High-Throughput Mechanoporation
Mechanoporation & The Scaling Challenge
Mechanoporation is a microfluidic technology that engineers precise cellular deformation to enable intracellular delivery. By driving cells through micro-scale constrictions at high velocity, the process induces transient pores in the cell membrane via controlled shear forces. This purely mechanical approach maintains high cell viability while allowing payloads—such as mRNA, CRISPR-Cas9, or proteins—to diffuse into the cytoplasm efficiently.
Scaling Constraint: The legacy device used a 2-channel silicon chip. Under biological load, debris and shear events caused rapid clogging, limiting throughput to ~1M cells per run and preventing meaningful scale-up.
Engineering Objective: I led the redesign of the consumable architecture to support >100M cells per run. This required developing a new 206-channel microfluidic chip and a scalable sealing + distribution system that preserved uniform shear conditions while providing channel-level redundancy.
The architecture evolved from a single 2-channel flow path to a 206-channel parallelized array, demanding precise control of hydraulic resistance and manifold geometry.
High Volume Microfluidic Chip, Fluid Flow Path
High-Volume Consumable Chip
The high-volume chip features 206 interconnected through-holes acting as vertical inlets and outlets. The chip footprint was constrained by photolithographic manufacturing limitations - expanding the active area further introduced unacceptable feature drift, necessitating a vertical stacking approach for scale. The gasket structure is therefore critical for both sealing and guiding fluid flow through this multi-layer assembly.
To debug the physical assembly, I designed a custom multi-port diagnostic fixture. This allowed us to isolate layer-by-layer failures (gasket interface vs. manifold) and verify the seal integrity of the intricate fluid paths.
High-Volume Consumable Architecture
Component Breakdown
The consumable consists of a polycarbonate lid with integrated pressure-sensor, fill, and pneumatic ports; an inlet reservoir that stabilizes upstream flow; and a polycarbonate top plate with tapered funnel features for uniform hydraulic distribution.
The core is a multi-chip silicon stack sealed using custom injection-molded 3D gaskets. This stack is constrained by precision spacers and clamped against a polycarbonate bottom plate, terminating in an outlet reservoir with a flow-sensor port and a lofted outlet funnel that reduces dead volume and mitigates air-entrainment artifacts.
Prototyping & Validation
Prototyping involved an extensive cycle of SLA/FDM 3D-printed components for rapid fit, tolerance, and flow testing. However, surface absorption and biocompatibility issues with printed materials ultimately drove a transition to machined polycarbonate for validation units.
I designed a multi-port diagnostic pressure fixture to isolate failures across manifold interfaces, gasket ridges, and chip-to-chip joints, enabling systematic leak debugging across the vertical stack.
High-Volume Consumable Architecture
Custom pressure-diagnostic fixture with a push-to-connect manifold
The Fracture & Leakage Mechanics Problem
The silicon microfluidic chips are fabricated via DRIE, producing high-aspect-ratio channels but resulting in an inherently brittle substrate with low fracture toughness. When multiple chips are stacked, the assembly becomes extremely sensitive to non-uniform clamping, torsional loading, surface flatness deviations, and gasket-induced bending moments - all of which can trigger catastrophic fracture.
A fundamental constraint defined the problem space:
- Too little compression → leakage.
- Too much compression → chip fracture.
The allowable process window between these two failure modes was only a few percent of gasket deflection, far narrower than standard sealing strategies could maintain. To diagnose and characterize these coupled failure modes, I designed a custom pressure-diagnostic fixture with a push-to-connect manifold architecture.
The Solution: Preventing substrate failure required rethinking both structural reinforcement and sealing mechanics to decouple sealing force from chip-level mechanical load. This drove the development of reinforced silicon bridge structures and a 3D gasket topology that localized compression only around fluid paths while offloading bending and torsional forces away from the chips.
