Overview
Project Background
Digital droplet PCR (ddPCR) requires precise, rapid thermal cycling between denaturation (~95 °C) and annealing (~62 °C) temperatures. The core engineering challenge: achieving sub-second step-function temperature transitions while maintaining uniform thermal distribution across thousands of droplets simultaneously — all within a compact, reliable bench-top platform deployable in clinical research settings.
This project integrated multidisciplinary domains of heat transfer, microfluidics, and actuation — resulting in one of the fastest ddPCR platforms demonstrated at the lab scale. The platform was deployed in active IRB-approved neurosurgery and pathology studies at NYU Langone for translational cancer research.
CAD & System Design
Hardware Architecture
SolidWorks-designed platform integrating thermal bed, microfluidic chip fixtures, fluid manifolds, and optical imaging stage into a single ruggedized bench unit.
Fluid Control ArrayPump manifold with 8-channel valve array for precise droplet transport and flow sequencing
Full Platform AssemblyComplete bench-top system — imaging stage, thermal subsystem, and motion control on optical breadboard
Chip Clamping StageOptical fixture and chip clamping assembly on precision breadboard with alignment features
Thermal Bed ModuleDual-zone thermal bed with water-channel ports for 95°C and 62°C zone circulation
Microfluidic Chip — Exploded ViewLayered chip construction: droplet generator, channel layer, gasket, cover plate, and substrate stack
Chip + Silicon SubstrateFabricated microfluidic chip on silicon substrate — 25×25mm dual-channel design generating 22,000+ droplets/cycle
Thermal Cycling PlatformFull thermal platform assembly with dual blower fans, chip stage, and wiring harness on optical table
Thermal Clamping FixturePrecision clamping fixture with silicone sealing gasket (red) and water-tight interface for chip-to-thermal-bed contact
Engineering Approach
System Design & Development
Thermal System
Engineered an active thermal bed capable of precise step-function temperature shifts from 95 °C to 62 °C — achieving sub-second transitions optimized through iterative thermal simulations and data-driven experimentation. Custom acrylic manifolds and thermocouple arrays provide closed-loop monitoring across both zones.
Multi-physics Model
Formulated a multi-physics control-volume model coupling thermal conduction, droplet kinetics, and actuator response. Model predictions were validated through SolidWorks design optimization and ANSYS thermal FEA, followed by empirical calibration against experimental measurements.
Microfluidic Chip
Developed a custom 25 × 25 mm dual-channel microfluidic chip to synchronize droplet formation (~22k per cycle) with alternating temperature zones, ensuring consistent amplification kinetics. Channel geometry and sealing interfaces iterated to achieve ±2% droplet size uniformity.
Fluid & Vacuum Control
Integrated pumps, pinch valves, and vacuum control into a modular manifold assembly for precise droplet transport and flow sequencing. Modular design allows independent replacement of fluid-path components without system disassembly.
Sensing & Embedded
Validated analog/digital sensors using oscilloscopes and DMMs. Identified and resolved grounding issues and noise sources to achieve <1% signal drift over complete thermal cycles. Arduino-based embedded control coordinates subsystem sequencing and data acquisition.
Image Analysis Pipeline
Developed automated fluorescence quantification pipeline in Python (FIJI + NumPy/Matplotlib) replacing manual ImageJ workflows. ROI segmentation, thresholding, and droplet classification routines reduced manual analysis time by 60% and improved classification consistency.
Key Achievements
Quantified Outcomes
<1s
Step-function thermal transitions 95°C → 62°C — record-speed ddPCR amplification with successful fluorescence detection
35%
Prototype failure rate reduction via sealing strategy, material selection & I/O validation before system-level testing
200+
Validation cycles completed, zero structural failures on load-path evaluated architecture in critical-care setting
25%
Assembly efficiency improvement — reduced part count, eliminated 3 assembly steps across two design revisions via DFM
Technical Challenges
Problem-Solving
- Sub-second thermal transitions — achieving step-function transitions required material and actuator selection optimized via data-driven design to minimize thermal lag and energy waste; culminated in the first successful <1s ddPCR amplification demonstrated at lab scale
- Thermal crosstalk — deliberate isolation architecture and insulation strategy between the 95°C and 62°C zones to maintain stable temperatures across 8-hour experimental windows
- Droplet uniformity — multiple channel geometry iterations and precise sealing interfaces; early prototypes showed high CV due to dimensional drift under thermal load, resolved through DFM-guided iteration
- Signal integrity — ground loops in mixed-power electronics layout caused ~8% signal drift; resolved through shield grounding and layout changes, achieving <1% drift
- Clinical deployment — ruggedization and SOP development to meet clinical-environment handling requirements for active use by neurosurgery and pathology staff
Project Info
Role
Mechatronics Engineer (R&D Systems)
Organization
NYU & NYU Langone
Timeline
Feb 2025 – Present
Location
New York, NY
Domain
Medical Device R&D · Microfluidics
Status
Deployed · IRB-Active
Tools & Technologies
SolidWorksANSYS FEAArduinoPythonNumPyMatplotlibFIJI/ImageJMicrofluidicsThermal SystemsVacuum SystemsPinch ValvesDFMSLA 3D PrintingOscilloscopeDMMThermocouples
Key Technical Areas
Thermal
Sub-second step transitions, dual-zone control, ANSYS FEA validation
Microfluidics
Chip design, channel geometry, 22k+ droplet generation
Electronics
Sensor calibration, signal integrity, embedded control
Software
Automated image analysis, ROI segmentation, Python pipeline
DFM
Iterative prototyping, sealing strategy, assembly optimization