Workstreams

Ti/Au microelectrode chip fabrication

I fabricate biosensor chips on glass substrates using photolithography and lift-off:

Substrate preparation through solvent and plasma cleaning
Photoresist spin-coating and soft-bake
UV exposure through a chrome mask defining electrode geometry
Development to define metal deposition windows
E-beam evaporation of Ti adhesion layer and Au sensing layer
Lift-off in acetone to define clean Ti/Au electrodes
Optical inspection, yield tracking, and failure-mode documentation

Tooling and process experience includes the O2 plasma cleaner, photoresist spin coater, hot plates, UV mask aligner, fume hood / chemical bench, e-beam evaporator, optical microscope, and manual substrate / photoresist handling. The sequence is the work: clean, coat, bake, expose, develop, deposit Ti/Au, lift off, inspect, and document what failed.

Design decisions

Decision	Selected direction	Why it mattered	Tradeoff / next step
Fabrication focus	Ti/Au electrodes on glass	Directly supports the lab’s biosensor assays	Yield and failure tracking remain central
Workflow improvement	Build small tools around bottlenecks	Saves researcher time without replacing the full assay system	Each tool has to survive real bench use
Validation style	Optical inspection plus electrical checks	Connects fabrication quality to measurable experiment output	More standardized data logging would help
Automation	Opentrons-compatible hardware and protocols	Makes deposition and assay steps more repeatable	Benchtop use still needs clear handoff documents
Documentation	Methods, labels, and run notes	Makes work transferable to other researchers	Needs ongoing cleanup as designs evolve

Inspection and data handling

After fabrication and deposition, I helped inspect chips optically, collect images, label data, and prepare results for downstream analysis. Some concentration analysis was completed by PhD students using MATLAB workflows.

ADOpt signal-delivery module

A compact 555-timer module that replaced a benchtop function generator in the deposition workflow. Two modules were deployed to Grenada. See ADOpt for full detail.

Opentrons OT-2 workflow support

Python protocols for the Opentrons OT-2 liquid-handling robot, including labware loading, pipette setup, reagent dispensing, incubation timing, wash cycles, and command sequencing for biosensor deposition and assay workflows.

Sensor Deposition Unit

An active electrochemical signal-routing subsystem adding deposition and sensing capability to Terry/ASATS. See Sensor Deposition Unit for full detail.

Manuscript and methods support

Documentation and methods writing in support of related hardware publications, including the ADOpt deposition module framework.

Validation

Validation depends on the workstream:

Fabrication: chip inspection, yield, failure modes, process repeatability
ADOpt: oscilloscope validation, optical deposition results, Grenada field deployment
OT-2 protocols: successful execution of workflow steps
Sensor Deposition Unit: pending board bring-up and electrochemical validation

Results

Fabrication and process experience with Ti/Au biosensor chips
Hands-on cleanroom and wet-lab equipment experience
Hardware development for automated deposition workflows
ADOpt deployment to Grenada
Optical inspection, data labeling, and methods support
Active development of multiplexed electrochemical deposition/sensing hardware

Future work

Continue improving chip fabrication repeatability and documentation
Bring up and validate the Sensor Deposition Unit
Expand automation around deposition and sensing workflows
Confirm exact equipment names for a more precise lab-process inventory

Biosensing workflow, end to end

Yanik Lab is where the biosensing hardware work starts. ADOpt and the Sensor Deposition Unit make more sense when the chip fabrication and assay workflow are visible first.

My work spans Ti/Au biosensor chip fabrication, deposition hardware, lab automation support, electrochemical workflow development, optical inspection, data labeling, and methods documentation. Those are not separate resume categories in the lab. They touch the same physical process.

A chip has to be fabricated, contacted, exposed to chemistry, measured, imaged, labeled, and handed to another person with enough procedure that the result can be repeated. The hardware projects came from that chain.

Row of clean biosensor chips — Clean biosensor chips lined up for workflow development and inspection.

Fabrication is procedural and unforgiving

The chip process is not one magic cleanroom step. It is a chain of machines and benches that only works if the previous step behaved: solvent cleaning at the chemical bench, O2 plasma cleaning, photoresist spin coating, hot-plate soft bake, UV mask alignment through the chrome mask, development, e-beam evaporation for the Ti/Au stack, acetone lift-off, and optical microscope inspection.

The cleanroom tools I used in that chain were the O2 plasma cleaner, spin coater, hot plates, UV mask aligner, e-beam evaporator, fume hood / chemical bench, and optical microscope. The important part is the process control: cleaning, exposure, metal deposition, lift-off, and inspection all have to line up before the chip is useful.

A small process error can become a failed electrode, bad adhesion, poor contact, or unusable assay data. Sometimes the failure looks electrical, sometimes chemical, sometimes mechanical, and sometimes it is just a dirty step from earlier in the process finally showing up.

That is why documentation matters here. Not because documentation is tidy, but because fabrication needs a memory. If a run fails, the notes are what let the lab ask a better question than "what happened?"

UV mask alignment work — UV mask alignment and inspection work during chip fabrication.

The hardware projects came from real bottlenecks

ADOpt, SDU, Opentrons workflow support, chip holders, and manifold tests are not isolated portfolio items. They came from repeated contact with the lab process: chips need to be fabricated, signals delivered, gaskets sealed, images labeled, and procedures handed to other researchers without losing the method.

ADOpt reduced a deposition signal bottleneck. SDU pushes the same workflow toward multiplexed electrochemical sensing. The manifold and gasket work exists because the electrical measurement is only meaningful if the fluid and contact geometry behave.

That is the larger lesson from the lab: the serious engineering problems are rarely contained inside one discipline boundary. The circuit, fixture, chemistry, image, and procedure all decide whether the result survives.

Fabrication process under yellow cleanroom lighting — Fabrication process context under yellow lighting.