Innovation: 3D Gasket Topology
I developed a 3D microstructured gasket featuring raised sealing ridges that localize compression forces only around fluid paths. This dramatically reduces total contact area - and therefore total required clamp force - while enabling the gasket to conform to micron-scale surface variations.
Technical advantages:
- Minimizes bending forces transmitted to silicon
- Maintains seal integrity under high differential pressures
- Compensates for micro-scale surface unevenness and manufacturing tolerances
- Optimized Pressure-to-Force Ratio: By reducing the contact area, we achieved high localized sealing pressure (psi) with significantly lower global clamping force (lbf), effectively decoupling the sealing requirement from the fracture risk.
I utilized FEA (Finite Element Analysis) to iterate on the fine features of the gasket geometry, optimizing the ridge profile and bridge structures to ensure uniform compression and prevent blowout without creating stress risers.
3D gasket ridges concentrating sealing force only where needed.
Reinforced gasket geometry with locator holes and thicker ridges.
Optimizing the 3D Gasket Geometry
Early iterations of the 3D gasket experienced ridge "blowout" under high pressure. Through iterative topology refinement, I resolved these issues by:
- Increasing ridge thickness to improve flexural rigidity
- Adding structural bridges for lateral reinforcement
- Reducing corner fillet radii to 0.4 mm to eliminate stress risers
- Relocating locator holes horizontally to provide material backing during pressurization
These changes produced a gasket capable of sustaining the required operational pressure envelope.
Validation Data: Sealing Performance
Extensive material characterization was conducted to define the process window. We tested various silicone rubber formulations, comparing Shore 60A vs. Shore 70A hardness at different compression percentages.
Once the optimal material properties (Shore 70A at ~19% compression) were validated to seal without fracturing the chips, I collaborated closely with an external injection molding vendor. We refined the geometry for manufacturability (DFM), ensuring the complex ridge features could be molded consistently at production scale.
| Stack Config | Nominal Gasket Dimension | Nominal Chip Thickness | Nominal Spacer Size | Actual Spacer Size | Actual Compression % | Shore 60A Results | Shore 70A Results |
|---|---|---|---|---|---|---|---|
| 1 Stack | 1.75 mm (2 Gaskets) | 1.39 mm (1 Chip) | 4.05 mm | [4.00, 4.05] | [19.9%, 18.4%] | Similar to 70A | 0.020 psi leakage |
| 2 Stack | 1.75 mm (3 Gaskets) | 1.39 mm (2 Chip) | 6.70 mm | [6.67, 6.73] | [20.0%, 19.4%] | 0.0226 psi leakage | 0.0284 psi leakage |
| 3 Stack | 1.75 mm (4 Gaskets) | 1.39 mm (3 Chip) | 9.45 mm | [9.45, 9.50] | [19.0%, 18.25%] | 0.1106 psi leakage | 0.0677 psi leakage |
| 4 Stack | 1.75 mm (5 Gaskets) | 1.39 mm (4 Chip) | 12.16 mm | [12.24, 12.30] | [19.5%, 19.0%] | 2.382 psi leakage | 0.0390 psi leakage |
Final Production Architecture
The validated production solution used a three-part injection-molded gasket set (Top, Middle, Bottom) that consistently sealed a 5-chip silicon stack without mechanical failure. This architecture ensured stable compression, predictable flow distribution, and robust manufacturability.
I validated the final geometry with COMSOL multiphysics simulations, analyzing inlet-to-outlet pressure drop distribution, lateral uniformity across 206 channels, and flow symmetry.
The results confirmed that the scaled architecture preserved the precise flow and shear regimes required for successful mechanoporation. This was further validated in real-world trials with live cell processing, confirming that the high-volume system achieved biological parity with the legacy low-throughput benchmark.
Assembled consumable for high-volume biological test
Engineering Artifacts Gallery
Scaling Concept
High-Volume Chip Stack
Validation Data
Failure Modes
3D Gasket Design
Optimized Geometry
Final Production